10-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

____________________________________________________

FORM 10-K

(Mark One)

x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2019

OR

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from ____ to ____

Commission File Number: 001-34885

____________________________________________________

AMYRIS, INC.

(Exact name of registrant as specified in its charter)

Delaware	55-0856151
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

5885 Hollis Street, Suite 100, Emeryville, California 94608

(Address of principal executive offices and Zip Code)

(510) 450-0761

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Trading symbol(s)	Name of each exchange on which registered
Common Stock, $0.0001 par value per share	AMRS	Nasdaq Global Select Market

Securities registered pursuant to Section 12(g) of the Act:

None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.   Yes ☐   No ☒

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.  Yes ☐   No ☒

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes ☐   No ☒

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).    Yes ☐   No ☒

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See definitions of “large accelerated filer”, “accelerated filer”, “smaller reporting company”, and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer ☐ Accelerated filer ☒ Non-accelerated filer ☐ Smaller reporting company ☒ Emerging growth company ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes ☐   No ☒

The aggregate market value of the registrant’s common stock held by non-affiliates of the registrant as of June 28, 2019, the last business day of the registrant's most recently completed second fiscal quarter, was $226.5 million based upon the closing price of the registrant’s common stock reported for such date on the Nasdaq Global Select Market.

Number of shares of the registrant’s common stock outstanding as of March 6, 2020: 163,843,407

DOCUMENTS INCORPORATED BY REFERENCE

None.

AMYRIS, INC.

FORM 10-K

FOR THE YEAR ENDED DECEMBER 31, 2019

TABLE OF CONTENTS

PART I
Item 1.	Business	1
Item 1A.	Risk Factors	10
Item 1B.	Unresolved Staff Comments	36
Item 2.	Properties	37
Item 3.	Legal Proceedings	37
Item 4.	Mine Safety Disclosures	37
PART II
Item 5.	Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities	38
Item 6.	Selected Financial Data	40
Item 7.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	40
Item 7A.	Quantitative and Qualitative Disclosures About Market Risk	47
Item 8.	Financial Statements and Supplementary Data	48
Item 9.	Changes in and Disagreements with Accountants on Accounting and Financial Disclosure	126
Item 9A.	Controls and Procedures	126
Item 9B.	Other Information	130
PART III
Item 10.	Directors, Executive Officers and Corporate Governance	131
Item 11.	Executive Compensation	131
Item 12.	Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters	131
Item 13.	Certain Relationships and Related Transactions, and Director Independence	131
Item 14.	Principal Accounting Fees and Services	131
PART IV
Item 15.	Exhibits and Financial Statement Schedule	132

Forward-Looking Statements

This Annual Report on Form 10-K contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. All statements contained in this Annual Report on Form 10-K other than statements of historical fact, including any projections of financing needs, revenue, expenses, earnings or losses from operations, or other financial items; any statements of the plans, strategies and objectives of management for future operations; any statements concerning product research, development and commercialization plans and timelines; any statements regarding expected production capacities, volumes and costs; any statements regarding anticipated benefits of our products and expectations for commercial relationships; any other statements of expectation or belief; and any statements of assumptions underlying any of the foregoing, are forward-looking statements. The words "believe," "may," "will," "estimate," "continue," "anticipate," "predict," "intend," "expect," and similar expressions are intended to identify forward-looking statements, but are not the exclusive means of identifying such statements. We have based these forward-looking statements largely on our current expectations and projections about future events and trends that we believe may affect our financial condition, results of operations, business strategy, short-term and long-term business operations and objectives, and financial needs. These forward-looking statements are subject to a number of risks, uncertainties and assumptions, including those described in Part I, Item 1A, "Risk Factors" in this Annual Report on Form 10-K. Moreover, we operate in a very competitive and rapidly changing environment. New risks emerge from time to time. It is not possible for our management to predict all risks, nor can we assess the impact of all factors on our business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in any forward-looking statements we may make. In light of these risks, uncertainties and assumptions, the future events and trends discussed in this Annual Report on Form 10-K may not occur, and actual results could differ materially and adversely from those anticipated or implied in the forward-looking statements contained herein.

We undertake no obligation to revise or publicly release the results of any revision to these forward-looking statements, except as required by law. Given these risks and uncertainties, readers are cautioned not to place undue reliance on such forward-looking statements.

Unless expressly indicated or the context requires otherwise, the terms "Amyris," the "Company," "we," "us," and "our" in this Annual Report on Form 10-K refer to Amyris, Inc., a Delaware corporation, and, where appropriate, its consolidated entities.

PART I

ITEM 1. BUSINESS

Overview

We are a leading industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets. Our proven technology platform enables us to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. Our biotechnology platform and industrial fermentation process replaces existing complex and expensive manufacturing processes. We have successfully used our technology to achieve nine molecules in production, leading to 17 commercial ingredients used by thousands of leading global brands.

We believe that industrial biotechnology represents a third industrial revolution, bringing together biology and engineering to generate new, more sustainable materials to meet the growing global demand for bio-based replacements for petroleum-based and traditional animal- or plant-derived ingredients. We continue to build demand for our current portfolio of products through an extensive sales network provided by our collaboration partners that represent the leading companies in the world for our target market sectors. We also have a small group of direct sales and distributors who support our Clean Beauty market. Via our partnership model, our partners invest in the development of each molecule to bring it from the lab to commercial scale and use their extensive sales forces to sell our ingredients and formulations to their customers as part of their core business. We capture long-term revenue through a combination of direct product sales, production and sale of the molecule to our partners, and royalty revenues from our partners' product sales to their customers.

We were founded in 2003 in the San Francisco Bay area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic acid, which is a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted royalty-free licenses to allow Sanofi S.A. to produce artemisinic acid using our technology. Building on our success with artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell sustainable alternatives to a broad range of markets.

We focused our initial development efforts primarily on the production of Biofene®, our brand of renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through fermentation using engineered microbes. Our farnesene derivatives are sold or included in thousands of products as nutrition, health, skincare, fragrances, solvents, and fragrance ingredients. The commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development process in the lab and drive manufacturing costs down. This investment has enabled our technology platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began manufacturing additional molecules for the Flavor & Fragrance industry. In 2015, we began investing to expand our capabilities to other small molecule chemical classes beyond terpenes, which comprised our initial research efforts (including through a Technology Investment Agreement with the Defense Advanced Research Projects Agency (DARPA)). In 2016 we expanded into the production of proteins.

Since the Company's inception, we have invested $700 million in infrastructure and technology to create microbes that produce molecules from sugar or other feedstocks at commercial scale. This platform has been used to design, build, optimize and upscale strains for nine molecules in production, leading to 17 commercial ingredients used by thousands of leading global brands. Our time to market for molecules has decreased from seven years to potentially less than a year, mainly due to our ability to leverage the technology platform we have built.

Our technology platform has been in active use since 2007 and has been integrated with our commercial production since 2011, creating an organism development process that we believe makes us an industry leader in the successful scale-up and commercialization of biotech-produced ingredients. The key performance characteristics of our platform that we believe differentiate us include our proprietary computational tools, strain construction tools, screening and analytics tools, and advanced lab automation and data integration. Full integration of the platform with our large-scale manufacturing capability enables us to engineer precisely with the end specification and commercial production requirements guiding our developments. Our state-of-the-art infrastructure includes industry-leading strain engineering and lab automation located in Emeryville, California, pilot-scale production facilities in Emeryville, California and Campinas, Brazil, a demonstration-scale facility in Campinas, Brazil and a commercial-scale production facility in Leland, North Carolina, which is owned and operated by our Aprinnova joint venture to convert our Biofene into squalane and other final products.

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We are able to use a wide variety of feedstocks for production but have focused on accessing non-GMO Brazilian sugarcane for our large-scale production because of its renewability, low cost and relative price stability.

Several years ago, we made the strategic decision to transition our business model from developing and commercializing molecules in low margin commodity markets to higher margin specialty markets. We began the transition by commercializing and supplying farnesene-derived squalane as a cosmetic ingredient sold to formulators and distributors. We then entered into collaboration and supply agreements for the development and commercialization of molecules within the Flavor & Fragrance and Clean Beauty markets where we utilize our strain generation technology to develop molecules that meet the customer’s rigorous specifications.

During this transition, we solidified the business model of partnering with our customers to create sustainable, high-performing, low-cost molecules that replace an ingredient in their supply chain, commercially scale and manufacture those molecules, and share in the profits earned by our customers once our customers sell their products into these specialty markets. These three steps constitute our grants and collaborations revenues, renewable product revenues, and royalty revenues.

In 2017, we decided to monetize the use of one of our lower margin molecules, farnesene, in certain fields of use while retaining any associated royalties. We began discussions with our partners and ultimately made the decision to license farnesene to Koninklijke DSM N.V. (DSM) for use in these fields. We also sold to DSM our subsidiary Amyris Brasil Ltda. (Amyris Brasil), which owned and operated the purpose-built, large-scale manufacturing facility in Brotas, Brazil that manufactures farnesene, a key, bio-based intermediate ingredient in certain of our products, in 2017.

The Brotas facility was built to batch manufacture one commodity product at a time (originally for high-volume production of biofuels, a business we have exited), which is an inefficient manufacturing process that is not suited for the high margin specialty markets in which we operate today. The inefficiencies we experienced at the Brotas facility included idling the facility for two weeks at a time to clean and prepare the plant for the production of the next molecule to be manufactured. These inefficiencies caused a significant increase in our cost of goods sold. We are in the process of constructing a new purpose-built, large-scale production facility in Brazil (see the Manufacturing section below), which we anticipate will allow for the manufacture of five products concurrently and over 10 different products annually. As part of the December 2017 sale of the Brotas facility, we contracted with DSM for the use of the Brotas facility to manufacture products for us to fulfill our product supply commitments to our customers until our new production facility becomes operational. In November 2018 and April 2019, we amended the supply agreement with DSM and entered into various other agreements with DSM. See Note 9, “Revenue Recognition” and Note 10, "Related Party Transactions" in Part II, Item 8 of this Annual Report on Form 10-K for a full listing and details of agreements with DSM. In September 2019, we obtained the necessary permits and broke ground on our Specialty Ingredients Plant (SIP). We expect facility construction to be completed in the second quarter of 2021. This facility will allow us to manufacture five products at once and to produce both our specialty ingredients portfolio and our alternative sweetener product.

As discussed above, on December 28, 2017, we completed the sale of Amyris Brasil, which operated our Brotas production facility, to DSM and concurrently entered into a series of commercial agreements and a credit agreement with DSM. At closing, we received $33.0 million in contractual cash consideration for the capital stock of Amyris Brasil, which was subject to certain post-closing working capital adjustments and reimbursements from DSM contingent on DSM’s utilization of certain Brazilian tax benefits it acquired with its purchase of Amyris Brasil. We used $12.6 million of the cash proceeds received to repay certain indebtedness of Amyris Brasil. The total fair value of the contractual consideration received in connection with the sales agreement for Amyris Brasil was $56.9 million and resulted in a pretax gain of $5.7 million from continuing operations, recognized in fiscal 2017.

Concurrent with the sale of Amyris Brasil, we entered into a series of commercial agreements with DSM including (i) a license agreement to DSM of our farnesene product for DSM to use in the Vitamin E and Lubricants specialty markets; (ii) a royalty agreement, pursuant to which DSM agreed to pay us specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene sold under the supply agreement with Nenter & Co., Inc. (“Nenter”), which was assigned to DSM; (iii) a performance agreement to perform research and development to optimize farnesene for production and sale of farnesene products; and (iv) a transition services agreement in which we provided finance, legal, logistics, and human resource services to support the Brotas facility under DSM ownership for a six-month period with a DSM option to extend for six additional months. At closing, DSM paid us a $27.5 million nonrefundable license fee and a $15.0 million nonrefundable minimum royalty revenue payment. DSM also agreed to pay us two additional future nonrefundable minimum annual royalty payments totaling $18.1 million related to 2019 and 2020 royalties. In June 2018, we received the 2019 non-refundable minimum royalty payment of $9.3 million (net of a $0.7 million early payment discount) and in March 2019, we received the 2020 payment of $7.4 million (net of a $0.7 million early payment discount).

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In the second quarter of 2018, we successfully demonstrated our industrial process at full-scale to produce a high-purity, zero calorie sweetener derived from sugarcane, and in December 2018, we received notification from the U.S. Food and Drug Administration (the FDA) that we received its "Generally Recognized As Safe" designation concurrence, and began producing commercial quantities of Steviol Glycoside Rebaudioside M (or Reb M) at DSM’s Brotas facility during the fourth quarter of 2018. Also, in the third and fourth quarters of 2019 we completed another successful campaign of Reb M utilizing the Brotas facility and a contract manufacturer for the purification steps and produced more than three times the volume of Reb M than in the December 2018/January 2019 campaign. We believe the Reb M molecule we are producing from sugarcane is one of the leading natural sweeteners. When derived from the Stevia plant, Reb M is found in very limited quantities. The Reb M we produce from sugarcane is more sustainable and lower cost than other natural sweeteners, and has a specific technical profile that we believe is advantaged in taste and total process economics for blends and formulations.

In June and December 2018, we and our contract manufacturer, Antibióticos de León (ADL), executed amendments to our January 2018 production agreement, thereby providing us additional tank capacity at ADL’s production facility in León, Spain. These amendments provide additional, cost-effective manufacturing capability to meet higher than expected product demand from our partners. The amended agreement includes a commitment to running a certain number of batches at ADL’s production facility from the period September 1, 2018 through December 31, 2019 for up to six of our products. In June 2019, we signed an additional amendment to this agreement extending our commitment through December 2020.

In the second quarter of 2018, we executed an agreement for a significant project consortium in Europe with the Universidade Católica Portuguesa (UCP) Porto Campus and AICEP Portugal Global (AICEP). UCP is a university system, including the leading biotech school in Portugal, and operates 15 research centers. AICEP is an independent public entity of the Government of Portugal, focused in encouraging foreign companies to invest in Portugal. In conjunction with this agreement, we opened a subsidiary in Porto, Portugal. The primary purpose of this subsidiary is to conduct a research and development project together with Escola Superior de Biotecnologia o Universidade Católica Portuguese. This subsidiary will be the second R&D center of Amyris and will be responsible for certain areas of research, namely valorization of fermentation residues and wastes and the advancement of the Company's Artificial Intelligence (AI) and Informatics platform. The overall multi-year project is valued up to approximately $50 million including investment funding and incentives allotted across the parties involved. We have sole responsibility for commercialization and majority ownership of all intellectual property (IP) generated. We believe this is the largest biotechnology grant ever awarded in Portugal and one of the largest ever approved by the AICEP for commercial applications.

In the third quarter of 2018, we entered into a supply and distribution agreement for our new, sugarcane-derived, zero calorie sweetener with ASR Group, the world’s largest cane sugar refiner. Also in the third quarter of 2018, we entered into a license and collaboration agreement with a subsidiary of Yifan Pharmaceutical Co., Ltd. (Yifan), which is one of the leading Chinese pharmaceutical companies. Such license and collaboration agreement was expanded in November 2018.

On May 2, 2019, we consummated a research, collaboration and license agreement (the Cannabinoid Agreement) with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million for the development, manufacture and commercialization of cannabinoids. Under the agreement, the Company will perform research and development activities and Lavvan will be responsible for the commercialization of the cannabinoids developed under the agreement. The Cannabinoid Agreement is being principally funded on a milestone basis, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. The Company could receive aggregate funding of up to $300 million over the term of the Cannabinoid Agreement if all of the milestones are achieved. Additionally, the agreement provides for royalties to the Company on Lavvan's gross profit margin once products are commercialized; these payments will be due for the next 20 years. Consummation of the transactions contemplated by the Cannabinoid Agreement included the formation of a special purpose entity to hold certain intellectual property created during the collaboration (the Cannabinoid Collaboration IP), the licensing of certain Company intellectual property to Lavvan, the licensing of the Cannabinoid Collaboration IP to the Company and Lavvan, and the granting by the Company to Lavvan of a lien on our background intellectual property being licensed to Lavvan under the Cannabinoid Agreement, which would be subordinated to the lien on such intellectual property under the Foris LSA debt facility; see Note 4, “Debt” in Part II, Item 8 of this Annual Report on Form 10-K for more information.

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into an agreement relating to the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products. In connection with the formation of the joint venture, among other things, (i) the joint venture will construct a manufacturing facility on land owned by Raizen and leased to the joint venture (the Sweetener Plant), (ii) the Company will grant to the joint venture an exclusive, royalty-free, worldwide, license to certain technology owned by the Company relevant to the joint venture’s business, and (iii) the Company and Raizen will enter into a shareholders agreement setting forth the rights and obligations of the parties with respect to, and the management of, the joint venture. The formation of the joint venture is subject

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to certain conditions, including certain regulatory approvals and the achievement of certain technological and economic milestones relating to the Company’s existing production of its alternative sweetener product. If such conditions are not satisfied by May 2020, the joint venture will automatically terminate. In addition, notwithstanding the satisfaction of the closing conditions, Raizen may elect not to consummate the formation and operation of the joint venture, in which event, the Company will retain the right to construct and operate the Sweetener Plant.

Technology

We have developed innovative microbial engineering and screening technologies that allow us to transform the way microbes metabolize sugars. Specifically, we engineer microbes, such as yeast, and use them as catalysts to convert sugar, through fermentation, into high-value molecules. In 2015, we were awarded a technology investment agreement with DARPA to expand the capabilities of our technology platform. The investment has resulted in us developing an integrated platform with artificial intelligence that will speed up the development and commercialization of small molecules across 15 different chemical classes. We have also developed our technology to be able to produce large molecules, such as proteins.

We devote substantial resources to our research and development efforts. As of December 31, 2019, our research and development organization included 192 employees, 55 of whom held Ph.D.s. We also have an additional 30 Ph.D.s throughout the organization who contribute to the success of our technology platform. We have invested $700 million to date in our research and development capabilities that has resulted in an almost 6x improvement in speed to market and in the scale-up of nine successful molecules. These achievements are due to the leading strain engineering and upscaling and commercialization capabilities we have developed from our investment.

Strain Engineering

Companies and researchers around the world are continuously learning how the complex biological processes in organisms work. Because there is so much that is still unknown, the best method for development of commercially viable strains is to test as many hypotheses as accurately and quickly as possible to accelerate the learning curve.

We have developed a high-throughput strain engineering system that is currently capable of producing and screening more than 100,000 yeast strains per month, which enables us to achieve an approximately 90% lower cost per strain than we achieved in 2009. We generated more than 360,000 unique strains in 2019, surpassing 6.3 million unique strains created since our inception, with each strain testing for improved production of the target molecules. In addition, through our lab-scale and pilot-plant fermentation operations, and our proprietary analytical tools, we are now able to predict, with high reliability, the performance of candidate strains at industrial scale.

Upscaling and Commercialization

The riskiest part of commercializing biotechnology is often the scale up and manufacturing due to the perceived unpredictability of biotechnology at different scales. We have built scale-up and manufacturing capabilities as our advantage by heavily investing in prediction models and analytics to quickly ascertain how a strain’s behavior at one scale will translate in another scale. We have successfully scaled-up and manufactured nine distinct molecules at commercial volumes to date, leading to 17 commercial ingredients used by thousands of leading global brands. The results of our advantage are accelerated speed to market, lower overall development costs, and a significantly lower risk profile for any project we undertake.

A strain must be improved to increase the level of efficiency of production, and tested for performance in pilot-scale facilities before it is implemented at commercial-scale manufacturing facilities. Our unique infrastructure to support this scale-up process includes lab-scale fermenters (0.5 to 2 liter), operating pilot plants in our facilities in Emeryville, California, which operates a 300-liter fermenter, and Campinas, Brazil, which operates 300- and 2,000-liter fermenters, and five years’ experience owning and operating the 1,200,000-liter production facility in Brotas, Brazil that we sold in late 2017. Each of these stages mimic the conditions found in larger-scale fermentation so that our findings may translate predictably from lab-scale to pilot and ultimately to commercial-scale. Our infrastructure is so accurate that we can typically go straight from lab-scale to commercial-scale for our fermentations, and generally the only reason we ever invest in the pilot-scale step is to produce enough product to accurately test our downstream processing since our fermentation process is already robust.

The complexities that can arise at industrial-scale manufacturing are significant and it takes an experienced team to not only address issues as they arise, but to also have the foresight to prevent issues from arising. With five years of experience operating the production facility in Brotas, Brazil that we designed (prior to selling the facility in late 2017), we have been able to develop a world-class manufacturing team. This team has successfully brought online a production facility and scaled up and manufactured nine molecules at commercial-scale that are currently used in thousands of consumer goods products around the

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world. Our effort also expands into continued strain and process improvements to ensure our manufacturing is robust and the most cost advantaged.

Product Markets and Partnerships

There are three market areas that are our primary focus and key to our growth: Health & Wellness, Clean Beauty and Flavor & Fragrance. Each of these markets embodies our core competencies of sustainably providing clean ingredients in markets where we can be the most impactful, not only from a growth and revenue standpoint, but also for healthier living.

We believe that our leadership in biotechnology is demonstrated by collaboration partners, who come to us to access our platform and industrial fermentation expertise. Together we seek to reduce environmental impact, enhance performance, reduce supply and price volatility, and improve profit margins. Our partners include Flavor & Fragrance companies such as Firmenich S.A. (Firmenich) and Givaudan International, SA (Givaudan), and nutrition companies such as DSM and Yifan. A portion of our work has also been funded by the U.S. government, including the Department of Energy (DOE) and DARPA, to develop technologies and processes capable of improving the ability to utilize biotechnology for the production of a broader range of molecules.

Health & Wellness

Our Health & Wellness focus includes alternative sweeteners, nutraceuticals, such as vitamins, and food ingredients. As consumers continue to demand higher nutritional performance, healthier ingredients and convenience from their food, the demand will continue to grow for specific ingredients that are often difficult and expensive to procure. Animal farming is also being impacted by the growing demand for protein and the need to change farming practices, such as reducing antibiotic use. Our technology can be employed to provide affordable access to these desired ingredients for both human and animal health. To date, product revenue in this area has been from a derivative made from our Biofene® product by our partner. In late 2018, we began to produce at commercial-scale an alternative, healthier sweetener. We introduced our product to the public during December 2018, at an investor event in NYC. In 2019, we ran two production campaigns that resulted in feedback that our Reb M product is distinguished by one of the best-tasting profiles in the industry to date. The market and commercial uptake has been significant. We have sold out the production for both campaigns. Also, by the end of 2019 we also introduced our B2C sweetener brand: Purecane. We currently offer this brand through our own website: www.purecane.com and we also plan to expand the distribution in Amazon in March. Finally, we currently offer Purecane in two product forms: a 100 sachet for table-top, and a culinary bag that has a cup for cup equivalency with sugar.

During 2015, we announced the signings of our first ingredient supply agreement and collaboration agreement for the global nutraceuticals market. Under the supply agreement, we sourced Biofene to our partner, which was then further processed into a nutraceutical product. In 2016, we made the first large-scale shipments of Biofene to our partner, who successfully produced and sold a nutraceutical product to its customers. In 2017 and 2018, we expanded our collaborations in nutraceuticals to four vitamins and a human nutrition ingredient.

Flavor & Fragrance Markets

Our technology enables us to cost-effectively produce natural oils and aroma chemicals that are commonly used in the Flavor & Fragrance market. Many of the natural ingredients used in the Flavor & Fragrance market are expensive because there is limited supply and the synthetic alternatives require complex chemical conversions. We offer Flavor & Fragrance companies a natural route to procure these high-value ingredients without sacrificing cost or quality. To date, we have successfully brought four Flavor & Fragrance ingredients to market with our collaboration partners. We also have several other ingredients under development.

In late 2013, we commenced commercial production of our first Flavor & Fragrance ingredient for a range of applications, from perfumes to laundry detergent, which is marketed by a collaboration partner which is a global Flavor & Fragrance leader. In 2014, we completed our first production campaign of this ingredient and shipped it to this collaboration partner. In late 2015, we commenced production and initial sales of our second Flavor & Fragrance ingredient to the same collaboration partner. During 2019, we added two new Flavor & Fragrance molecules to our list of successfully scaled products and we shipped seven compounds destined for the Flavor & Fragrance market (including compounds converted by our partners to Flavor & Fragrance ingredients) to our partners.

We continue to work to develop and commercialize a variety of Flavor & Fragrance ingredients that are either direct fermentation products or derivatives of fermentation products.

Clean Beauty

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Our Clean Beauty focus includes clean skincare and cosmetic ingredients we develop and commercialize with our partners and our branded Biossance product line. In September 2019, we launched a new clean beauty baby brand, Pipette. We have several cosmetic ingredients currently under development. Our Biossance and Pipette products are discussed further in the Amyris-branded Product Markets section below.

Amyris-branded Product Markets

Through basic chemical finishing steps, we are able to convert our farnesene into squalane, which is used today as a premium emollient in clean skincare products. We believe that our squalane offers performance attributes equal or superior to those of squalane derived from conventional sources. The ingredient traditionally has been manufactured from olive oil or extracted from deep-sea shark liver oil, which requires that the shark be killed in order to harvest its liver oil. The relatively high price and unstable supply of squalane in the past meant that its use was generally limited to luxury products or small quantities in mass-market product formulations. With our ability to produce a reliable supply of low-cost squalane that eliminates the need to harvest shark liver oil, we offer this ingredient at a price that we believe will drive increasing adoption by formulators. In addition to squalane, we offer a second, lower-cost cosmetic ingredient, hemisqualane, for the cosmetics market. In December 2016, we and Nikko Chemicals Co., Ltd. (Nikko) formed a joint venture, in which we hold a 50% interest, for our business-to-business sales of Neossance squalane and hemisqualane. See below under “Joint Venture” for more information regarding our Aprinnova joint venture. The joint venture currently has supply agreements with several regional distributors, including those with locations in Japan, South Korea, Europe, Brazil and North America, and, in some cases, directly with cosmetics formulators, which we transferred to the joint venture during the formation process.

Our consumer clean skincare products, sold under our Biossance brand, feature our Biofene-derived squalane. Under our Biossance brand, we market and sell our products directly to retailers and consumers. Biossance was initially sold solely through our ecommerce branded website and in 2016, we expanded the product line to include an expansive line of clean high-performance skincare products and opened up sales through Home Shopping Network (HSN). In October 2016, we announced our Biossance product line would begin to be carried at Sephora in 2017. In February 2017, we launched a full squalane-based consumer cosmetic line at participating Sephora stores and Sephora online. All of the products are based on our commitment to No Compromise®. Since the launch of Biossance, sales have grown, and with Sephora’s partnership, we continued to expand to more stores through 2019.

We launched a clean beauty brand, Pipette, in September 2019 with an initial offering of seven products developed for babies and moms to support and nurture the skin. Currently, the brand now offers nine unique products.

Pipette is available for purchase at Pipettebaby.com, buybuyBABY.com, Amazon.com, Walmart.com, and Dermstore.com, in-store exclusively at buybuy BABY® stores nationwide, and at our own direct website. Pipette recently became available for purchase at Target.com, as well. The brand is seeking further expansion through online and brick-and-mortar retailers.

Manufacturing

Until December 2017, we owned and operated a purpose-built, large-scale production facility located in Brotas, Brazil. In December 2017, we sold the facility to a unit of DSM and entered into a supply agreement with DSM for us to purchase output from the facility. See Note 12, “Divestiture” and Note 10, "Related Party Transactions" in Part II, Item 8 of this Annual Report on Form 10-K for additional information regarding our December 2017 transaction with DSM.

In September 2019, we obtained the necessary permits and broke ground on our Specialty Ingredients Plant (SIP). We expect facility construction to be completed in the second quarter of 2021. This facility will allow us to manufacture five products at once and to produce both our specialty ingredients portfolio and our alternative sweetener product. During construction, we are manufacturing our products at six contract manufacturing sites in Brazil, the U.S., Italy and Spain. In addition, in May 2019 we entered into an agreement with Raizen Energia S.A. (Raizen) for the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products whereby the parties would construct a manufacturing facility exclusively for sweetener molecules on land owned by Raizen and leased to the joint venture; see Note 1, “Basis of Presentation and Summary of Significant Accounting Policies” in Part II, Item 8 of this Annual Report on Form 10-K for more details.

For many of our products, we perform additional distillation or chemical finishing steps to convert initial target molecules into other finished products, such as renewable squalane. We have agreements with several facilities in the U.S. and Brazil to perform these downstream steps for such products. We may enter into additional agreements with other facilities for finishing

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services and to access flexible production capacity and an array of other services as we develop additional products. In December 2016, we purchased a manufacturing facility in Leland, North Carolina, which had been previously operated by Glycotech Inc. (Glycotech) to convert our Biofene into squalane and other final products. We subsequently contributed that facility to our Aprinnova joint venture. See below under "Joint Venture" for more information regarding our Aprinnova joint venture.

Joint Venture

Aprinnova, LLC

In December 2016, we entered into joint venture agreements with Nikko related to the formation of a joint venture to focus on the worldwide commercialization of our Neossance cosmetic ingredients business. We formed the joint venture under the name Neossance, LLC, and later changed the name to Aprinnova, LLC (the Aprinnova JV), which is jointly owned by us and Nikko. Pursuant to the joint venture agreements, we contributed certain assets to the Aprinnova JV, including certain intellectual property and other commercial assets relating to our Neossance cosmetic ingredients business, as well as the production facility in Leland, North Carolina and related assets purchased by us from Glycotech in December 2016. We also agreed to provide the Aprinnova JV with licenses to certain intellectual property necessary to make and sell products associated with the Neossance business. At the closing of the formation of the joint venture, Nikko purchased a 50% interest in the Aprinnova JV in exchange for an initial payment to Amyris of $10.0 million and payment to Amyris of any profits distributed in cash to Nikko from the Aprinnova JV during the three year period following December 12, 2016, up to a maximum of $10.0 million. In addition, as part of the formation of the Aprinnova JV, we and Nikko agreed to make certain working capital loans to the Aprinnova JV and executed a supply agreement to supply farnesene to the Aprinnova JV, to purchase all of our requirements for the Aprinnova JV products from the Aprinnova JV, to transfer all of our customers for the Aprinnova JV products to the Aprinnova JV, to guarantee a maximum production cost for certain Aprinnova JV products, and to bear any cost of production above such guaranteed costs.

Product Distribution and Sales

We distribute and sell our products directly to distributors or collaboration partners, or through joint ventures, depending on the market. For most of our products, we sell directly to our collaboration partners, except for our consumer care products, which we sell to distributors and formulators (other than our Biossance brand, which we sell directly to retailers and consumers). Generally, our collaboration agreements include commercial terms, and sales are contingent upon achievement of technical and commercial milestones.

For the year ended December 31, 2019, revenue from 10%-or-more customers and from all other customers was as follows:

(In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total Revenue		% of Total Revenue
DSM	$	10	$	49,051	$	4,120	$	53,181	34.9	%
Lavvan	—		—		18,342		18,342		12.0	%
All other customers	59,862		4,992		16,180		81,034		53.1	%
Total revenue	$	59,872	$	54,043	$	38,642	$	152,557	100.0	%

Intellectual Property

Our success depends in large part upon our ability to obtain and maintain proprietary protection for our products and technologies, and to operate without infringing on the proprietary rights of others. We seek to avoid the latter by monitoring patents and publications in our product areas and technologies to be aware of developments that may affect our business, and to the extent we identify such developments, evaluate and take appropriate courses of action. With respect to the former, our policy is to protect our proprietary position by, among other methods, filing for patent applications on inventions that are important to the development and conduct of our business with the U.S. Patent and Trademark Office (the USPTO), and its foreign counterparts.

As of December 31, 2019, we had 633 issued U.S. and foreign patents and 238 pending U.S. and foreign patent applications that are owned or co-owned by or licensed to us. We also use other forms of protection (such as trademark, copyright, and trade secret) to protect our intellectual property, particularly where we do not believe patent protection is appropriate or obtainable. We aim to take advantage of all of the intellectual property rights that are available to us and believe that this comprehensive approach provides us with a strong proprietary position.

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Patents extend for varying periods according to the date of patent filing or grant and the legal term of patents in various countries where patent protection is obtained. The actual protection afforded by patents, which can vary from country to country, depends on the type of patent, the scope of its coverage and the availability of legal remedies in the country. See “Risk Factors - Risks Related to Our Business - Our proprietary rights may not adequately protect our technologies and product candidates.”

We also protect our proprietary information by requiring our employees, consultants, contractors and other advisers to execute nondisclosure and assignment of invention agreements upon commencement of their respective employment or engagement. Agreements with our employees also prevent them from bringing the proprietary rights of third parties to us. In addition, we also require confidentiality or material transfer agreements from third parties that receive our confidential data or materials.

Trademarks

Amyris, the Amyris logo, Biofene, Biossance, Pipette, Purecane and No Compromise are trademarks or registered trademarks of Amyris, Inc or its subsidiaries. This report also contains trademarks and trade names of other businesses that are the property of their respective holders.

Competition

We expect that our renewable products will compete with products produced from traditional sources as well as from alternative production methods (including the intellectual property underlying such methods) that established enterprises and new companies are seeking to develop and commercialize.

Health & Wellness

Many active ingredients in the nutraceutical market are made via chemical synthesis by suppliers that have a deep chemistry knowhow and production facilities, including ingredient suppliers. We may compete directly with these companies with respect to specific ingredients or attempt to provide customers with more cost effective or higher performing alternatives. For food ingredients, we compete with companies that produce products from plant- and animal-derived sources as well as with companies that are also developing biotechnology production solutions to produce specific molecules.

Flavor & Fragrance

The main competition in the Flavor & Fragrance and cosmetic actives markets is from products derived from plant and animal sources as well as chemical synthesis. The products derived from plant and animal sources are typically produced at a higher cost, lower purity and create a greater impact on the environment compared to our products. Products derived from chemical synthesis are often produced at a low cost but may have ramifications on sustainability and on non-natural sourcing. There are also companies that are working to develop products using similar technology to us.

Clean Beauty

We develop and sell active cosmetic ingredients and consumer products in the Clean Beauty market, creating a competitive landscape that includes ingredient suppliers as well as consumer goods companies, such as Procter & Gamble and Estee Lauder. Most skincare ingredients are derived from plant and animal sources or created using chemical synthesis. Plant- and animal-sourced ingredients are typically higher in cost, lower in purity and have a greater impact on the environment versus our products. Products derived from chemical synthesis are often produced at a low cost but have ramifications on sustainability as well as non-natural sourcing. There are also companies that are working to develop products using similar technology to us.

Competitive Factors

We believe the primary competitive factors in our target markets are:

•product price;

•product performance and other measures of quality;

•product cost;

•infrastructure compatibility of products;

•sustainability; and

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•dependability of supply.

We believe that, for our products to succeed in the market, we must demonstrate that our products are comparable or better alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, pricing, availability, performance, and consumer preference characteristics.

Regulatory Matters

Environmental Regulations

Our development and production processes involve the use, generation, handling, storage, transportation and disposal of hazardous chemicals and radioactive and biological materials. We are subject to a variety of federal, state, local and international laws, regulations and permit requirements governing the use, generation, manufacture, transportation, storage, handling and disposal of these materials in the United States, Brazil, Europe, China and other countries where we operate or may operate or sell our products in the future. These laws, regulations and permits can require expensive fees, pollution control equipment or operational changes to limit actual or potential impact of our technology on the environment and violation of these laws could result in significant fines, civil sanctions, permit revocation or costs from environmental remediation. We believe we are currently in substantial compliance with applicable environmental regulations and permitting. However, future developments including the commencement of or changes in the processes relating to commercial manufacturing of one or more of our products, more stringent environmental regulation, policies and enforcement, the implementation of new laws and regulations or the discovery of unknown environmental conditions may require expenditures that could have a material adverse effect on our business, results of operations or financial condition. See “Risk Factors - Risks Relating to Our Business - We may incur significant costs to comply with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.”

GMM Regulations

The use of genetically modified microorganisms (GMMs), such as our yeast strains, is subject to laws and regulations in many countries. In the United States, the Environmental Protection Agency (EPA) regulates the commercial use of GMMs as well as potential industrial products produced from the GMMs. Various states within the United States could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we use, S. cerevisiae, is eligible for exemption from EPA review because it is generally recognized as safe, we must satisfy certain criteria to achieve this exemption, including but not limited to, use of compliant containment structures and safety procedures. In Brazil, GMMs are regulated by the National Biosafety Technical Commission (CTNBio) under its Biosafety Law No. 11.105-2005. We have obtained commercial approvals from CTNBio to use our GMMs in a contained environment in our Brazil facilities for research and development purposes, in manufacturing and at contract manufacturing facilities in Brazil.

We expect to encounter GMM regulations in most if not all of the countries in which we may seek to make our products; however, the scope and nature of these regulations will likely vary from country to country. In addition, such regulations may change over time. If we cannot meet the applicable requirements in countries in which we intend to produce our products using our yeast strains, then our business will be adversely affected. See “Risk Factors - Risks Related to Our Business - Our use of genetically modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.”

Chemical Regulations

Our renewable products may be subject to government regulations in our target markets. In the United States, the EPA administers the requirements of the Toxic Substances Control Act (TSCA), which regulates the commercial registration, distribution and use of many chemicals. Before an entity can manufacture or distribute significant volumes of a chemical, it needs to determine whether that chemical is listed in the TSCA inventory. If the substance is listed, then manufacture or distribution can commence immediately. If not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice must be filed with the EPA, which has 90 days to review the filing. A similar requirement exists in Europe under the Registration, Evaluation, Authorization and Restriction of Chemical Substances (REACH) regulation. See “Risk Factors - Risks Related to Our Business - We may not be able to obtain regulatory approval for the sale of our renewable products.” In 2013, the EPA registered farnesane as a new chemical substance under the TSCA, which enables us to manufacture and sell farnesane without restriction in the United States.

Other Regulations

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Certain of our current or emerging products in the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets, including alternative sweeteners, nutraceuticals, Flavor & Fragrance ingredients, skincare ingredients, cosmetic actives, and our proposed cannabinoid products, are subject to regulation by either the FDA or the Drug Enforcement Administration (DEA) or both, as well as similar agencies of states and foreign jurisdictions where these products are manufactured, sold or proposed to be sold. Pursuant to the Federal Food, Drug, and Cosmetic Act (the FDCA), the FDA regulates the processing, formulation, safety, manufacture, packaging, labeling and distribution of food ingredients, vitamins, and cosmetics. Generally, in order to be marketed and sold in the United States, a relevant product must be generally recognized as safe, approved and not adulterated or misbranded under the FDCA and relevant regulations issued thereunder. The FDA has broad authority to enforce the provisions of the FDCA applicable to food ingredients, vitamins, drugs and cosmetics, including powers to issue a public warning letter to a company, to publicize information about illegal products, to request a recall of illegal products from the market, and to request the United States Department of Justice to initiate a seizure action, an injunction action, or a criminal prosecution in the U. S. courts. Failure to obtain requisite approval from, or comply with the laws and regulations of, the FDA or similar agencies of states and applicable foreign jurisdictions could prevent us from fully commercializing certain of our products. See “Risk Factors - Risks Related to Our Business - We may not be able to obtain regulatory approval for the sale of our renewable products.” Our proposed cannabinoid products may also be subject to regulation under various federal, state and foreign-controlled substance laws and regulations. See “Risk Factors - Our cannabinoid initiative is uncertain and may not yield commercial results and is subject to significant regulatory risks.”

In addition, our end-user products such as our Biossance and Pipette brands clean skincare products will be subject to the Natural Cosmetics/Personal Care Products Safety Act, if enacted. Cosmetic products are regulated by or under the FDA’s oversight. Also, our end-user products are subject to the regulations of the United States Federal Trade Commission (FTC) and similar agencies of states and foreign jurisdictions where these products are sold or proposed to be sold regarding the advertising of such products. In recent years, the FTC has instituted numerous enforcement actions against companies for failure to have adequate substantiation for claims made in advertising or for the use of false or misleading advertising claims. The FTC has broad authority to enforce its laws and regulations applicable to cosmetics, including the ability to institute enforcement actions which often result in consent decrees, injunctions, and the payment of civil penalties by the companies involved. Failure to comply with the laws and regulations of the FTC or similar agencies of states and applicable foreign jurisdictions could impair our ability to market our end-user products.

Employees

As of December 31, 2019, we had 561 full-time employees, of whom 440 were in the United States, 103 were in Brazil and 18 were in Portugal. Except for labor union representation for Brazil-based employees based on labor code requirements in Brazil, none of our employees is represented by a labor union or is covered by a collective bargaining agreement. We have never experienced any employment-related work stoppages, and we consider relations with our employees to be good.

Corporate Information

We were originally incorporated in California in 2003 under the name Amyris Biotechnologies, Inc. and then reincorporated in Delaware in 2010 and changed our name to Amyris, Inc. Our principal executive offices are located at 5885 Hollis Street, Suite 100, Emeryville, California 94608, and our telephone number is (510) 450-0761. Our common stock is listed on The Nasdaq Global Select Market under the symbol "AMRS".

Available Information

Our website address is www.amyris.com. Our Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q, Current Reports on Form 8-K, and other reports filed pursuant to Sections 13(a) and 15(d) of the Securities Exchange Act of 1934 (the Exchange Act), as well as amendments thereto, are filed with the U.S. Securities and Exchange Commission (the SEC) and are available free of charge on our website at investors.amyris.com promptly after such reports are available on the SEC's website. We may use our investors.amyris.com website as a means of disclosing material non-public information and complying with our disclosure obligations under Regulation FD.

The SEC maintains an Internet site that contains reports, proxy and information statements, and other information regarding issuers that file electronically with the SEC at www.sec.gov.

The information contained in or accessible through our website or contained on other websites is not incorporated into this filing. Further, any references to URLs contained in this report are intended to be inactive textual references only.

ITEM 1A. RISK FACTORS

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Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described below, together with all of the other information set forth in this Annual Report on Form 10-K, including the consolidated financial statements and related notes, which could materially affect our business, financial condition or future results. If any of the following risks actually occurs, our business, financial condition, results of operations and future prospects could be materially and adversely harmed. The trading price of our common stock could decline due to any of these risks, and, as a result, you may lose all or part of your investment.

Risks Related to Our Business

We have identified a material weakness in our internal control over financial reporting which, if not corrected, could affect the reliability of our consolidated financial statements and have other adverse consequences.

Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rule 13a-15(f) under the Exchange Act. Section 404 of the Sarbanes-Oxley Act of 2002 (Section 404) and related SEC rules require management to assess the effectiveness of our internal control over financial reporting. Based on the assessment as of December 31, 2019, our management believes that our internal control over financial reporting was not effective at that date due to a material weakness we identified. A material weakness is a deficiency, or combination of control deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim financial statements will not be prevented or detected on a timely basis.

Based on management's assessment, we have identified the following material weakness:

•We did not have an effective internal and external information and communication process to ensure that relevant and reliable information was communicated timely across the organization, to enable financial personnel to effectively carry out their financial reporting and internal control roles and responsibilities.

As a consequence of the ineffective communication components, we did not design, implement, and maintain effective control activities at the transaction level over debt-related liability accounts to mitigate the risk of material misstatement in financial reporting, specifically:

•We did not design and operate effective controls over significant non-routine transactions related to certain debt-related contractual obligations.

Control deficiencies in 2017 and 2018 contributed to the restatement of our audited consolidated financial statements for the year ended December 31, 2017 and resulted in material errors to our interim condensed consolidated financial statements for the quarterly and year-to-date periods ended March 31, 2017, June 30, 2017, September 30, 2017, March 31, 2018, June 30, 2018 and September 30, 2018. Also, a control deficiency in 2019 contributed to a material misstatement, as described above, to the preliminary unissued consolidated financial statements as of and for the three and nine months ended September 30, 2019. While the material misstatement was corrected prior to the issuance of the condensed consolidated financial statements as of and for the three and nine months ended September 30, 2019, we concluded this control deficiency was a material weakness and our internal control over financial reporting was not effective as of December 31, 2019, and creates a reasonable possibility that a further material misstatement of our annual or interim consolidated financial statements would not be prevented or detected on a timely basis.

See Part II, Item 9A “Controls and Procedures” of this Annual Report on Form 10-K for additional information. If not remediated, the material weakness could result in further material misstatements to our annual or interim consolidated financial statements that would not be prevented or detected on a timely basis, or in delayed filing of required periodic reports. Our management has developed, and begun to implement, a plan to remediate the material weakness. We cannot, however, assure you that we will be able to implement the plan, or to remediate the material weakness in a timely manner. Furthermore, during the course of re-design of existing processes and controls, implementation of additional processes and controls and testing of the operating effectiveness of such re-designed and additional processes and controls, we may identify additional control deficiencies that could give rise to other material weaknesses, in addition to the currently identified material weakness. We expect the remediation plan to extend over multiple financial reporting periods in 2020. If our remedial measures are insufficient to address the material weakness, or if additional material weaknesses or significant deficiencies in our internal controls are discovered or occur in the future, we may be unable to report our financial results accurately or on a timely basis, which could cause our reported financial results to be materially misstated and result in the loss of investor confidence and adversely affect the market price of our common stock and our ability to access the capital markets, and we could be subject to sanctions or investigations by the Nasdaq Stock Market (Nasdaq), the SEC or other regulatory authorities.

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If we fail to maintain an effective system of internal controls, we may not be able to report our financial results accurately or in a timely manner or prevent fraud; in that case, our stockholders could lose confidence in our financial reporting, which would harm our business and could negatively impact the price of our stock.

Effective internal controls are necessary for us to provide reliable financial reports and help us to prevent fraud. In addition, Section 404 of the Sarbanes-Oxley Act of 2002 (Section 404) requires us and our independent registered public accounting firm to evaluate and report on our internal control over financial reporting. The process of implementing our internal controls and complying with Section 404 is expensive and time consuming, and requires significant continuous attention of management. We cannot be certain that these measures will ensure that we maintain adequate controls over our financial processes and reporting in the future. In addition, to the extent we create joint ventures or have any variable interest entities and the financial statements of such entities are not prepared by us, we will not have direct control over their financial statement preparation. As a result, we will, for our financial reporting, depend on what these entities report to us, which could result in us adding monitoring and audit processes to those operations and increase the difficulty of implementing and maintaining adequate internal control over our financial processes and reporting in the future, which could lead to delays in our external reporting. In particular, this may occur in instances in which where we are establishing such entities with commercial partners that do not have sophisticated financial accounting processes in place, or where we are entering into new relationships at a rapid pace, straining our integration capacity. Additionally, if we do not receive the information from the joint venture or variable interest entity on a timely basis, it could cause delays in our external reporting. Even if we conclude in the future, and our independent registered public accounting firm concurs, that our internal control over financial reporting provides reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles, because of its inherent limitations, internal control over financial reporting may not prevent or detect fraud or misstatements. Failure to implement required new or improved controls, or difficulties encountered in their implementation, could harm our results of operations or cause us to fail to meet our reporting obligations, which could reduce the market’s confidence in our financial statements and harm our stock price. In addition, failure to comply with Section 404 could subject us to a variety of administrative sanctions, including SEC action, the suspension or delisting of our common stock from the stock exchange on which it is listed, and the inability of registered broker-dealers to make a market in the Company’s common stock, which could further reduce our stock price and could harm our business.

We have incurred losses to date, anticipate continuing to incur losses in the future, and may never achieve or sustain profitability.

We have incurred significant operating losses since our inception, and we expect to continue to incur losses and negative cash flows from operations for at least the next 12 months following the issuance of this Annual Report on Form 10-K. As of December 31, 2019, we had negative working capital of $87.5 million and an accumulated deficit of $1.8 billion.

As of December 31, 2019, our debt, net of a $20.3 million debt discount and a $15.4 million fair value adjustment, totaled $261.8 million, of which $63.8 million is classified as current. Our debt agreements contain various covenants, including certain restrictions on our business that could cause us to be at risk of contractual defaults, such as restrictions on additional indebtedness, material adverse effect and cross default clauses. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding indebtedness. We have in the past, including in July 2019, had certain of our debt instruments accelerated for failure to make a payment when due. While we have been able to cure these defaults to date to avoid additional cross-acceleration, we may not be able to cure such a default promptly in the future. See Note 15, “Subsequent Events” in Part II, Item 8 of this Annual Report on Form 10-K for additional information.

Our cash and cash equivalents of $0.3 million as of December 31, 2019 is not sufficient to fund expected future negative cash flows from operations and cash debt service obligations through March 31, 2021. These factors raise substantial doubt about our ability to continue as a going concern within one year after the date that these financial statements are issued. The financial statements do not include any adjustments that might result from the outcome of this uncertainty. Our ability to continue as a going concern will depend, in large part, on our ability to raise additional proceeds through financings, achieve positive cash flows from operations during the 12 months from the date of this filing, and refinance or extend other existing debt maturities currently past due and those occurring later in 2020, all of which is uncertain and outside our control. Further, our operating plan for 2020 contemplates a significant reduction in our net operating cash outflows as compared to the year ended December 31, 2019, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) reduced spending in general and administrative areas, and (iv) cash inflows from collaborations and grants. If we are unable to complete these actions, we expect to be unable to meet our operating cash flow needs and our obligations under our existing debt facilities.

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This could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and the Company may be forced to obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all, and/or liquidate our assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these financial statements.

Our consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty, which could have a material adverse effect on our financial condition and cause investors to suffer the loss of all or a substantial portion of their investment.

We will require significant cash inflows from the sales of renewable products, licenses and royalties, and grants and collaborations and, if needed, financings to fund our anticipated operations and to service our debt obligations and may not be able to obtain such funding on favorable terms, if at all.

Our planned working capital needs and operating and capital expenditures for 2020, and our ability to service our outstanding debt obligations, are dependent on significant inflows of cash from grants and collaborations, licenses and royalties, and product sales and, if needed, additional financing arrangements. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, procurement, storage, distribution and other aspects of our business. Some of our anticipated funding sources, such as research and development collaborations, are subject to the risks that we may not be able to meet milestones, or that collaborations may end prematurely for reasons that may be outside of our control (including technical infeasibility of the project or a collaborator’s right to terminate without cause). The inability to generate sufficient cash flow, as described above, could have an adverse effect on our ability to continue with our business plans and our status as a going concern.

If we are unable to raise additional funding, or if other expected sources of funding are delayed or not received, our ability to continue as a going concern would be jeopardized and we would take the following actions:

•Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts;

•Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors;

•Reduce or delay uncommitted capital expenditures, including expenditures related the construction and commissioning of the new production facility in Brazil, nonessential facilities and lab equipment, and information technology projects; and

•Closely monitor our working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

•Achieve planned production levels;

•Develop and commercialize products within planned timelines or at planned scales; and

•Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have an adverse effect on our ability to meet contractual requirements and increase the severity of the consequences described above.

Our existing financing arrangements provide our secured lenders with liens on substantially all of our assets, including our intellectual property, and contain financial covenants and other restrictions on our actions, which may cause significant risks to our stockholders and may impact our ability to pursue certain transactions and operate our business.

As of December 31, 2019, our debt, net of a $20.3 million debt discount and a $15.4 million fair value adjustment, totaled $261.8 million, of which $63.8 million is classified as current. Our cash balance is substantially less than the principal amount of our outstanding debt, and we will be required to generate cash from operations and raise additional working capital through future financings or sales of assets to enable us to repay this indebtedness as it becomes due. There can be no assurance that we will be able to do so.

In addition, we have granted liens on substantially all of our assets, including our intellectual property, as collateral in connection with certain financing arrangements with a current aggregate principal amount outstanding of $133.2 million, and have agreed to significant covenants in connection with such transactions (see Note 4, “Debt” in Part II, Item 8 of this Annual Report on Form 10-K), including covenants that materially limit our ability to take certain actions, including our ability to pay dividends, make certain investments and other payments, incur additional indebtedness, undertake certain mergers and

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consolidations, and encumber and dispose of assets, and customary events of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse effect events, certain cross defaults and judgements, and insolvency. For example, the loan and security agreements relating to our secured term loan credit facilities that closed in June 2018 and August 2019 (as further amended and restated in October 2019) prevent us from incurring additional indebtedness, making investments, encumbering our assets, engaging in certain corporate transactions, such as mergers and consolidations, and transferring or otherwise disposing of assets, subject in each case to certain exceptions, and also require us to maintain certain liquidity and asset coverage levels and meet certain revenue requirements. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of such indebtedness and could result in a material adverse effect on us. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of a substantial portion of our indebtedness. Any required repayment of our indebtedness as a result of acceleration or otherwise would lower our current cash on hand such that we would not have those funds available for use in our business or for payment of other outstanding indebtedness.

If we are at any time unable to generate sufficient cash flow from operations to service our indebtedness when payment is due, we may be required to attempt to renegotiate the terms of the instruments relating to the indebtedness, seek to refinance all or a portion of the indebtedness or obtain additional financing. There can be no assurance that we would be able to successfully renegotiate such terms, that any such refinancing would be possible or that any additional financing could be obtained on terms that are favorable or acceptable to us, if at all. Any debt financing that is available could cause us to incur substantial costs and subject us to covenants that significantly restrict our ability to conduct our business. If we seek to complete additional equity financings, the interests of existing equity holders may be diluted. If we are unable to make payment on our secured debt instruments when due, the lenders under such instruments may foreclose on and sell the assets securing such indebtedness to satisfy our payment obligations, which could prevent us from accessing those assets for our business and conducting our business as planned, which could materially harm our financial condition and results of operations.

In addition, certain of our outstanding securities contain anti-dilution adjustment provisions that may be triggered by future issuances of equity or equity-linked instruments in financing transactions. If such adjustment provisions are triggered, the conversion or exercise price of such securities will decrease and/or the number of shares issuable upon conversion or exercise of such securities will increase. In such event, existing stockholders will be further diluted and the effective issuance price of such equity or equity-linked instruments will be reduced, which may harm our ability to engage in future financing transactions to fund our business.

Our substantial leverage may place us at a competitive disadvantage in our industry.

We continue to have substantial debt outstanding and we may incur additional indebtedness from time to time to finance working capital, product development efforts, strategic acquisitions, investments and partnerships, or capital expenditures, or for other general corporate purposes, subject to the restrictions contained in our debt agreements. Our significant indebtedness and debt service requirements could adversely affect our ability to operate our business and may limit our ability to take advantage of potential business opportunities. For example, our high level of indebtedness presents the following risks:

•we will be required to use a substantial portion of our cash flow from operations to pay principal and interest on our indebtedness, thereby reducing the availability of our cash flow to fund working capital, capital expenditures, product development efforts, acquisitions, investments and strategic alliances and for other general corporate requirements;

•our substantial leverage increases our vulnerability to economic downturns and adverse competitive and industry conditions and could place us at a competitive disadvantage compared to those of our competitors that are less leveraged;

•our debt service obligations could limit our flexibility in planning for, or reacting to, changes in our business and our industry and could limit our ability to pursue other business opportunities, borrow more money for operations or capital in the future and implement our business strategies;

•our level of indebtedness and the covenants in our debt instruments may restrict us from raising additional financing on satisfactory terms to fund working capital, capital expenditures, product development efforts, strategic acquisitions, investments and alliances, and for other general corporate requirements;

•our secured loan agreements restrict our ability to grant additional liens on our assets, which may make it more difficult to secure additional financing in the future; and

•our substantial leverage may make it difficult for us to attract additional financing when needed.

We are currently ineligible to use a registration statement on Form S-3 to register the offer and sale of securities, which could adversely affect our ability to raise future capital.

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As a result of the delayed filing of our Annual Report on Form 10-K for the year ended December 31, 2018, our Quarterly Report on Form 10-Q for the fiscal quarter ended March 31, 2019 and our Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 2019 with the SEC, we will not be eligible to register the offer and sale of our securities using a registration statement on Form S-3 until one year from the date we regain and maintain status as a current filer. Should we wish to register the offer and sale of our securities to the public prior to the time we are eligible to use Form S-3, both our transaction costs and the amount of time required to complete the transaction could increase, potentially harming our financial condition.

Future revenues are difficult to predict, and our failure to predict revenue accurately may cause our results to be below our expectations or those of analysts or investors and could result in our stock price declining.

Our revenues are comprised of product revenues, licenses and royalties revenues, and grants and collaborations revenues. We generate the substantial majority of our product revenues from sales to collaboration partners and distributors, and only a small portion from direct sales. Our collaboration, supply and distribution agreements do not usually include any specific purchase obligations. The sales volume of our products in any given period has been difficult to predict. A significant portion of our product sales is dependent upon the interest and ability of third-party distributors to create demand for, and generate sales of, such products to end-users. For example, if such distributors are unsuccessful in creating pull-through demand for our products with their customers, such distributors may purchase less of our products from us than we expect. Also, under revenue recognition rules, we are required to estimate royalties. These estimates could be subject to material adjustment in subsequent periods.

In addition, many of our new and novel products are intended to be a component of other companies’ products; therefore, sales of our products may be contingent on our collaboration partners and/or customers’ timely and successful development and commercialization of end-use products that incorporate our products, and price volatility in the markets for such end-use products, which may include commodities, could adversely affect the demand for our products and the margin we receive for our product sales, which could harm our financial results. While we maintain certain clawback rights to our technology in the event our collaboration partners are unable or unwilling to commercialize the products we create for them, we may be restricted from or unable to market or sell such products or technologies to other potential collaboration partners, which could hinder the growth of our business. In addition, certain of our collaboration partners have the right to terminate their agreements with us if we undergo a change of control or a sale of our business, which could discourage a potential acquirer from making an offer to acquire us.

Further, we have in the past entered into, and expect in the future to enter into, research and development collaboration arrangements pursuant to which we receive payments from our collaboration partners. Some of such collaboration arrangements include advance payments in consideration for grants of exclusivity or research and development activities to be performed by us. It has in the past been difficult for us to know with certainty when we will sign a new collaboration arrangement and receive payments thereunder. In addition, a portion of the advance payments we receive under our collaboration agreements is typically classified as contract liabilities and recognized over multiple quarters or years. As a result, achievement of our quarterly and annual financial goals has been difficult to forecast with certainty. Once a collaboration agreement has been signed, receipt of cash payments and/or recognition of related revenues may depend on our achievement of research, development, production or cost milestones, which may be difficult to predict. Our collaboration arrangements may also include future royalty payments upon commercialization of the products subject to the collaboration arrangements, which is uncertain and depends in part on the success of the counterparty in commercializing the relevant product. As a result, our receipt of royalty revenues and the timing thereof is difficult to predict with certainty.

Furthermore, we market and sell some of our products directly to end-consumers, initially in the cosmetics market. Because we have limited experience in marketing and selling directly to consumers, it is difficult to predict how successful our efforts will be and we may not achieve the product sales we expect to achieve on the timeline we anticipate, if at all. These factors have made it difficult to predict future revenues and have resulted in our revenues being below our previously announced guidance or analysts’ estimates. We continue to face these risks in the future, which may cause our stock price to decline.

Our financial results could vary significantly from quarter to quarter and are difficult to predict.

Our revenues and results of operations could vary significantly from quarter to quarter because of a variety of factors, many of which are outside of our control. As a result, comparing our results of operations on a period-to-period basis may not be meaningful. Factors that could cause our quarterly results of operations to fluctuate include:

•achievement, or failure, with respect to technology, product development or manufacturing milestones needed to allow us to enter identified markets on a cost-effective basis or obtain milestone-related payments from collaboration partners;

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•delays or greater than anticipated expenses associated with the completion, commissioning, acquisition or retrofitting of new production facilities, or the time to ramp up and stabilize production at a new production facility or the transition (including ramp up) to producing new molecules at existing facilities or with a new contract manufacturer;

•impairment of assets based on shifting business priorities and working capital limitations;

•disruptions in the production process at any manufacturing facility, including disruptions due to seasonal or unexpected downtime as a result of feedstock availability, contamination, safety or other technical difficulties, or scheduled downtime as a result of transitioning equipment to the production of different molecules;

•losses of, or the inability to secure new, major customers, collaboration partners, suppliers or distributors;

•losses associated with producing our products as we ramp to commercial production levels;

•failure to recover value added tax (VAT) that we currently reflect as recoverable in our financial statements (e.g., due to failure to meet conditions for reimbursement of VAT under local law);

•the timing, size and mix of product sales to customers;

•increases in price or decreases in availability of feedstock;

•the unavailability of contract manufacturing capacity altogether or at reasonable cost;

•exit costs associated with terminating contract manufacturing relationships;

•fluctuations in foreign currency exchange rates;

•change in the fair value of derivative instruments;

•fluctuations in the price of and demand for sugar, ethanol, petroleum-based and other products for which our products are alternatives;

•seasonal variability in production and sales of our products;

•competitive pricing pressures, including decreases in average selling prices of our products;

•unanticipated expenses or delays associated with changes in governmental regulations and environmental, health, labor and safety requirements;

•departure of executives or other key management employees resulting in transition and severance costs;

•our ability to use our net operating loss carryforwards to offset future taxable income;

•business interruptions such as earthquakes, tsunamis and other natural disasters, including pandemics;

•our ability to integrate businesses that we may acquire;

•our ability to successfully collaborate with joint venture partners;

•risks associated with the international aspects of our business; and

•changes in general economic, industry and market conditions, both domestically and in our foreign markets.

Due to the factors described above, among others, the results of any quarterly or annual period may not meet our expectations or the expectations of our investors and may not be meaningful indications of our future performance.

A limited number of customers, collaboration partners and distributors account for a significant portion of our revenues, and the loss of major customers, collaboration partners or distributors could harm our operating results.

Our revenues have varied significantly from quarter to quarter and are dependent on sales to, and collaborations with, a limited number of customers, collaboration partners and/or distributors. We cannot be certain that customers, collaboration partners and/or distributors that have accounted for significant revenues in past periods, individually or as a group, will continue to generate similar revenues in any future period. If we fail to renew with, or if we lose, a major customer, collaborator or distributor, or group of customers, collaboration partners or distributors, our revenues could decline if we are unable to replace the lost revenues with revenues from other sources. Further, since our business depends in part on such collaboration agreement, it may be difficult for us to replace any such lost revenues through additional collaborations in any period, as revenue from such new collaborations will often be recognized over multiple quarters or years.

If we do not meet technical, development and commercial milestones in our collaboration agreements, our future revenues and financial results will be adversely impacted.

We have entered into a number of agreements regarding the development of certain of our products and, in some cases, for ultimate sale of certain products to the customer under the agreement. Most of these agreements do not affirmatively obligate the other party to purchase specific quantities of any products, and most contain important conditions that must be satisfied before additional research and development funding or product purchases would occur. These conditions include research and development milestones and technical specifications that must be achieved to the satisfaction of our collaboration partners, which we cannot be certain we will achieve. If we do not achieve these contractual milestones or specifications, our revenues and financial results will be adversely affected.

We face challenges producing our products at commercial-scale or at reduced cost and may not be able to commercialize our products to the extent necessary to make a profit or sustain and grow our current business.

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To commercialize our products, we must be successful in using our yeast strains to produce target molecules at commercial-scale and at a commercially viable cost. If we cannot achieve commercially-viable production economics for enough products to support our business plan, including through establishing and maintaining sufficient production-scale and volume, we will be unable to achieve a sustainable products business.

In order to be competitive in the markets we are targeting, our products must have superior qualities or be competitively priced relative to alternatives available in the market. Our production costs depend on many factors that could have a negative effect on our ability to offer our planned products at competitive prices, including, in particular, our ability to establish and maintain sufficient production scale and volume, and feedstock and contract manufacturing costs.

We face financial risk associated with scaling up production to reduce our production costs. To reduce per-unit production costs, we must increase production to achieve economies of scale and to be able to sell our products with positive margins. However, if we do not sell production output in a timely manner or in sufficient volumes, our investment in production will harm our cash position and generate losses. Additionally, we may incur added costs in storage and we may face issues related to the decrease in quality of our stored products, which could adversely affect the value of such products. Since achieving competitive product prices generally requires increased production volumes and our manufacturing operations and cash flows from sales are in their early stages, we have had to produce and sell products at a loss in the past, and may continue to do so as we build our business. If we are unable to achieve adequate revenues from a combination of product sales and other sources, we may not be able to invest in production and we may not be able to pursue our business plans. In addition, in order to attract potential collaboration or joint venture partners, or to meet payment milestones under existing or future collaboration agreements, we have in the past and may in the future be required to guarantee or meet certain levels of production costs. If we are unable to reduce our production costs to meet such guarantees or milestones, our net cash flow will be further reduced.

If we are not able to successfully commence, scale-up or sustain operations at existing and planned manufacturing facilities, our customer relationships, business and results of operations may be adversely affected.

A substantial component of our planned production capacity in the near and long term depends on successful operations at our existing and potential large-scale production plants. We commenced operations at our first purpose-built, large-scale production facility located in Brotas, Brazil in 2012. In December 2016, we acquired a production facility in Leland, North Carolina, which facility had been previously operated by our partner Glycotech Inc. to perform chemical conversion and production of certain of our end-products, and which facility was subsequently transferred to our joint venture with Nikko, as further described in Note 10, “Related Party Transactions” in Part II, Item 8 of this Annual Report on Form 10-K. In December 2017, we sold the Brotas facility to DSM and concurrently entered into a supply agreement with DSM for us to purchase output from the facility, which represents a significant portion of our expected supply needs (see Note 12, “Divestiture”, Note 9, "Revenue Recognition" and Note 10, "Related Party Transactions" in Part II, Item 8 of this Annual Report on Form 10-K for more information). We are building a new purpose-built, large-scale specialty ingredients plant in Brazil, which we anticipate will allow for the manufacture of five products concurrently and to produce both our specialty ingredients portfolio and our alternative sweetener product. We currently anticipate facility construction to be completed in the second quarter of 2021; however, there can be no assurances that we will be able to complete such facility on our expected timeline, if at all. In addition, in May 2019 we entered into a joint venture agreement with Raizen for the production, sale and commercialization of alternative sweetener products, pursuant to which the parties would construct a manufacturing facility exclusively for alternative sweetener products on land owned by Raizen and leased to the joint venture. The consummation of the transactions contemplated by the opportunity to launch a joint venture with Raizen, including the construction of a manufacturing facility for the production of alternative sweetener products, is subject to conditions, including certain regulatory approvals and the achievement of certain technological and economic milestones relating to the production of our alternative sweetener product, and there can be no assurances that the construction of such facility will occur on our expected timeline, if at all. Delays or problems in the construction, start-up or operation of such facilities could cause delays in our ramp-up of production and hamper our ability to reduce our production costs. Delays in construction can occur due to a variety of factors, including regulatory requirements and our ability to fund construction and commissioning costs.

Once our large-scale production facilities are built, acquired or retrofitted, we must successfully commission them, if necessary, and they must perform as we expect. If we encounter significant delays, cost overruns, engineering issues, contamination problems, equipment or raw material supply constraints, unexpected equipment maintenance requirements, safety issues, work stoppages or other serious challenges in bringing these facilities online and operating them at commercial-scale, we may be unable to produce our renewable products in the time frame and at the cost we have planned. It is difficult to predict the effects of scaling up production of industrial fermentation to commercial-scale, as it involves various risks to the quality and consistency of our molecules. In addition, in order to produce molecules at existing and potential future plants, we have been and may in the future be required to perform thorough transition activities, and modify the design of the plant. Any

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modifications to the production plant could cause complications in the operations of the plant, which could result in delays or failures in production. If any of these risks occur, or if we are unable to create or obtain additional manufacturing capacity necessary to meet existing and potential customer demand, we may need to continue to use, or increase our use of, contract manufacturing sources, which may not be available on terms acceptable to us, if at all, and generally entail greater cost to us to produce our products and would therefore reduce our anticipated gross margins and may also prevent us from accessing certain markets for our products. Further, if our efforts to increase (or commence, as the case may be) production at these facilities are not successful, our partners may decide not to work with us to develop additional production facilities, demand more favorable terms or delay their commitment to invest capital in our production. If we are unable to create and sustain manufacturing capacity and operations sufficient to satisfy the existing and potential demand of our customers and partners, our business and results of operations may be adversely affected.

In addition, the production of our products at our planned purpose-built, large-scale production facilities will require large volumes of feedstock. For our planned large-scale production facilities in Brazil, we plan to rely primarily on Brazilian sugarcane. While in certain cases we have entered into feedstock agreements with suppliers, including Raizen, which we expect to supply the sugarcane feedstock necessary to produce our products at our planned large-scale production facilities in Brazil, that specify the pricing, quantity and product specifications for our feedstocks, we cannot predict the future availability or price of these various feedstocks, nor can we be sure that our mill partners, including Raizen, will be able to supply it in sufficient quantities or in a timely manner. Furthermore, to the extent we are required to rely on sugar feedstock other than Brazilian sugarcane, the cost of such feedstock may be higher than we expect, increasing our anticipated production costs. Feedstock crop yields and sugar content depend on weather conditions, such as rainfall and temperature. Weather conditions have historically caused volatility in the ethanol and sugar industries by causing crop failures or reduced harvests. Excessive rainfall can adversely affect the supply of sugarcane and other sugar feedstock available for the production of our products by reducing the sucrose content and limiting growers' ability to harvest. Crop disease and pestilence can also occur from time to time and can adversely affect feedstock growth, potentially rendering useless or unusable all or a substantial portion of affected harvests. With respect to sugarcane, our initial primary feedstock, seasonal availability and price, the limited amount of time during which it keeps its sugar content after harvest, and the fact that sugarcane is not itself a traded commodity, increases these risks and limits our ability to substitute supply in the event of such an occurrence. If production of sugarcane or any other feedstock we may use to produce our products is adversely affected by these or other conditions, our production will be impaired, increasing costs to our operations and adversely affecting our business.

Our use of contract manufacturers exposes us to risks relating to costs, contractual terms and logistics.

In addition to our existing and planned production facilities discussed above, we must commercially produce, process and manufacture our products through the use of contract manufacturers, including DSM, and we anticipate that we will continue to use contract manufacturers for the foreseeable future. Establishing and operating contract manufacturing facilities requires us to make significant capital expenditures, which reduces our cash and places such capital at risk. Also, contract manufacturing agreements may contain terms that commit us to pay for capital expenditures and other costs and amounts incurred or expected to be earned by the plant operators and owners, which can result in contractual liability and losses for us even if we terminate a particular contract manufacturing arrangement or decide to reduce or stop production under such an arrangement. Further, we cannot be sure that contract manufacturers will be available when we need their services, that they will be willing to dedicate a portion of their capacity to our projects, or that we will be able to reach acceptable price, delivery and other terms with them for the provision of their production services.

The locations of contract manufacturers can pose additional cost, logistics and feedstock challenges. If production capacity is available at a plant that is remote from usable chemical finishing or distribution facilities, or from customers, we will be required to incur additional expenses in shipping products to other locations. Such costs could include shipping costs, compliance with export and import controls, tariffs and additional taxes, among others. In addition, we may be required to use feedstock from a particular region for a given production facility. The feedstock available in such region may not be the least expensive or most effective feedstock for production, which could significantly raise our overall production cost or reduce our product’s quality until we are able to optimize the supply chain.

Loss or termination of contract manufacturing relationships could harm our ability to meet our production goals.

As discussed above, we rely on contract manufacturers, including DSM, to produce and/or provide downstream processing of our products, and we anticipate that we will need to use contract manufacturers for the foreseeable future. If we are unable to secure the services of contract manufacturers when and as needed, we may lose customer opportunities and the growth of our business may be impaired. If we shift priorities and adjust anticipated production levels (or cease production altogether) at contract manufacturing facilities, such adjustments or cessations could also result in disputes or otherwise harm our business relationships with contract manufacturers. In addition, reliance on external sources for our other target molecules

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could create a risk for us if a single source or a limited number of sources of manufacturing runs into operational issues, creating risk of loss of sales and profitability. Reducing or stopping production at one facility while increasing or starting up production at another facility generally results in significant losses of production efficiency, which can persist for significant periods of time. Also, in order for production to commence under our contract manufacturing arrangements, we generally must provide equipment for such operations, and we cannot be assured that such equipment can be ordered or installed on a timely basis, at acceptable costs, or at all. Further, in order to establish operations at new contract manufacturing facilities, we need to transfer our yeast strains and production processes from our labs to commercial plants controlled by third parties, which may pose technical or operational challenges that delay production or increase our costs.

Our ability to establish substantial commercial sales of our products is subject to many risks, any of which could prevent or delay revenue growth and adversely impact our customer relationships, business and results of operations.

There can be no assurance that our products will be approved or accepted by customers, including customers of our branded products, or that we will be able to sell our products profitably at prices and with features sufficient to establish demand. The potential customers for our products generally have well developed manufacturing processes and arrangements with suppliers of the chemical components of their products and may have a resistance to changing these processes and components. These potential customers frequently impose lengthy and complex product qualification procedures on their suppliers, influenced by consumer preference, manufacturing considerations such as process changes and capital and other costs associated with transitioning to alternative components, supplier operating history, established business relationships and agreements, regulatory issues, product liability and other factors, many of which are unknown to, or not well understood by, us. Satisfying these processes may take many months. Similarly, customers of our branded products may have a resistance to accept our alternative compositions for such products. Additionally, we may be subject to product safety testing and may be required to meet certain regulatory and/or product safety standards. Meeting these standards can be a time consuming and expensive process, and we may invest substantial time and resources into such qualification efforts without ultimately securing approval. If we are unable to convince these potential customers, the consumers who purchase end-products containing our products and the customers of our direct to consumer products that our products are comparable to the chemicals that they currently use or that the use of our products is otherwise to their benefit, we will not be successful in entering these markets and our business will be adversely affected. Moreover, in order to successfully market our direct to consumer products, we must continue to build our sales, marketing, managerial, compliance, and related capabilities or make arrangements with third parties to perform these services. If we are unable to establish adequate sales, marketing, and distribution capabilities, whether independently or with third parties, we may not be able to appropriately commercialize such products.

The price and availability of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products.

In Brazil, Conselho dos Produtores de Cana-de-Açúcar, Açúcar e Etanol do Estado de São Paulo (Council of Sugarcane, Sugar and Ethanol Producers in the State of São Paulo, or “Consecana”), an industry association of producers of sugarcane, sugar and ethanol, sets market terms and prices for general supply, lease and partnership agreements for sugarcane. If Consecana makes changes to such terms and prices, it could result in higher sugarcane prices and/or a significant decrease in the volume of sugarcane available for the production of our products. In addition, if the availability of sugarcane juice or syrup or other feedstocks is restricted or limited due to weather conditions, land conditions or any other reason, we may not be able to manufacture our products in a timely or cost-effective manner, or at all, which would have a material adverse effect on our business.

We expect to face competition for our products from existing suppliers, including from price declines in petroleum and petroleum-based products, and if we cannot compete effectively against these companies, products or prices, we may not be successful in bringing our products to market, demand for some of our renewable products may decline, or we may be unable to further grow our business.

We expect that our renewable products will compete with both the traditional products that are currently being used in our target markets and with the alternatives to these existing products that established enterprises and new companies are seeking to produce. In the markets that we have entered, and in other markets that we may seek to enter in the future, we will compete primarily with the established providers of ingredients currently used in products in these markets. Producers of these incumbent products include global health and nutrition companies, large international chemical companies and companies specializing in specific products, such as flavor or fragrance ingredients, squalane or essential oils. We may also compete in one or more of these markets with products that are offered as alternatives to the traditional products being offered in these markets.

With the emergence of many new companies seeking to produce products from renewable sources, we may face increasing competition from such companies. As they emerge, some of these companies may be able to establish production

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capacity and commercial partnerships to compete with us. If we are unable to establish production and sales channels that allow us to offer comparable products at attractive prices, we may not be able to compete effectively with these companies.

We believe the primary competitive factors in our target markets are:

•product price;

•product performance and other measures of quality;

•product cost;

•infrastructure compatibility of products;

•sustainability; and

•dependability of supply.

The global health and nutrition companies, large international chemical companies and companies specializing in specific products with whom we compete are much larger than us, have, in many cases, well developed distribution systems and networks for their products, have valuable historical relationships with the potential customers we are seeking to serve and have much more extensive sales and marketing programs in place to promote their products. In order to be successful, we must convince customers that our products are at least as effective as the traditional products they are seeking to replace and we must provide our products on a cost basis that does not greatly exceed these traditional products and other available alternatives. Some of our competitors may use their influence to impede the development and acceptance of renewable products of the type that we are seeking to produce.

While most of our products do not compete with, and do not serve as alternatives to, petroleum-based products, we anticipate that some of our renewable products will be marketed as alternatives to corresponding petroleum-based products. We believe that for our renewable products to succeed in the market, we must demonstrate that our products are comparable or better alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, availability, performance, and consumer preference characteristics.

We are subject to risks related to our reliance on collaboration arrangements to fund development and commercialization of our products, and our financial results may be adversely impacted if we fail to meet technical, development or commercial milestones in such agreements.

For most product markets we are seeking to enter, we have collaboration partners to fund the research and development, commercialization and production efforts required for the target products. Typically, we provide limited exclusive rights and revenue sharing with respect to the production and sale of particular products in specific markets in exchange for such up-front funding. These exclusivity, revenue-sharing and other similar terms limit our ability to commercialize our products and technology, and may impact the size of our business or our profitability in ways that we do not currently envision. In addition, most of these agreements do not affirmatively obligate the other party to purchase specific quantities of any products, and most contain important conditions that must be satisfied before additional research and development funding or product purchases would occur. These conditions include research and development programs and milestones, and technical specifications that must be achieved to the satisfaction of our collaboration partners. We may focus our efforts and resources on potential discovery efforts, product targets or candidates that require substantial technical, financial and human resources which we cannot be certain we will achieve.

In addition, we may encounter numerous uncertainties and difficulties in developing, manufacturing and commercializing any new products subject to these collaboration arrangements that may delay or prevent us from realizing their expected benefits or enhancing our business, including uncertainties on the feasibility of taking new molecules to commercial-scale. Any failure to successfully develop, produce and commercialize products under our existing and future collaboration arrangements could have a material adverse effect on our business, financial conditions, earnings and prospects.

Revenues from these types of relationships are a key part of our cash plan for 2020 and beyond. If we fail to collect expected collaboration revenues, or to identify and add sufficient additional collaborations to fund our planned operations, we may be unable to fund our operations or pursue development and commercialization of our planned products. To achieve our collaboration revenue targets from year to year, we may be obliged to enter into agreements that contain less favorable terms. Historically, the process of negotiating and finalizing collaboration arrangements with our partners has at times been lengthy and unpredictable. Furthermore, as part of our current and future collaboration arrangements, we may be required to make significant capital investments at our existing or planned production facilities in order to develop, produce and commercialize molecules or other products. Any failure or difficulties in maintaining existing collaboration arrangements or establishing new collaboration arrangements, or building up or retooling our operations to meet the demands of our collaboration partners could have a significant negative impact on our business, including our ability to achieve commercial viability for our products, lead

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to the inability to meet our contractual obligations and could cause us to allocate or divert capital, personnel and other resources from our organization which could adversely affect our business and reputation.

Our collaboration arrangements may restrict or prevent our future business activity in certain markets or industries, which could harm our ability to grow our business.

As part of our collaboration arrangements in the ordinary course of business, we may grant to our partners exclusive rights with respect to the development, production and/or commercialization of particular products or types of products in specific markets in exchange for up-front funding and/or downstream royalty arrangements. These rights may inhibit potential collaboration or strategic partners or potential customers from entering into negotiations with us about further business opportunities, and we may be restricted or prevented from engaging with other partners or customers in those markets, which may limit our ability to grow our business or influence our strategic focus, and may lead to an inefficient allocation of capital resources.

In the past, we have had to grant concessions to existing partners in exchange for such partners waiving or modifying their exclusive rights with respect to a particular product, type of product or market so that we could engage with a third party with respect to such product, product type or market. There can be no assurance that existing partners will be willing to grant waivers of or modify their exclusive rights in the future on favorable terms, if at all. If we are unable to engage other potential partners with respect to particular products, product types or markets for which we have previously granted exclusive rights, our ability to grow our business would be harmed and our results of operations may be adversely affected.

Certain rights we have granted to Total S.A., DSM and other existing stockholders, including in relation to our future securities offerings, could substantially impact our company.

In connection with certain investments of Total S.A. (Total) in our company, our Certificate of Incorporation includes a provision that excludes Total from prohibitions on business combinations between us and an “interested stockholder.” This provision could have the effect of discouraging potential acquirers from making offers to acquire us, and give Total more access to Amyris than other stockholders if Total decides to pursue an acquisition.

In addition, each of Total, DSM, Vivo Capital LLC and Naxyris S.A. has the right to designate one or more directors to serve on our Board of Directors pursuant to agreements between us and such investors.

In May 2017, we entered into an agreement with DSM, which was amended and restated in August 2017, pursuant to which we agreed (i) that for as long as there is a DSM-designated director serving on our Board of Directors, we will not engage in certain commercial or financial transactions or arrangements without the consent of such director, and (ii) to provide DSM with certain exclusive negotiating rights in connection with certain future commercial projects and arrangements. These provisions could discourage other potential partners from approaching us with business opportunities, and could restrict, delay or prevent us from pursuing or engaging in such opportunities, which could adversely affect our business.

Additionally, in connection with their investments in Amyris, we granted certain investors, including DSM, a right of first investment if we propose to sell securities in certain financing transactions. With these rights, such investors may subscribe for a portion of any such new financing and require us to comply with certain notice periods, which could discourage other investors from participating in, or cause delays in our ability to close, such a financing.

Our relationship with DSM exposes us to financial and commercial risks.

In May 2017, DSM made an investment in our company and, in connection therewith, we entered into a stockholder agreement with DSM (subsequently amended) which provides DSM with certain rights, including the right to designate two members of our board of directors as well as exclusive negotiating rights in connection with certain future commercial projects and arrangements. Subsequently, in July and September 2017, we entered into collaboration agreements (and related license agreements) with DSM to jointly develop three new molecules in the Health and Nutrition field using the Company’s technology, which the Company would produce and DSM would commercialize. In December 2017, we completed the sale of our Brotas, Brazil production facility to DSM and, in connection therewith, entered into several commercial agreements with DSM, including a supply agreement to procure a substantial portion of our product supply requirements, and borrowed $25 million from DSM. For more information regarding these and other transactions and arrangements with DSM, please see Note 4, “Debt,” Note 6, “Stockholders’ Deficit,” Note 9, “Revenue Recognition”, Note 10, “Related Party Transactions” and Note 12, “Divestiture” in Part II, Item 8 of this Annual Report on Form 10-K.

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There can be no assurance that our partnership with DSM will be successful, and the partnership may prevent us from pursuing other business opportunities in the future. If the partnership is unsuccessful, our ability to continue with our business plans could be adversely affected. In addition, negative developments in one aspect of our relationship with DSM could negatively affect other aspects of our relationship with DSM. In such event, our financial condition and business operations could be adversely affected.

In addition, DSM, due to the presence of its representatives on our board of directors, equity ownership in our company, and commercial relationships with us, may be able to control or significantly influence our management, operations and affairs, as well as matters requiring stockholder approval, including the election of directors and the approval of significant corporate transactions, such as the disposition of our intellectual property, mergers, consolidations or the sale of all or substantially all of our assets. Due to its various relationships with the Company, DSM may have interests different than, and may not act in the best interests of, our other stockholders. Consequently, our relationship with DSM may have the effect of delaying or preventing a change of control, or a change in our management or board of directors, or discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control of our company, even if such actions would benefit our other stockholders.

A significant portion of our operations are centered in Brazil, and our business will be adversely affected if we do not operate effectively in that country.

For the foreseeable future, we will be subject to risks associated with the concentration of essential product sourcing and operations in Brazil. The Brazilian government has changed in the past, and may change in the future, monetary, taxation, credit, tariff, labor, export and other policies to influence the course of Brazil's economy. For example, the government's actions to control inflation have involved interest rate adjustments. We have no control over, and cannot predict what policies or actions the Brazilian government may take in the future. Our business, financial performance and prospects may be adversely affected by, among others, the following factors:

•delays or failures in securing licenses, permits or other governmental approvals necessary to build and operate facilities, use our yeast strains to produce products and export such products for sale outside Brazil;

•rapid consolidation in the sugar and ethanol industries in Brazil, which could result in a decrease in competition;

•political, economic, diplomatic or social instability in, or in the region surrounding, Brazil;

•changing interest rates;

•tax burden and policies;

•effects of changes in currency exchange rates;

•any changes in currency exchange policy that lead to the imposition of exchange controls or restrictions on remittances abroad;

•export or import restrictions that limit our ability to move our products out of Brazil or interfere with the import of essential materials into Brazil;

•changes in, or interpretations of foreign regulations that may adversely affect our ability to sell our products or repatriate profits to the United States;

•tariffs, trade protection measures and other regulatory requirements;

•compliance with United States and foreign laws that regulate the conduct of business abroad;

•compliance with privacy, anti-corruption and anti-bribery laws, including certain anti-corruption and privacy laws recently enacted in Brazil;

•an inability, or reduced ability, to protect our intellectual property in Brazil including any effect of compulsory licensing imposed by government action; and

•difficulties and costs of staffing and managing foreign operations.

We cannot predict whether the current or future Brazilian government will implement changes to existing policies on taxation, exchange controls, monetary strategy, labor relations, social security and the like, nor can we estimate the impact of any such changes on the Brazilian economy or our operations.

Brazil’s economy has recently experienced quarters of slow gross domestic product growth. Although recent data has shown signs of an economic recovery in Brazil, there is no assurance that such recovery will continue. In addition, major corruption scandals involving members of the executive, state-controlled enterprises and large private sector companies have been disclosed and are the subject of ongoing investigation by federal authorities. Although these investigations continued to evolve through 2019, their final outcome and impact on the Brazilian economy is not yet known and cannot be predicted with certainty.

We are subject to the risks of doing business globally.

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We maintain operations in foreign jurisdictions other than Brazil, and may in the future expand, or seek to expand, our operations to additional foreign jurisdictions. For example, in 2018 we announced plans to increase our commercial activities in China. Operating in China exposes us to political, legal and economic risks. In particular, the political, legal and economic climate in China, both nationally and regionally, is fluid and unpredictable. Our ability to operate in China may be adversely affected by changes in U.S. and Chinese laws and regulations such as those related to taxation, import and export tariffs, environmental regulations, genetically modified microorganisms (GMM), land use rights, product testing requirements, intellectual property, currency controls, network security and other matters. In addition, we may not obtain or retain the requisite permits to operate in China, and costs or operational limitations may be imposed in connection with obtaining and complying with such permits. In addition, Chinese trade regulations are in a state of flux, and we may become subject to other forms of taxation, tariffs and duties in China. Furthermore, our counterparties in China may use or disclose our confidential information or intellectual property to competitors or third parties, which could result in the illegal distribution and sale of counterfeit versions of our products. If any of these events occur, our business, financial condition and results of operations could be materially and adversely affected.

In addition, a significant percentage of the production, downstream processing and sales of our products occurs outside the United States or with vendors, suppliers or customers located outside the United States. If tariffs or other restrictions are placed by the United States on foreign imports from Brazil, European or other countries where we operate or seek to operate, or any related counter-measures are taken, our business, financial condition and results of operations may be harmed. In 2018, President Trump imposed tariffs on steel and aluminum imports and additional tariffs on goods imported from certain specified countries and regions, including China and Europe, and has indicated potential future tariffs on a range of goods from certain countries and regions. In response, certain countries, including China, have imposed retaliatory tariffs on U.S. goods imported into such countries. If further tariffs are imposed on a broader range of imports, or if further retaliatory trade measures are taken by other countries in response to additional tariffs, our operating performance could be harmed. Tariffs may increase our cost of goods, which could result in lower gross margin on certain of our products. If we raise prices to account for any such increase in costs of goods, the competitiveness of the affected products could potentially be reduced. In either case, increased tariffs on imports from Brazil, European or other countries where we operate or seek to operate could materially and adversely affect our business, financial condition and results of operations. Furthermore, in retaliation for any tariffs imposed by the United States, other countries may implement tariffs on a wide range of American products, which could increase the cost of our products for non-U.S. customers located in such countries. Any increase in the cost of our products for non-U.S. customers, which represent a substantial portion of our sales, could result in a decrease in demand for our products by such customers. Trade restrictions implemented by the United States or other countries could materially and adversely affect our business, financial condition and results of operations.

Many, if not all of the above-mentioned risks also apply to our operations in other foreign jurisdictions where we operate or seek to operate. If any of these risks were to occur, our operations and business would be adversely affected.

We are subject to new U.S. foreign investment regulations which may impose additional burdens on or may limit certain investors' ability to purchase our common stock, potentially making our common stock less attractive to investors.

In October 2018, the U.S. Department of Treasury announced a pilot program to implement part of the Foreign Investment Risk Review Modernization Act (FIRRMA), effective November 10, 2018. The pilot program expands the jurisdiction of the Committee on Foreign Investment in the United States (CFIUS), to include certain direct or indirect foreign investments in a defined category of U.S. companies, including companies involved in critical infrastructure and critical technologies. Among other things, FIRRMA empowers CFIUS to require certain mandatory filings in connection with certain foreign investments in U.S. companies and permits CFIUS to charge filing fees related to such filings. Such filings are subject to review by CFIUS, which will have the authority to recommend that the President block or impose conditions on certain foreign investments in companies subject to CFIUS’s oversight. Any such restrictions on the ability of foreign investors to invest in our company could limit our ability to engage in strategic transactions that may benefit our stockholders, including a change of control, and may prevent our stockholders from receiving a premium for their shares of our common stock in connection with a change of control, and could also affect the price that some investors are willing to pay for our common stock.

Ethical, legal and social concerns about products using genetically modified microorganisms could limit or prevent the use of our products and technologies and could harm our business.

Our technologies and products involve the use of genetically modified microorganisms (GMMs). Public perception about the safety of, and ethical, legal or social concerns over, genetically engineered products, including GMMs, could affect public acceptance of our products. If we are not able to overcome any such concerns relating to our products, our technologies may not be accepted by our customers or end-users. In addition, the use of GMMs has in the past received negative publicity, which

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could lead to greater regulation or restrictions on imports of our products. If our technologies and products are not accepted by our customers or their end-users due to negative publicity or lack of public acceptance, our business could be significantly harmed.

Our use of genetically modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.

The use of GMMs, such as our yeast strains, is subject to laws and regulations in many countries, some of which are new and some of which are still evolving. In the United States, the Environmental Protection Agency (EPA), regulates the commercial use of GMMs as well as potential products produced from GMMs. Various states or local governments within the United States could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we currently use for the development and commercial production of our target molecules, S. cerevisiae, is eligible for exemption from EPA review because it is generally recognized as safe, we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant containment structures, waste disposal and safety procedures, and we cannot be sure that we will meet such criteria in a timely manner, or at all. If exemption of S. cerevisiae is not obtained, our business may be substantially harmed. In addition to S. cerevisiae, we may seek to use different GMMs in the future that will require EPA approval. If approval of different GMMs is not secured, our ability to grow our business could be adversely affected.

In Brazil, GMMs are regulated by the National Biosafety Technical Commission (CTNBio). We have obtained approvals from CTNBio to use GMMs in a contained environment in our Brazil facilities for research and development purposes as well as at contract manufacturing facilities in Brazil for industrial-scale production of target products. In addition, we have obtained initial commercial approvals from CTNBio for five of our yeast strains, with two of these strains being approved for feed purposes. As we continue to develop new yeast strains and deploy our technology at new production facilities in Brazil, we will be required to obtain further approvals from CTNBio in order to use these strains in industrial-scale commercial production in Brazil. We may not be able to obtain such approvals on a timely basis, or at all, and if we do not, our ability to produce our products in Brazil could be impaired, which would adversely affect our results of operations and financial condition.

In addition to our production operations in the United States and Brazil, we have been party to contract manufacturing agreements with parties in other production locations around the world, including Europe. The use of GMM technology is regulated in the European Union, which has established various directives for member states regarding regulation of the use of such technology, including notification processes for contained use of such technology. We expect to encounter GMM regulations in most, if not all, of the countries in which we may seek to establish production capabilities and/or conduct sales to customers or end-use consumers, and the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable regulatory requirements in the countries in which we produce or sell, or intend to produce or sell, products using our yeast strains, or if it takes longer than anticipated to obtain the necessary regulatory approvals, our business could be adversely affected. Furthermore, there are various governmental, non-governmental and quasi-governmental organizations that review and certify products with respect to the determination of whether products can be classified as “natural” or other similar classifications. While the certification from such governmental organizations, and verification from non-governmental and quasi-governmental organizations are generally not mandatory, some of our current or prospective customers, collaboration partners or distributors may require that we meet the standards set by such organizations as a condition precedent to purchasing or distributing our products. We cannot be certain that we will be able to satisfy the standards of such organizations, and any delay or failure to do so could harm our ability to sell or distribute some or all of our products to certain customers and prospective customers, which could have a negative impact on our business.

We may not be able to obtain regulatory approval for the sale of our renewable products.

Our renewable chemical products may be subject to government regulation in our target markets. In the United States, the EPA administers the Toxic Substances Control Act (the TSCA), which regulates the commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or distribute a new chemical subject to the TSCA, it must file a Pre-Manufacture Notice, or PMN, to add the chemical to a product. The EPA has 180 days to review the filing but may request additional data, which could significantly extend the timeline for approval. As a result, we may not receive EPA approval to list future molecules on the TSCA registry as expeditiously as we would like, resulting in delays or significant increases in testing requirements. A similar program exists in the European Union, called REACH. Under this program, chemicals imported or manufactured in the European Union in certain quantities must be registered with the European Chemicals Agency, and this process could cause delays or entail significant costs. To the extent that other countries in which we are producing or selling (or seeking to produce or sell) our products, such as Brazil and various countries in Asia, rely on TSCA or REACH (or similar laws and programs) for chemical registration or regulation in their jurisdictions, delays with the United States or European authorities, or any relevant authorities in such other countries, may delay entry into these markets as well. In addition, some of

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our Biofene-derived products are sold for the cosmetics market, and some countries may impose additional regulatory requirements or permits for such uses, which could impair, delay or prevent sales of our products in those markets. Also, certain of our current or proposed products in the Flavor & Fragrance, Clean Beauty and Health & Wellness markets, including alternative sweeteners, nutraceuticals, Flavor & Fragrance ingredients, skincare ingredients and cosmetic actives, may be subject to the approval of and regulation by the FDA, the European Food Safety Authority, as well as similar agencies of states and foreign jurisdictions where these products are sold or proposed to be sold.

We expect to encounter regulations in most, if not all, of the countries in which we may seek to produce, import or sell our products (and our customers may encounter similar regulations in selling end-use products to consumers), and we cannot assure you that we (or our customers) will be able to obtain necessary approvals and third-party verifications in a timely manner or at all. If our products do not meet applicable regulatory requirements in a particular country, then we (or our customers) may not be able to commercialize our products in such country and our business will be adversely affected. In addition, any enforcement action taken by regulators against us or our products could cause us to suffer adverse publicity, which could harm our reputation and our relationship with our customers and vendors.

In addition, many of our products are intended to be a component of our collaboration partners and/or customers’ (or their customers’) end-use products. Such end-use products may be subject to various regulations, including regulations promulgated by the EPA, the FDA, or the European Food Safety Authority. If our company or our collaboration partners and customers (or their customers) are not successful in obtaining any required regulatory approval or third-party verifications for their end-use products that incorporate our products, or fail to comply with any applicable regulations for such end-use products, whether due to our products or otherwise, demand for our products may decline and our revenues will be adversely affected.

Changes in government regulations, including subsidies and economic incentives, could have a material adverse effect on our business.

The markets where we sell our products are heavily influenced by foreign, federal, state and local government regulations and policies. Changes to existing or adoption of new foreign or domestic federal, state and local legislative initiatives that impact the production, distribution or sale of products may harm our business. The uncertainty regarding future standards and policies, including developing legislation in the Clean Beauty industry, may also affect our ability to develop our products or to license our technologies to third parties and to sell products to our end customers. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

Furthermore, the production of our products will depend on the availability of feedstock, especially sugarcane. Agricultural production and trade flows are subject to government policies and regulations. Governmental policies affecting the agricultural industry, such as taxes, tariffs, duties, subsidies, incentives and import and export restrictions on agricultural commodities and commodity products can influence the planting of certain crops, the location and size of crop production, whether unprocessed or processed commodity products are traded, the volume and types of imports and exports, and the availability and competitiveness of feedstocks as raw materials. Future government policies may adversely affect the supply of feedstocks, restrict our ability to use sugarcane or other feedstocks to produce our products, or encourage the use of feedstocks more advantageous to our competitors, which would put us at a commercial disadvantage and could negatively impact our future revenues and results of operations.

Our cannabinoid initiative is uncertain and may not yield commercial results and is subject to significant regulatory risks.

In 2019, we announced a new collaboration arrangement aimed at developing, producing and commercializing fermentation-derived cannabinoids. While we believe there are substantial business opportunities for us in this field, there can be no assurance that our activities will be successful, or that any research and development and product testing efforts will result in commercially saleable products, or that the market will accept or respond positively to our products.

In addition, the market for cannabinoids is heavily regulated. Synthetic cannabinoids may be viewed as qualifying as controlled substances under the federal Controlled Substances Act of 1970 (CSA), and may be subject to a high degree of regulation including, among other things, certain registration, licensing, manufacturing, security, record keeping, reporting, import, export, clinical and non-clinical studies, insurance and other requirements administered by the U.S. Drug Enforcement Administration (DEA) and/or the FDA.

Individual states and countries have also established controlled substance laws and regulations, which may differ from U.S. federal law. We or our partner may be required to obtain separate state or country registrations, permits or licenses in order to be able to develop produce, sell, store and transport cannabinoids.

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Complying with laws and regulations relating to cannabinoids is evolving, complex and expensive, and may divert management’s attention and resources from other aspects of our business. Failure to maintain compliance with such laws and regulations may result in regulatory action that could have a material adverse effect on our business, results of operations and financial condition. The DEA, FDA or state agencies may seek civil penalties, refuse to renew necessary registrations, or initiate proceedings to revoke those registrations. In certain circumstances, violations could lead to criminal proceedings.

We may incur significant costs to comply with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We use intermediate substances, hazardous chemicals and radioactive and biological materials in our business, and such materials are subject to a variety of federal, state and local laws and regulations governing the use, generation, manufacture, storage, handling and disposal of these materials in the United States, European Union and Brazil. Although we have implemented safety procedures for handling and disposing of these materials and related waste products in an effort to comply with these laws and regulations, we cannot be sure that our safety measures and those of our contractors will prevent accidental injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of contamination or injury, we could be held liable for any resulting damages, and any liability could exceed our insurance coverage. There can be no assurance that violations of environmental, health and safety laws will not occur in the future as a result of human error, accident, equipment failure or other causes. Compliance with applicable environmental laws and regulations may be expensive, and the failure to comply with past, present, or future laws could result in the imposition of fines, third party property damage, product liability and personal injury claims, investigation and remediation costs, the suspension of production, or a cessation of operations, and our liability may exceed our total assets. Liability under environmental laws can be joint and several, without regard to comparative fault, and may be punitive in nature. Furthermore, environmental laws could become more stringent over time, imposing greater compliance costs and increasing risks and penalties associated with violations, which could impair our research, development or production efforts and otherwise harm our business.

Our proprietary rights may not adequately protect our technologies and product candidates.

Our commercial success will depend substantially on our ability to obtain patents and maintain adequate legal protection for our technologies and product candidates in the United States and other countries. As of December 31, 2019, we had 633 issued United States and foreign patents and 238 pending United States and foreign patent applications that were owned or co-owned by or licensed to us. We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies and future products are covered by valid and enforceable patents or are effectively maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate. However, filing, prosecuting, maintaining and defending patents on product candidates in all countries throughout the world would be prohibitively expensive, and our intellectual property rights in some countries outside the United States are less extensive than those in the United States. We may also fail to apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing and future patents may not be sufficiently broad to prevent others from practicing our technologies or from designing products around our patents or otherwise developing competing products or technologies. In addition, the patent positions of companies like ours are highly uncertain and involve complex legal and factual questions for which important legal principles remain unresolved. No consistent policy regarding the breadth of patent claims has emerged to date in the United States and the landscape is expected to become even more uncertain in view of recent rule changes by the United States Patent Office, or USPTO. Additional uncertainty may result from legal decisions by the United States Federal Circuit and Supreme Court as they determine legal issues concerning the scope and construction of patent claims and inconsistent interpretation of patent laws or from legislation enacted by the U.S. Congress. The patent situation outside of the United States is also difficult to predict. As a result, the validity and enforceability of patents cannot be predicted with certainty. Moreover, we cannot be certain whether:

•we (or our licensors) were the first to make the inventions covered by each of our issued patents and pending patent applications;

•we (or our licensors) were the first to file patent applications for these inventions;

•others will independently develop similar or alternative technologies or duplicate any of our technologies;

•any of our or our licensors' patents will be valid or enforceable;

•any patents issued to us (or our licensors) will provide us with any competitive advantages, or will be challenged by third parties;

•we will be able to identify when others are infringing our (or our licensed) valid patent claims;

•we will develop additional proprietary products or technologies that are patentable; or

•the patents of others will have an adverse effect on our business.

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We do not know whether any of our pending patent applications or those pending patent applications that we license will result in the issuance of any patents. Even if patents are issued, they may not be sufficient to protect our technology or product candidates. The patents we own or license and those that may be issued in the future may be challenged, invalidated, rendered unenforceable, or circumvented, and the rights granted under any issued patents may not provide us with proprietary protection or competitive advantages. Moreover, third parties could practice our inventions in territories where we do not have patent protection or in territories where they could obtain a compulsory license to our technology where patented. Such third parties may then try to import products made using our inventions into the United States or other territories. Accordingly, we cannot ensure that any of our pending patent applications will result in issued patents, or even if issued, predict the breadth, validity and enforceability of the claims upheld in our and other companies' patents.

Many companies have encountered significant problems in protecting and defending intellectual property rights in foreign jurisdictions. The legal systems of certain countries do not favor the enforcement of patents or other intellectual property rights, which could hinder us from preventing the infringement of our patents or other intellectual property rights. Proceedings to enforce our patent rights in the United States or foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business, could put our patents at risk of being invalidated or interpreted narrowly and our patent applications at risk of not issuing and could provoke third parties to assert patent infringement or other claims against us. We may not prevail in any lawsuits that we initiate and the damages or other remedies awarded, if any, may not be commercially meaningful. Accordingly, our efforts to enforce our intellectual property rights around the world may be inadequate to obtain a significant commercial advantage from the intellectual property that we develop or license from third parties.

Moreover, we have granted certain of our lenders liens on substantially all of our assets, including our intellectual property, as collateral. If we default on our payment obligations under these secured loans, such lenders have the right to foreclose upon and control the disposition of our assets, including our intellectual property assets, to satisfy our payment obligations under such instruments. If such default occurs, and our intellectual property assets are sold or licensed, our business could be materially adversely affected.

Unauthorized parties may attempt to copy or otherwise obtain and use our products or technology. Monitoring unauthorized use of our intellectual property is difficult, and we cannot be certain that the steps we have taken will prevent unauthorized use of our technology, particularly in certain foreign countries where the local laws may not protect our proprietary rights as fully as in the United States or may provide, today or in the future, for compulsory licenses. Moreover, in some cases our ability to determine if our intellectual property is being unlawfully used by a competitor may be limited. If competitors are able to use our technology, our ability to compete effectively could be harmed. Moreover, others may independently develop and obtain patents for technologies that are similar to, or superior to, our technologies. If that happens, we may need to license these technologies, and we may not be able to obtain licenses on reasonable terms, if at all, which could cause harm to our business.

We rely in part on trade secrets to protect our technology, and our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

We rely on trade secrets to protect some of our technology, particularly where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to maintain and protect. Our strategy for contract manufacturing and scale-up of commercial production requires us to share confidential information with our international business partners and other parties. Our product development collaborations with third parties, including with Givaudan, Firmenich, DSM and Yifan, require us to share certain confidential information. While we use reasonable efforts to protect our trade secrets, our or our business partners' employees, consultants, contractors or scientific and other advisors may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims that a third party has illegally obtained and is using trade secrets is expensive, time consuming and uncertain. In addition, foreign courts are sometimes less willing than United States courts to protect trade secrets. If our competitors lawfully obtain or independently develop equivalent knowledge, methods and know-how, we would not be able to assert our trade secrets against them.

We require new employees and consultants to execute proprietary information and inventions agreements upon the commencement of an employment or consulting arrangement with us. We additionally require contractors, advisors, corporate collaboration partners, outside scientific collaboration partners and other third parties that may receive trade secret information to execute such agreements or confidentiality agreements. These agreements generally require that all confidential information developed by the individual or made known to the individual by us during the course of the individual's relationship with us be kept confidential and not be disclosed to third parties. These agreements also generally provide that inventions conceived by the individual in the course of rendering services to us shall be our exclusive property. Nevertheless, our proprietary information

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may be disclosed, or these agreements may be unenforceable or difficult to enforce. If any of our trade secrets were to be lawfully obtained or independently developed by a competitor, we would have no right to prevent such third party, or those to whom they communicate such technology or information, from using that technology or information to compete with us. Additionally, trade secret law in Brazil differs from that in the United States, which requires us to take a different approach to protecting our trade secrets in Brazil. Some of these approaches to trade secret protection may be novel and untested under Brazilian law and we cannot guarantee that we would prevail if our trade secrets are contested in Brazil. If any of the above risks materializes, our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

Third parties and former employees may misappropriate our trade secrets including those embodied in our yeast strains.

Third parties, including collaboration partners, contract manufacturers, other contractors and shipping agents, as well as exiting employees, often have access to our trade secrets and custody or control of our yeast strains. If our trade secrets or yeast strains were stolen, misappropriated or reverse engineered, they could be used by other parties who may be able to reproduce the yeast strains for their own commercial gain. If this were to occur, it would be difficult for us to challenge and prevent this type of use, especially in countries where we have limited intellectual property protection or that do not have robust intellectual property law regimes.

If we or one of our collaboration partners is sued for infringing intellectual property rights or other proprietary rights of third parties, litigation could be costly and time consuming and could prevent us from developing or commercializing our future products.

Our commercial success depends on our and our collaboration partners' ability to operate without infringing the patents and proprietary rights of other parties and without breaching any agreements we have entered into with regard to our technologies and product candidates. We cannot determine with certainty whether patents or patent applications of other parties may materially affect our ability to conduct our business. Our industry spans several sectors, including biotechnology, renewable fuels, renewable specialty chemicals and other renewable molecules, and is characterized by the existence of a significant number of patents and disputes regarding patent and other intellectual property rights. Because patent applications remain unpublished and confidential for eighteen months and can take several years to issue, there may currently be pending applications, unknown to us, that may result in issued patents that cover our technologies or product candidates. There may be a significant number of patents and patent applications relating to aspects of our technologies filed by, and issued to, third parties. The existence of third-party patent applications and patents could significantly reduce the coverage of patents owned by or licensed to us and our collaboration partners and limit our ability to obtain meaningful patent protection. If we wish to make, use, sell, offer to sell, or import the technology or compound claimed in issued and unexpired patents owned by others, we may need to obtain a license from the owner, develop or obtain alternative technologies, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the event that the owner asserts that we infringe its patents. If patents containing competitive or conflicting claims are issued to third parties and these claims are ultimately determined to be valid, we and our collaboration partners may be enjoined from pursing research, development, or commercialization of products, or be required to obtain licenses to these patents, or to develop or obtain alternative technologies.

If a third party asserts that we infringe upon its patents or other proprietary rights, we could face a number of issues that could seriously harm our competitive position, including:

•infringement and other intellectual property claims, which could be costly and time consuming to litigate, whether or not the claims have merit, and which could prevent or delay getting our products to market and divert management attention from our business;

•substantial damages for past infringement, which we may have to pay if a court determines that our products or technologies infringe a third party's patent or other proprietary rights;

•a court prohibiting us from selling or licensing our technologies or future products unless the holder licenses the patent or other proprietary rights to us, which it is not required to do;

•the International Trade Commission (ITC) prohibiting us from importing our products into the United States; and

•if a license is available from a third party, such third party may require us to pay substantial royalties or grant cross licenses to our patents or proprietary rights.

The industries in which we operate, and the biotechnology industry in particular, are characterized by frequent and extensive litigation and patent agency procedures regarding patents and other intellectual property rights. Many biotechnology companies have employed intellectual property litigation as a way to gain a competitive advantage. If any of our competitors have filed patent applications or obtained patents that claim inventions also claimed by us, we may have to participate in interference proceedings declared by the relevant patent regulatory agency to determine priority of invention and, thus, the right to the patents for these inventions in the United States. In addition, third parties may be able to challenge the validity of one or

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more of our patents using available post-grant procedures including oppositions and inter partes reviews (IPR). These proceedings could result in substantial cost to us even if the outcome is favorable. Even if successful, an interference or post-grant proceeding may result in loss of certain of our patent claims. Our involvement in litigation, interferences, opposition proceedings or other intellectual property proceedings inside and outside of the United States, to defend our intellectual property rights, or as a result of alleged infringement of the rights of others, may divert management time from focusing on business operations and could cause us to spend significant resources, all of which could harm our business and results of operations.

Many of our employees were previously employed at universities, biotechnology, specialty chemical or oil companies, including our competitors or potential competitors. We may be subject to claims that these employees or we have inadvertently or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. If we fail in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel and be enjoined from certain activities. A loss of key research personnel or their work product, especially to our competitors or potential competitors, could hamper or prevent our ability to commercialize our product candidates, which could severely harm our business. Even if we are successful in prosecuting or defending against these claims, litigation could result in substantial costs and demand on management resources.

We may need to commence litigation to enforce our intellectual property rights, which would divert resources and management's time and attention and the results of which would be uncertain.

Enforcement of claims that a third party is using our proprietary rights without permission is expensive, time consuming and uncertain. Significant litigation would result in substantial costs, even if the eventual outcome is favorable to us and would divert management's attention from our business objectives. In addition, an adverse outcome in litigation could result in a substantial loss of our proprietary rights and we may lose our ability to exclude others from practicing our technology or producing our product candidates.

The laws of some foreign countries do not protect intellectual property rights to the same extent as do the laws of the United States. Many companies have encountered significant problems in protecting and defending intellectual property rights in certain foreign jurisdictions. The legal systems of certain countries, particularly certain developing countries, do not favor the enforcement of patents by foreign holders and other intellectual property protection, particularly those relating to biotechnology and/or bioindustrial technologies. This could make it difficult for us to stop the infringement of our patents or misappropriation of our other intellectual property rights. Proceedings to enforce our patent rights in foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business. Moreover, our efforts to protect our intellectual property rights in such countries may be inadequate.

We do not have exclusive rights to intellectual property we develop under U.S. federally funded research grants and contracts, including with DARPA and DOE, and we could ultimately share or lose the rights we do have under certain circumstances.

Some of our intellectual property rights have been or may be developed in the course of research funded by the U.S. government, including under our agreements with DARPA and DOE. As a result, the U.S. government may have certain rights to intellectual property embodied in our current or future products pursuant to the Bayh-Dole Act of 1980. Government rights in certain inventions developed under a government-funded program include a non-exclusive, non-transferable, irrevocable worldwide license to use inventions for any governmental purpose. In addition, the U.S. government has the right to require us, or an assignee or exclusive licensee to such inventions, to grant licenses to any of these inventions to a third party if they determine that: (i) adequate steps have not been taken to commercialize the invention; (ii) government action is necessary to meet public health or safety needs; (iii) government action is necessary to meet requirements for public use under federal regulations; or (iv) the right to use or sell such inventions is exclusively licensed to an entity within the U.S. and substantially manufactured outside the U.S. without the U.S. government’s prior approval. Additionally, we may be restricted from granting exclusive licenses for the right to use or sell our inventions created pursuant to such agreements unless the licensee agrees to additional restrictions (e.g., manufacturing substantially all of the invention in the U.S.). The U.S. government also has the right to take title to these inventions if we fail to disclose the invention to the government and fail to file an application to register the intellectual property within specified time limits. In addition, the U.S. government may acquire title in any country in which a patent application is not filed within specified time limits. Additionally, certain inventions are subject to transfer restrictions during the term of these agreements and for a period thereafter, including sales of products or components, transfers to foreign subsidiaries for the purpose of the relevant agreements, and transfers to certain foreign third parties. If any of our intellectual property becomes subject to any of the rights or remedies available to the U.S. government or third parties pursuant to the Bayh-Dole Act of 1980, this could impair the value of our intellectual property and could adversely affect our business.

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Loss of, or inability to secure government contract revenues could impair our business.

We have contracts or subcontracts with certain governmental agencies or their contractors, including DARPA. Generally, these agreements, as they may be amended or modified from time to time, have fixed terms and may be terminated, modified or be subject to recovery of payments by the government agency under certain conditions (such as failure to comply with detailed reporting and governance processes or failure to achieve milestones). Under these agreements, we are also subject to audits, which can result in corrective action plans and penalties up to and including termination. If these governmental agencies terminate these agreements with us, it could reduce our revenues which could harm our business. Additionally, we anticipate securing additional government contracts as part of our business plan for 2020 and beyond. If we are unable to secure such government contracts, it could harm our business.

Our products subject us to product-safety risks, and we may be sued for product liability.

The design, development, production and sale of our products involve an inherent risk of product liability claims and the associated adverse publicity. Our products could be used by a wide variety of consumers with varying levels of sophistication. Although safety is a priority for us, we are not always in control of the final uses and formulations of the products we supply or their use as ingredients. Our products could have detrimental impacts or adverse impacts we cannot anticipate. Despite our efforts, negative publicity about Amyris, including product safety or similar concerns, whether real or perceived, could occur, and our products could face withdrawal, recall or other quality issues. In addition, we may be named directly in product liability suits relating to our products, even for defects resulting from errors of our commercial partners, contract manufacturers, chemical finishers, customers or end users of our products. These claims could be brought by various parties, including customers who are purchasing products directly from us or other users who purchase products from our customers. We could also be named as co-parties in product liability suits that are brought against the contract manufacturers with whom we partner to produce our products. Insurance coverage is expensive, may be difficult to obtain and may not be available in the future on acceptable terms. We cannot be certain that our contract manufacturers or the sugar and ethanol producers who partner with us to produce our products will have adequate insurance coverage to cover against potential claims. Any insurance we do maintain may not provide adequate coverage against potential losses, and if claims or losses exceed our liability insurance coverage, our business would be adversely impacted. In addition, insurance coverage may become more expensive, which would harm our results of operations.

We may become subject to lawsuits or indemnity claims in the ordinary course of business, which could materially and adversely affect our business and results of operations.

From time to time, we may in the ordinary course of business be named as a defendant in lawsuits, indemnity claims and other legal proceedings. These actions may seek, among other things, compensation for alleged personal injury, employment discrimination, breach of contract, property damage and other losses or injunctive or declaratory relief. In the event that such actions, claims or proceedings are ultimately resolved unfavorably to us at amounts exceeding our accrued liability, or at material amounts, the outcome could materially and adversely affect our reputation, business and results of operations. In addition, payments of significant amounts, even if reserved, could adversely affect our liquidity position. For more information regarding our current legal proceedings, please refer to the section entitled “Legal Proceedings” in Part I, Item 3 of this Annual Report on Form 10-K.

We may not be able to fully enforce covenants not to compete with and not to solicit our employees, and therefore we may be unable to prevent our competitors from benefiting from the expertise of such employees.

Our proprietary information and inventions agreements with our employees contain non-compete and non-solicitation provisions. These provisions prohibit our employees from competing directly with our business or proposed business or working for our competitors during their term of employment, and from directly or indirectly soliciting our employees or consultants to leave our company for any purpose. Under applicable U.S. and Brazilian law, we may be unable to enforce these provisions. If we cannot enforce these provisions with our employees, we may be unable to prevent our competitors from benefiting from the expertise of such employees. Even if these provisions are enforceable, they may not adequately protect our interests. The defection of one or more of our employees to a competitor could materially adversely affect our business, results of operations and ability to capitalize on our proprietary information.

Loss of key personnel, including key management personnel, and/or failure to attract and retain additional personnel could delay our product development programs and harm our research and development efforts and our ability to meet our business objectives.

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Our business involves complex, global operations across a variety of markets and requires a management team and employee workforce that is knowledgeable in the many areas in which we operate. As we continue to build our business, we will need to hire and retain qualified research and development, management and other personnel to succeed. The process of hiring, training and successfully integrating qualified personnel into our operations in the United States, Brazil and other countries in which we may seek to operate, can be a lengthy and expensive one. The market for qualified personnel is very competitive because of the limited number of people available who have the necessary technical skills and understanding of our technology and products. Our failure to hire and retain qualified personnel could impair our ability to meet our research and development and business objectives and adversely affect our results of operations and financial condition.

The loss of any key member of our management or key technical and operational employees, or the failure to attract or retain such employees, could prevent us from developing and commercializing our products for our target markets and executing our business strategy. In addition, we may not be able to attract or retain qualified employees in the future due to the intense competition for qualified personnel among biotechnology and other technology-based businesses. Furthermore, any reductions to our workforce as part of potential cost-saving measures, such as those discussed above with respect to our planned actions to continue as a going concern, may make it more difficult for us to attract and retain key employees. If we do not maintain the necessary personnel to accomplish our business objectives, we may experience staffing constraints that will adversely affect our ability to meet the demands of our collaboration partners and customers in a timely fashion or to support our internal research and development programs and operations. In particular, our product and process development programs depend on our ability to attract and retain highly skilled technical and operational personnel. Competition for such personnel from numerous companies and academic and other research institutions may limit our ability to do so on acceptable terms. All of our U.S. employees are “at-will” employees, which means that either the employee or we may terminate their employment at any time.

Our operations rely on sophisticated information technology and equipment systems, a disruption of which could harm our operations.

We rely on various information technology and equipment systems, some of which are dependent on services provided by third parties, to manage our technology platform and operations. These systems provide critical data and services for internal and external users, including research and development activities, procurement and inventory management, transaction processing, financial, commercial and operational data, partner and joint venture activities, human resources management, legal and tax compliance and other processes necessary to operate and manage our business. These systems are complex and are frequently updated as technology improves, and include software and hardware that is licensed, leased or purchased from third parties. If our information technology and equipment systems experience breaches or other failures or disruptions, our systems and the information contained therein could be compromised. While we have implemented security measures and disaster recovery plans designed to mitigate the effects of any failures or disruption of these systems, such measures may not adequately prevent adverse events such as breaches or failures from occurring or mitigate their severity if they do occur. If our information technology or equipment systems are breached, damaged or fail to function properly due to internal errors or defects, implementation or integration issues, catastrophic events or power outages, we may experience a material disruption in our ability to manage our business operations. Failure or disruption of these systems could have an adverse effect on our operating results and financial condition.

Increased information systems security threats and more sophisticated, targeted computer invasions could pose a risk to our technology platform and operations.

Increased information systems security threats, cyber- or phishing-attacks and more sophisticated, targeted computer invasions pose a risk to the security of our systems and networks, and the confidentiality, availability, and integrity of our data, operations, and communications. Cyber-attacks against our technology platform and infrastructure could result in exposure of confidential information, the modification of critical data, and/or the failure of critical operations. Likewise, improper or inadvertent employee behavior, including data privacy breaches by employees and others with permitted access to our systems may pose a risk that sensitive data may be exposed to unauthorized persons or to the public. While we attempt to mitigate these risks by employing a number of measures, including security measures, employee training, comprehensive monitoring of our networks and systems, maintenance of backup and protective systems and incident response procedures, if these measures prove inadequate, we could be adversely affected by, among other things, loss or damage of intellectual property, proprietary and confidential information, data integrity, and communications or customer data, increased costs to prevent, respond to, or mitigate these cyber security threats and interruptions of our business operations.

Growth may place significant demands on our management and our infrastructure.

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We have experienced, and expect to continue to experience, expansion of our business as we continue to make efforts to develop and bring our products to market. We have grown from 18 employees at the end of 2005 to 561 full-time employees at December 31, 2019. Our growth and diversified operations have placed, and may continue to place, significant demands on our management and our operational and financial infrastructure. In particular, continued growth could strain our ability to:

•manage multiple research and development programs;

•operate multiple manufacturing facilities around the world;

•develop and improve our operational, financial and management controls;

•enhance our reporting systems and procedures;

•recruit, train and retain highly skilled personnel;

•develop and maintain our relationships with existing and potential business partners;

•maintain our quality standards; and

•maintain customer satisfaction.

Managing our growth will require significant expenditures and allocation of valuable management resources. If we fail to achieve the necessary level of efficiency in our organization as it grows, our business, results of operations and financial condition would be adversely impacted.

Our international operations expose us to the risk of fluctuation in currency exchange rates and rates of foreign inflation, which could adversely affect our results of operations.

We currently incur significant costs and expenses in Brazilian real and may in the future incur additional expenses in foreign currencies and derive a portion of our revenues in the local currencies of customers throughout the world. As a result, our revenues and results of operations are subject to foreign exchange fluctuations, which we may not be able to manage successfully. During the past few decades, the Brazilian currency in particular has faced frequent and substantial exchange rate fluctuations in relation to foreign currencies mostly because of political and economic conditions. There can be no assurance that the Brazilian real will not significantly appreciate or depreciate against the United States dollar in the future. We also bear the risk that the rate of inflation in the foreign countries where we incur costs and expenses or the decline in value of the United States dollar compared to those foreign currencies will increase our costs as expressed in United States dollars. For example, future measures by the Central Bank of Brazil to control inflation, including interest rate adjustments, intervention in the foreign exchange market and actions to fix the value of the real, may weaken the United States dollar in Brazil. Whether in Brazil or elsewhere, we may not be able to adjust the prices of our products to offset the effects of inflation or foreign currency appreciation on our cost structure, which could increase our costs and reduce our net operating margins. If we do not successfully manage these risks through hedging or other mechanisms, our revenues and results of operations could be adversely affected.

Our U.S. GAAP operating results could fluctuate substantially due to the accounting for embedded derivatives in our convertible debt and equity instruments, and debt that we measure at fair value.

Features in several of our outstanding convertible debt and equity instruments are accounted for under Accounting Standards Codification 815, Derivatives and Hedging (ASC 815), as embedded derivatives. ASC 815 requires companies to bifurcate conversion options from their host instruments and account for them as free standing derivative financial instruments according to certain criteria. The current fair value of the derivative is remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the change in the fair value of the derivative being charged to earnings (loss) in the statement of operations. We have determined that we must bifurcate and account for certain features of our convertible debt and equity instruments as embedded derivatives in accordance with ASC 815. We have recorded these embedded derivative liabilities as non-current liabilities on our consolidated balance sheet with a corresponding discount at the date of issuance that is netted against the principal amount of the applicable instrument. The derivative liabilities are remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the change in the fair value of the derivative liabilities being recorded in other income or expenses. There is no current observable market for this type of derivative and, as such, we determine the fair value of the embedded derivatives using the binomial lattice model. The valuation model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. Changes in the inputs for these valuation models may have a significant impact on the estimated fair value of the embedded derivative liabilities. For example, an increase in our stock price would result in an increase in the estimated fair value of the embedded derivative liabilities, if in this example, each of the other elements of the valuation model remained substantially unchanged from the last measurement date. The embedded derivative liabilities may have, on a U.S. GAAP basis, a substantial effect on our balance sheet from quarter to quarter and it is difficult to predict the effect on our future U.S. GAAP financial results, since valuation of these embedded derivative liabilities are based on factors largely outside of our control and may have a negative impact on our statement of operations and balance sheet. The effects of these embedded derivatives may cause our U.S. GAAP operating results to be below expectations, which may cause our stock price to decline. See Note 3, “Fair Value Measurement”

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in Part II, Item 8 of this Annual Report on Form 10-K for more information regarding the valuation of embedded derivatives in certain of our outstanding debt and equity instruments.

In addition, we account for one of our outstanding debt instruments at fair value. That instrument is remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss from change in fair value of debt recorded in other income or expense.

Our ability to use our net operating loss carryforwards to offset future taxable income may be subject to certain limitations.

In general, under Section 382 of the Internal Revenue Code (the Code), a corporation that undergoes an “ownership change”, as defined in the Code, is subject to limitations on its ability to utilize its pre-ownership change net operating loss carryforwards (NOLs) to offset future taxable income. During the three years ended December 31, 2017 and the two years ended December 31, 2019, changes in our share ownership resulted in significant reductions in our NOLs pursuant to Section 382 of the Code. Future changes in our stock ownership, some of which are outside of our control, could result in an ownership change under Section 382 of the Code; if that occurs, our ability to utilize NOLs could be further limited. Furthermore, our ability to utilize NOLs of companies that we may acquire in the future may be subject to limitations under Section 382 of the Code. For these reasons, we may not be able to utilize a material portion of our reported NOLs as of December 31, 2019, even if we attain profitability, which could adversely affect our results of operations.

Our headquarters and other facilities are located in active earthquake and tsunami or in active hurricane zones, and an earthquake, hurricane or other type of natural disaster affecting us or our suppliers could cause resource shortages, disrupt our business and harm our results of operations.

We conduct our primary research and development operations in the San Francisco Bay Area in an active earthquake and tsunami zone, and certain of our suppliers conduct their operations in the same region or in other locations that are susceptible to natural disasters. In addition, California and some of the locations where certain of our suppliers are located have experienced shortages of water, electric power and natural gas from time to time. The occurrence of a hurricane or associated flooding in the Wilmington, North Carolina area could cause damage to our facility located in Leland or result in localized extended outages of utilities or transportation systems. The occurrence of a natural disaster, such as an earthquake, hurricane, drought or flood, or localized extended outages of critical utilities or transportation systems, or any critical resource shortages, affecting us or our suppliers could cause a significant interruption in our business, damage or destroy our facilities, production equipment or inventory or those of our suppliers and cause us to incur significant costs or result in limitations on the availability of our raw materials, any of which could harm our business, financial condition and results of operations. The insurance we maintain against fires, earthquakes and other natural disasters may not be adequate to cover our losses in any particular case. Our facilities undergo annual loss control audits and both our Emeryville and Leland facilities have emergency actions plans outlining emergency response practices for these and other emergency scenarios. Training on emergency response is provided to all employees at hire and annually thereafter as a refresh.

Our stock price may be volatile.

The market price of our common stock has been, and we expect it to continue to be, subject to significant volatility, and it has declined significantly from our initial public offering price. Market prices for securities of early stage companies have historically been particularly volatile. Such fluctuations could be in response to, among other things, the factors described in this “Risk Factors” section, or other factors, some of which are beyond our control, such as:

•fluctuations in our financial results or outlook or those of companies perceived to be similar to us;

•changes in estimates of our financial results or recommendations by securities analysts;

•changes in market valuations of similar companies;

•changes in the prices of commodities associated with our business such as sugar and petroleum or changes in the prices of commodities that some of our products may replace, such as oil and other petroleum sourced products;

•changes in our capital structure, such as future issuances of securities or the incurrence of debt;

•announcements by us or our competitors of significant contracts, acquisitions or strategic partnerships;

•regulatory developments in the United States, Brazil, and/or other foreign countries;

•litigation involving us, our general industry or both;

•additions or departures of key personnel;

•investors’ general perception of us; and

•changes in general economic, industry and market conditions.

Furthermore, stock markets have experienced price and volume fluctuations that have affected, and continue to affect, the market prices of equity securities of many companies. These fluctuations often have been unrelated or disproportionate to the

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operating performance of those companies. These broad market fluctuations, as well as general economic, political and market conditions, such as recessions, interest rate changes and international currency fluctuations, may negatively affect the market price of our common stock.

In the past, many companies that have experienced volatility and sustained declines in the market price of their stock have become subject to securities class action and derivative action litigation. We were involved in two such lawsuits that were dismissed in 2014, were involved in five such lawsuits that were dismissed in September 2017, July 2018 and September 2018, respectively, are currently involved in two such lawsuits, as described in more detail below under “Legal Proceedings,” and we may be the target of this type of litigation in the future. Securities litigation against us could result in substantial costs and divert our management’s attention from other business concerns, which could seriously harm our business.

The concentration of our capital stock ownership with insiders will limit the ability of other stockholders to influence corporate matters and presents risks related to the operations of our significant stockholders.

As of January 31, 2020, significant stockholders held an aggregate total of 56.9% of the Company's total common shares outstanding, as follows: Foris Ventures, LLC (Foris) (33.3%), DSM (8.1%), Total (6.2%), Loyola Capital (5.2%) and Vivo Capital LLC (Vivo) (4.1%). Furthermore, each of these parties holds some or a combination of convertible preferred stock, warrants and purchase rights, pursuant to which they may acquire additional shares of our common stock and thereby increase their ownership interest in our company. Additionally, Foris is indirectly owned by John Doerr, one of our current directors, and each of DSM, Total and Vivo have the right to designate one or more directors to serve on our Board of Directors pursuant to agreements between us and such stockholders. This significant concentration of share ownership may adversely affect the trading price of our common stock because investors often perceive disadvantages in owning stock in companies with stockholders with significant interests. Also, these stockholders, acting together, may be able to control or significantly influence our management and affairs and matters requiring stockholder approval, including the election of directors and the approval of significant corporate transactions, such as mergers, consolidations or the sale of all or substantially all of our assets, and may not act in the best interests of our other stockholders. Consequently, this concentration of ownership may have the effect of delaying or preventing a change of control, or a change in our management or Board of Directors, or discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control of our company, even if such actions would benefit our other stockholders.

In addition, certain of our significant stockholders are also our commercial partners and have various rights in connection with their security ownership in us. These stockholders may have interests that are different from those of our other stockholders, including with respect to our company’s commercial transactions. While we have a related-party transactions policy that requires certain approvals of any transaction between our company and a significant stockholder or its affiliates, there can be no assurance that our significant stockholders will act in the best interests of our other stockholders, which could harm our results of operations and cause our stock price to decline.

The market price of our common stock could be negatively affected by future sales of our common stock.

If our existing stockholders, particularly our largest stockholders, our directors, their affiliates, or our executive officers, sell a substantial number of shares of our common stock in the public market, the market price of our common stock could decrease significantly. The perception in the public market that these stockholders might sell our common stock could also depress the market price of our common stock and could impair our future ability to obtain capital, especially through an offering of equity securities.

We have in place, or have agreed to file, registration statements for the resale of certain shares of our common stock held by, or issuable to, certain of our largest stockholders. All of our common stock sold pursuant to an offering covered by such registration statements will be freely transferable. In addition, shares of our common stock issued or issuable under our equity incentive plans have been registered on Form S-8 registration statements and may be freely sold in the public market upon issuance, except for shares held by affiliates who have certain restrictions on their ability to sell.

The restatement of our previously issued financial statements was time-consuming and expensive and could expose us to additional risks that could materially adversely affect our financial position, results of operations and cash flows.

On April 5, 2019, our Audit Committee, after consultation with management and KPMG LLP (KPMG), our former independent registered public accounting firm, determined that we would restate our interim condensed consolidated financial statements for the quarterly and year-to-date periods ended March 31, 2018, June 30, 2018 and September 30, 2018, included in our Quarterly Reports on Form 10-Q for the fiscal quarters ended March 31, 2018, June 30, 2018 and September 30, 2018, respectively. In addition, on May 14, 2019, our Board of Directors, upon the recommendation of the Audit Committee after

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consultation with senior management and KPMG, determined that we would restate our audited consolidated financial statements for the year ended December 31, 2017. The consolidated financial statements and related information included in our previously filed Annual Report on Form 10-K for the year ended December 31, 2017 and Quarterly Reports on Form 10-Q for the periods ended March 31, 2018, June 30, 2018 and September 30, 2018 and all earnings press releases and similar communications issued by us for such periods should not be relied upon and are superseded in their entirety by the Annual Report on Form 10-K/A for the year ended December 31, 2018.

Accordingly, the Annual Report on Form 10-K/A as of and for the year ended December 31, 2018 includes: (1) changes to our consolidated financial statements to reflect the restatement of our audited consolidated financial statements for the year ended December 31, 2017 and our unaudited interim condensed consolidated financial statements for the quarterly and year-to-date periods ended March 31, 2018, June 30, 2018 and September 30, 2018; (2) changes as to reflect the restatement of our unaudited quarterly and year-to-date periods ended March 31, 2017, June 30, 2017 and September 30, 2017 for additional errors identified during the re-audit of our consolidated financial statements for the year ended December 31, 2017; (3) expanded risk factor disclosures within Part I, Item 1A; and (4) additional disclosures and conclusions regarding our disclosure controls and procedures and internal control over financial reporting in Part II, Item 9A.

As a result of the restatement and associated non-reliance on previously issued financial information, we became subject to a number of additional expenses and risks, including unanticipated expenses for accounting and legal fees in connection with or related to the restatement. Likewise, the attention of our management team has been diverted by these efforts. In addition, we could also be subject to additional shareholder, governmental, regulatory or other actions or demands in connection with the restatement or other matters. Any such proceedings will, regardless of the outcome, consume a significant amount of management’s time and attention and may result in additional legal, accounting, insurance and other expenses. If we do not prevail in any such proceeding, we could be required to pay damages or settlement costs. In addition, the restatement and related matters could impair our reputation or could cause our customers, shareholders, or other counterparties to lose confidence in us. Any of these occurrences could have a material adverse effect on our business, results of operations, financial condition and stock price.

If securities or industry analysts do not publish or cease publishing research or reports about us, our business or our market, or if they change their recommendations regarding our stock adversely, our stock price and trading volume could decline.

The trading market for our common stock will be influenced by the research and reports that industry or securities analysts may publish about us, our business, our market or our competitors. If any of the analysts who cover us change their recommendation regarding our stock adversely, or provide more favorable relative recommendations about our competitors, our stock price would likely decline. If any analyst who may cover us were to cease coverage of our company or fail to regularly publish reports on us, we could lose visibility in the financial markets, which in turn could cause our stock price or trading volume to decline.

We do not expect to declare any cash dividends in the foreseeable future.

We do not anticipate declaring any cash dividends to holders of our common stock in the foreseeable future. In addition, certain of our equipment leases and credit facilities currently restrict our ability to pay dividends. Consequently, investors may need to rely on sales of their shares of our common stock after price appreciation, which may never occur, as the only way to realize any future gains on their investment. Investors seeking cash dividends should not purchase our common stock.

Anti-takeover provisions contained in our Certificate of Incorporation and Bylaws, as well as provisions of Delaware law, could impair a takeover attempt.

Our Certificate of Incorporation and Bylaws contain provisions that could delay or prevent a change in control of our company. These provisions could also make it more difficult for stockholders to nominate directors and take other corporate actions. These provisions include:

•a staggered Board of Directors;

•authorizing the Board of Directors to issue, without stockholder approval, preferred stock with rights senior to those of our common stock;

•authorizing the Board of Directors to amend our Bylaws, to increase the number of directors and to fill board vacancies until the end of the term of the applicable class of directors;

•prohibiting stockholder action by written consent;

•limiting the liability of, and providing indemnification to, our directors and officers;

•eliminating the ability of our stockholders to call special meetings; and

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•requiring advance notification of stockholder nominations and proposals.

Section 203 of the Delaware General Corporation Law prohibits, subject to some exceptions, “business combinations” between a Delaware corporation and an “interested stockholder,” which is generally defined as a stockholder who becomes a beneficial owner of 15% or more of a Delaware corporation’s voting stock, for a three-year period following the date that the stockholder became an interested stockholder. We have agreed to opt out of Section 203 through our Certificate of Incorporation, but our Certificate of Incorporation contains substantially similar protections to our company and stockholders as those afforded under Section 203, except that we have agreed with Total that it and its affiliates will not be deemed to be “interested stockholders” under such protections.

These and other provisions in our Certificate of Incorporation and our Bylaws could discourage potential takeover attempts, reduce the price that investors are willing to pay in the future for shares of our common stock and result in the market price of our common stock being lower than it would be without these provisions.

Our business is subject to risks arising from epidemic diseases, such as the recent outbreak of the COVID-19 illness.

The recent outbreak of the Coronavirus Disease 2019, or COVID-19, which has been declared by the World Health Organization to be a “public health emergency of international concern,” has spread across the globe and is impacting worldwide economic activity. A public health epidemic, including COVID-19, poses the risk that we or our employees, contractors, suppliers, and other partners may be prevented from conducting business activities for an indefinite period of time, including due to shutdowns that may be requested or mandated by governmental authorities. While it is not possible at this time to estimate the impact that COVID-19 could have on our business, the continued spread of COVID-19 and the measures taken by the governments of countries affected could disrupt the supply chain and the manufacture or shipment of our products and adversely impact our business, financial condition or results of operations. The COVID-19 outbreak and mitigation measures may also have an adverse impact on global economic conditions which could have an adverse effect on our business and financial condition. The extent to which the COVID-19 outbreak impacts our results will depend on future developments that are highly uncertain and cannot be predicted, including new information that may emerge concerning the severity of the virus and the actions to contain its impact.

ITEM 1B. UNRESOLVED STAFF COMMENTS

Not applicable.

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ITEM 2. PROPERTIES

The following is a summary of our principal facilities as of December 31, 2019. We lease our principal office and research and development facilities located in Emeryville, California. We hold a 50% ownership interest in a manufacturing facility and related land located in Leland, North Carolina and lease a pilot plant and demonstration facility and related office and laboratory space located in Campinas, Brazil. Our lease agreements expire at various dates through the year 2031.

Location	Approximate Square Feet	Operations
U.S.
Emeryville, California	136,000	Executive offices; research and development, administrative and pilot plant
Leland, North Carolina	19,400	Manufacturing (joint venture with Nikko)
BRAZIL
Campinas, Brazil	44,000	Pilot plant, research and development and administrative

We believe that our current facilities are suitable and adequate to meet our needs and that suitable additional space will be available to accommodate the foreseeable expansion of our operations. Based on our anticipated volume requirements for 2020 and beyond, we will likely need to identify and secure access to additional production capacity in 2020 and beyond, which we plan to obtain by constructing new facilities and by increasing our use of contract manufacturers, including our collaboration partner, DSM. We are currently making plans to secure such additional capacity.

ITEM 3. LEGAL PROCEEDINGS

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all persons and entities that purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The complaint, which was amended by the lead plaintiff on September 13, 2019, alleges securities law violations based on statements and omissions made by the Company during such period. On October 25, 2019, the defendants filed a motion to dismiss the securities class action complaint. The hearing on such motion to dismiss was held on February 18, 2020 and we are awaiting a ruling from the Court. Subsequent to the filing of the securities class action complaint described above, on June 21, 2019 and October 1, 2019, respectively, two separate purported shareholder derivative complaints were filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr, et al., and Carlson v. Doerr, et al.) based on similar allegations to those made in the securities class action complaint described above and named the Company and certain of the Company’s current and former officers and directors as defendants. The derivative lawsuits sought to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and omissions made in connection with the Company’s securities filings. The derivative lawsuits were dismissed on October 18, 2019 (Bonner) and December 10, 2019 (Carlson), without prejudice. We believe the securities class action complaint lacks merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

We may be involved, from time to time, in legal proceedings and claims arising in the ordinary course of our business. Such matters are subject to many uncertainties and there can be no assurance that legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, results of operations, financial position or cash flows. For additional information, see "Other Matters" in Note 9, "Commitments and Contingencies" in Part II, Item 8 of this Annual Report on Form 10-K.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

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PART II

ITEM 5. MARKET FOR REGISTRANT’S COMMON EQUITY AND RELATED STOCKHOLDER MATTERS

Market Information for Common Stock

Our common stock is traded on the Nasdaq Global Select Market under the symbol AMRS.

At March 6, 2020, there were 71 holders of record (not including beneficial holders of stock held in street names) of our common stock.

Dividend Policy

We have never declared or paid any cash dividend on our common stock. We intend to retain any future earnings and do not expect to pay cash dividends in the foreseeable future.

Recent Sales of Unregistered Equity Securities and Use of Proceeds

For information regarding unregistered sales of our equity securities during the two years ended December 31, 2019, see the financial statements included in Part II, Item 8 of this Annual Report on Form 10-K.

See Note 15, “Subsequent Events” in Part II, Item 8 of this Annual Report on Form 10-K for information regarding unregistered sales of our equity securities subsequent to December 31, 2019.

Securities Authorized for Issuance under Equity Compensation Plans

The following table shows certain information concerning our common stock reserved for issuance in connection with our 2005 Stock Option/Stock Issuance Plan, our 2010 Equity Incentive Plan and our 2010 Employee Stock Purchase Plan, all as of December 31, 2019:

Plan category	Number of securities to be issued upon exercise of outstanding options, warrants and rights	Weighted-average exercise price of outstanding options		Number of securities to be issued upon vesting of outstanding restricted stock units	Number of securities remaining available for future issuance under equity compensation plans(1)(2)
Equity compensation plans approved by security holders	5,620,419	$	10.27	5,782,651	4,079,422
Equity compensation plans not approved by security holders	—	—		—	—
Total	5,620,419	$	10.27	5,782,651	4,079,422

(1) Includes 3,815,625 shares reserved for future issuance under our 2010 Equity Incentive Plan and 263,797 shares reserved for future issuance under our 2010 Employee Stock Purchase Plan. No shares are reserved for future issuance under our 2005 Stock Option/Stock Issuance Plan other than shares issuable upon exercise of equity awards outstanding under such plan.

(2) Effective January 1, 2019, the number of shares available for future issuance under our 2010 Equity Incentive Plan increased by 5,887,133 shares pursuant to the automatic increase provision contained in the 2010 Equity Incentive Plan and the number of shares available for future issuance under our 2010 Employee Stock Purchase Plan increased by 588,713 shares, in each case pursuant to automatic increase provisions contained in the respective plans, as discussed in more detail below.

Our 2010 Equity Incentive Plan includes all shares of our common stock reserved for issuance under our 2005 Stock Option/Stock Issuance Plan immediately prior to our initial public offering that were not subject to outstanding grants as of the completion of such offering. In addition, any shares of our common stock (i) issuable upon exercise of stock options granted under our 2005 Stock Option/Stock Issuance Plan that cease to be subject to such options and (ii) issued under our 2005 Stock Option/Stock Issuance Plan that are forfeited or repurchased by us at the original issue price, will become part of our 2010 Equity Incentive Plan reserve.

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The number of shares available for grant and issuance under our 2010 Equity Incentive Plan is increased on January 1 of each year during the term of the plan by an amount equal to the lesser of (1) five percent (5%) of our shares outstanding on the immediately preceding December 31 and (2) a number of shares as may be determined by our Board of Directors or the Leadership Development and Compensation Committee in their discretion. In addition, shares will again be available for grant and issuance under our 2010 Equity Incentive Plan that are:

•subject to issuance upon exercise of an option or stock appreciation right granted under our 2010 Equity Incentive Plan and that cease to be subject to such award for any reason other than the award’s exercise;

•subject to an award granted under our 2010 Equity Incentive Plan and that are subsequently forfeited or repurchased by us at the original issue price;

•surrendered pursuant to an exchange program; or

•subject to an award granted under our 2010 Equity Incentive Plan that otherwise terminates without shares being issued.

The number of shares reserved for issuance under our 2010 Employee Stock Purchase Plan is increased on January 1 of each year during the term of the plan by an amount equal to the lesser of  (1) one percent (1%) of our shares outstanding on the immediately preceding December 31 and (2) a number of shares as may be determined by our Board of Directors or the Leadership Development and Compensation Committee of the Board in their discretion, provided that the aggregate number of shares issued over the term of our 2010 Employee Stock Purchase Plan shall not exceed 1,666,666 shares.

For more information regarding our 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan, see Note 11, “Stock-based Compensation” in Part II, Item 8 of this Annual Report on Form 10-K.

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ITEM 6. SELECTED FINANCIAL DATA

Not applicable for smaller reporting companies.

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Overview

As a leading industrial biotechnology company, we apply our technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets. Our proven technology platform enables us to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. Our biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. We have successfully used our technology to develop and produce nine distinct molecules at commercial volumes, leading to more than 17 commercial ingredients used by thousands of leading global brands.

We believe that industrial synthetic biology represents a third industrial revolution, bringing together biology and engineering to generate new, more sustainable materials to meet the growing global demand for bio-based replacements for petroleum-based and traditional animal- or plant-derived ingredients. We continue to build demand for our current portfolio of products through an extensive sales network provided by our collaboration partners that represent leading companies for our target market sectors. We also have a small group of direct sales and distributors who support our Clean Beauty market. Via our partnership model, our partners invest in the development of each molecule to bring it from the lab to commercial-scale and use their extensive sales force to sell our ingredients and formulations to their customers as part of their core business. We capture long-term revenue both through the production and sale of the molecule to our partners and through royalty revenues from our partners' product sales to their customers.

We were founded in 2003 in the San Francisco Bay area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic acid, which is a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted royalty-free licenses to allow Sanofi-Aventis to produce artemisinic acid using our technology. Building on our success with artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell sustainable alternatives to a broad range of markets.

We focused our initial development efforts primarily on the production of Biofene®, our brand of renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through fermentation using engineered microbes. Our farnesene derivatives are sold in hundreds of products as nutraceuticals, skincare products, fragrances, solvents, polymers, and lubricant ingredients. The commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development process in the lab and drive manufacturing costs down. This investment has enabled our technology platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began manufacturing additional molecules for the Flavor & Fragrance industry; in 2015 we began investing to expand our capabilities to other small molecule chemical classes beyond terpenes via our collaboration with the Defense Advanced Research Projects Agency (DARPA); and in 2016 we expanded into proteins.

We have invested over $700 million in infrastructure and technology to create microbes that produce molecules from sugar or other feedstocks at commercial-scale. This platform has been used to design, build, optimize and upscale strains producing nine distinct molecules at commercial volumes, leading to more than 17 commercial ingredients used by thousands of leading global brands. Our time to market for molecules has decreased from seven years to less than a year for our most recent molecule, mainly due to our ability to leverage the technology platform we have built.

Our technology platform has been in active use since 2007 and has been integrated with our commercial production since 2011, creating an organism development process that we believe makes us an industry leader in the successful scale-up and commercialization of biotech-produced ingredients. The key performance characteristics of our platform that we believe differentiate us include our proprietary computational tools, strain construction tools, screening and analytics tools, and advanced lab automation and data integration. Having this fully integrated with our large-scale manufacturing process and capability enables us to always engineer with the end specification and requirements guiding our technology. Our state-of-the-

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art infrastructure includes industry-leading strain engineering and lab automation located in Emeryville, California, pilot-scale production facilities in Emeryville, California and Campinas, Brazil, a demonstration-scale facility in Campinas, Brazil and a commercial-scale production facility in Leland, North Carolina, which is owned and operated by our Aprinnova joint venture to convert our Biofene into squalane and other final products.

We are able to use a wide variety of feedstocks for production, but have focused on accessing Brazilian sugarcane for our large-scale production because of its renewability, low cost and relative price stability. We have also successfully used other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars at various manufacturing facilities.

Several years ago, we made the strategic decision to transition our business model from collaborating and commercializing molecules in low margin commodity markets to higher margin specialty markets. We began the transition by first commercializing and supplying farnesene-derived squalane as a cosmetic ingredient sold to formulators and distributors. We also entered into collaboration and supply agreements for the development and commercialization of molecules within the Flavor & Fragrance and Clean Beauty markets where we utilize our strain generation technology to develop molecules that meet the customer’s rigorous specifications.

During this transition, we solidified the business model of partnering with our customers to create sustainable, high performing, low-cost molecules that replace an ingredient in their supply chain, commercially scale and manufacture those molecules, and share in the profits earned by our customers once our customer sells its product into these specialty markets. These three steps constitute our grants and collaborations revenues, renewable product revenues, and royalty revenues.

During 2017, we completed several development agreements with DSM and others for new products such as Vitamin A, a human nutrition molecule and others, and in late 2018 we began commercial production and shipment of an alternative sweetener product developed from the Reb M molecule, which is a superior sweetener and sugar replacement. Our goal is to bring two to three new molecules per year to commercial production in the future.

In 2017, we monetized the use of one of our lower margin molecules, farnesene, in the Vitamin E and Lubricants specialty markets while retaining any associated royalties, and licensed farnesene to Koninklijke DSM N.V. (DSM) for use in these fields. Also in 2017, we sold to DSM our subsidiary Amyris Brasil Ltda. (Amyris Brasil), which operated our purpose-built, large-scale manufacturing facility located in Brotas, Brazil.

The Brotas facility was built to batch manufacture one commodity product at a time (originally for high-volume production of biofuels, a business Amyris has exited), which is an inefficient manufacturing process that is not suited for the high margin specialty markets in which we operate today. We currently manufacture nine specialty products and expect to increase the number of specialty products we manufacture by two to three products a year. The inefficiencies we experienced included having to idle the facility for two weeks at a time to prepare for the next product batch manufacture. These inefficiencies caused our cost of goods sold to be significantly higher. As a result, we are building a new purpose-built, large-scale specialty ingredients plant in Brazil, which we anticipate will allow for the manufacture of five products concurrently, including our alternative sweetener product, and over 10 different products annually. In September 2019, we obtained the necessary permits and broke ground on our new specialty ingredients plant and expect the facility to be fully operational in the first quarter of 2021. During construction, we are manufacturing our products at four contract manufacturing sites in Brazil, the U.S. and Spain.

Also, as part of the December 2017 sale of Brotas, we contracted with DSM for the use of Brotas to manufacture products for us to fulfill our product supply commitments to our customers until the new production facility is built and becomes operational, and in November 2018, we amended the supply agreement with DSM to secure capacity at the Brotas facility for production of our alternative sweetener product through 2022.

In May 2019 we entered into an agreement with Raizen Energia S.A. (Raizen) for the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products whereby the parties would construct a manufacturing facility exclusively for sweetener molecules on land owned by Raizen and leased to the joint venture.

Also, in May 2019, we consummated a research, collaboration and license agreement with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids. Under the Cannabinoid Agreement, we would perform research and development activities and Lavvan would be responsible for the commercialization of the cannabinoids developed under the agreement. The Cannabinoid Agreement is being principally funded on a milestone basis, with Amyris also entitled to receive certain supplementary research and development funding from Lavvan. We could receive aggregate funding of up to $300 million over the term of the Cannabinoid

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Agreement if all of the milestones are achieved. Additionally, the Cannabinoid Agreement provides for profit share to Amyris on Lavvan's gross profit margin once products are commercialized; these payments will be due for the next 20 years.

Sales and Revenue

We recognize revenue from product sales, license fees and royalties, and grants and collaborations.

We have research and development collaboration arrangements for which we receive payments from our collaboration partners, which include DARPA, DSM, Firmenich SA (Firmenich), Givaudan International SA (Givaudan), Lavvan and others. Some of our collaboration arrangements provide for advance payments to us in consideration for grants of exclusivity or research efforts that we will perform. In 2017 we signed collaboration agreements for an infant nutrition ingredient, and in 2018 and 2019 we signed a collaboration agreement for four vitamins that we expect will contribute to our collaboration revenue and ultimately product sales. Also, in 2019 we signed a collaboration agreement for up to $300 million to develop cannabinoids. Our collaboration agreements, which may require us to achieve milestones prior to receiving payments, are expected to contribute revenues from product sales and royalties if and when they are commercialized. See Note 9, “Revenue Recognition” in Part II, Item 8 of this Annual Report on Form 10-K for additional information.

All of our non-government partnerships include commercial terms for the supply of molecules we successfully upscale and produce at commercial volumes. The first molecule to generate revenue for us outside of farnesene was a fragrance molecule launched in 2015. Since the launch, the product has continued to grow in sales year over year. In 2016, we launched our second fragrance molecule and in 2017, we launched our third fragrance molecule as well as our first cosmetic active ingredient. Our partners for these molecules are indicating continued strong growth due to their cost advantaged position, high purity and sustainable production method. We are continuing to identify new opportunities to apply our technology and deliver sustainable access to key molecules. As a result, we have a pipeline that we believe can deliver two to three new molecules each year over the coming years with a flavor ingredient, a cosmetic active ingredient and a fragrance molecule. In 2019, we commercially produced and shipped our Reb M product that is a sweetener and sugar replacement for food and beverages.

Concurrent with the December 2017 sale of Amyris Brasil and the Brotas facility, we entered into a series of commercial agreements with DSM that included (i) a license agreement to DSM of our farnesene product for DSM to use in the Vitamin E and lubricant specialty markets and (ii) a royalty agreement, pursuant to which DSM agreed to pay us specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene sold under a supply agreement with Nenter & Co., Inc. (Nenter) which was assigned to DSM. Under the terms of the royalty agreement, DSM was obligated to pay us minimum royalties totaling $18.1 million for 2019 and 2020. In June 2018, we received the 2019 non-refundable minimum royalty payment totaling $9.3 million (net of a $0.7 million early payment discount) and in March 2019, we received the 2020 non-refundable payment totaling $7.4 million (net of a $0.7 million early payment discount). In April 2019, we assigned the right to receive such royalty payments under the Vitamin E royalty agreement to DSM for total consideration of $57 million, of which approximately $40.3 million was recognized as royalty revenue in 2019. See Note 9, “Revenue Recognition” and Note 10, "Related Party Transactions" in Part II, Item 8 of this Annual Report on Form 10-K for information regarding the accounting treatment of the assignment of Vitamin E royalty agreement and for a full listing of our agreements with DSM.

We have several other collaboration molecules in our development pipeline with partners including DSM, Givaudan, Firmenich and Lavvan that we expect will contribute revenues from product sales and royalties if and when they are commercialized.

Critical Accounting Policies and Estimates

Management's discussion and analysis of results of operations and financial condition are based on our consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the U.S. (U.S. GAAP). We believe that the critical accounting policies described in this section are those that significantly impact our financial condition and results of operations and require the most difficult, subjective or complex judgements, often as a result of the need to make estimates about the effects of matters that are inherently uncertain. Because of this uncertainty, actual results may vary from these estimates.

Our most critical accounting estimates include:

•Recognition of revenue including arrangements with multiple performance obligations;

•Valuation and allocation of fair value to various elements of complex related party transactions;

•The valuation of freestanding and embedded derivatives, which impacts gains or losses on such derivatives, the carrying value of debt, interest expense and deemed dividends; and

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•The valuation of debt for which we have elected fair value accounting.

For a more detailed discussion of our critical accounting estimates and policies, see Note 1, "Basis of Presentation and Summary of Significant Accounting Policies" in Part II, Item 8 of this 2019 Form 10-K.

Results of Operations

Revenue

Years Ended December 31, (In thousands)	2019		2018		2019 vs 2018 % Change
Revenue:
Renewable products	$	59,872	$	33,598	78	%
Licenses and royalties	54,043		7,658		606	%
Grants and collaborations	38,642		22,348		73	%
Total revenue	$	152,557	$	63,604	140	%

Total revenue increased by 140% to $152.6 million in 2019. Renewable products revenue increased by 78% to $59.9 million in 2019, primarily due to (i) $15.9 million of consumer products revenue in 2019 through a combination of retail and direct e-commerce sales, as compared to $4.6 million in 2018; (ii) a $4.9 million increase in product revenue from sales to Firmenich; (iii) a $3.4 million increase from sales to Givaudan; and (iv) a $2.8 million increase in squalane sales.

Licenses and royalties revenue increased by 606% to $54.0 million in 2019, primarily due to a $43.1 million increase in royalty revenues as the result of our sale and assignment of the Vitamin E Value Sharing Agreement to DSM, and a $3.3 million increase in royalties from fragrance product sales.

Grants and collaborations revenue increased by 73% to $38.6 million in 2019, primarily due to $18.3 million of revenue from Lavvan in 2019 in connection with a CBD collaboration agreement, and $5.7 million of vitamin-related collaboration revenue from Yifan, less a $4.3 million decrease in collaboration revenue from Firmenich, a $2.9 million decrease in grant revenue from DARPA and a $2.9 million decrease in collaboration revenue from Givaudan.

Our revenues are dependent on the timing and nature of arrangements entered into with our customers, which may include multiple performance obligations for which revenue accounting requires significant judgement and estimates. Based on the nature of our customer arrangements, our revenues may vary significantly from one period to the next.

Cost and Operating Expenses

Years Ended December 31, (In thousands)	2019		2018		2019 vs 2018 % Change
Cost of products sold	$	76,185	$	36,698	108	%
Research and development	71,460		68,722		4	%
Sales, general and administrative	126,586		90,902		39	%
Impairment of other assets	216		3,865		(94)	%
Total cost and operating expenses	$	274,447	$	200,187	37	%

Cost of Products Sold

Cost of products sold includes the costs of raw materials, labor and overhead, amounts paid to contract manufacturers, inventory write-downs resulting from applying lower of cost or net realizable value inventory adjustments, and costs related to production scale-up. Because of our product mix, our cost of products sold does not change proportionately with changes in renewable product revenue.

Cost of products sold increased by 108% to $76.2 million in 2019, primarily due to a 78% increase in renewable products revenue, and significant non-recurring production costs related to the launch of certain new products.

Research and Development Expenses

Research and development expenses increased by 4% to $71.5 million in 2019, primarily due to increases in laboratory supplies and employee compensation. The laboratory supplies increase was related to the procurement of additional leased

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equipment to expand research and product development. Employee compensation increased primarily as the result of competitive changes to the Company’s base salary and bonus structure for most personnel at the beginning of 2019, and higher employee benefits costs.

Sales, General and Administrative Expenses

Sales, general and administrative expenses increased by 39% to $126.6 million in 2019, primarily due to increases in employee staffing, outside services, sales and marketing spending to support the growth of our Biossance, Pipette and Purecane product lines, and significantly increased audit fees and accounting advisory services related to the 2017 annual and 2018 quarterly financial restatements performed in 2019.

Impairment of Other Assets

In 2019 and 2018, we impaired $0.2 million and $3.9 million, respectively, of contingent consideration that had been recorded in 2017 in connection with the December 2017 sale of our factory in Brasil.

Other Income (Expense), Net

Years Ended December 31, (In thousands)	2019		2018		2019 vs 2018 % Change
Loss on divestiture	$	—	$	(1,778)	(100)	%
Interest expense	(58,665)		(42,703)		37	%
Gain (loss) from change in fair value of derivative instruments	2,777		(30,880)		(109)	%
(Loss) gain from change in fair value of debt	(19,369)		2,082		nm
Loss upon extinguishment of debt	(44,208)		(17,424)		154	%
Other expense, net	(783)		(2,949)		(73)	%
Total other expense, net	$	(120,248)	$	(93,652)	28	%

______________

nm = not meaningful

Total other expense, net was $120.2 million in 2019, compared to $93.7 million in 2018. The $26.6 million increase was primarily comprised of a $26.8 million increase in loss upon extinguishment of debt, a $21.5 million unfavorable swing in change in fair value of debt from a gain to a loss, and a $16.0 million increase in interest expense, partly offset by a $33.7 million favorable swing in change in fair value of derivative instruments from a loss to a gain. The increases in loss upon extinguishment of debt, loss from change in fair value of debt and interest expense were primarily related to (i) the write-off of unamortized debt discounts upon the modification of a debt instrument accounted for as an extinguishment, (ii) upfront expense recognition of the fair value of warrants issued in connection with new borrowings, refinancings and maturity date extensions with existing lenders, (iii) upfront expense recognition of debt discounts paid and end of term fees due to existing lenders in connection with additional borrowings and maturity date extensions, and (iv) penalties, waiver fees and default interest related to covenant violations, events of default under certain debt instruments and in connection with forbearance agreements. See Note 1, “Basis of Presentation and Summary of Significant Accounting Policies–Fair Value Measures” in Part II, Item 8 of this Annual Report on Form 10-K for a discussion regarding how our closing stock price at the end of the period or immediately prior to the extinguishment of an embedded derivative or debt or warrant instrument can affect the fair value of our derivative liabilities and our debt.

Income Taxes

For 2019, we recorded $0.6 million income tax expense related to accrued interest on uncertain tax positions. For 2018, we recorded $0 income tax expense as a result of recording a full valuation allowance against our net deferred tax assets due to our history of losses and the unlikelihood of timely recovery of such tax assets.

See Note 13, "Income Taxes" in Part II, Item 8 of this Annual Report on Form 10-K for additional information.

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Liquidity and Capital Resources

Years Ended December 31, (In thousands)	2019		2018
Net cash (used in) provided by:
Operating activities	$	(156,933)	$	(109,366)
Investing activities	$	(13,080)	$	(12,472)
Financing activities	$	124,910	$	107,957

Liquidity

We have incurred significant operating losses since our inception, and we expect to continue to incur losses and negative cash flows from operations through at least the next 12 months following the issuance of this Annual Report on Form 10-K. As of December 31, 2019, we had negative working capital of $87.5 million, an accumulated deficit of $1.8 billion, and cash and cash equivalents of $0.3 million.

As of December 31, 2019, our debt (including amounts owed to related parties), net of a $20.3 million discount and a $15.4 million fair value adjustment, totaled $261.8 million, of which $63.8 million is classified as current. However, $75.0 million of debt was converted into equity in January 2020; see Note 15, “Subsequent Events” for more information. Our debt agreements contain various covenants, including certain restrictions on our business — including restrictions on additional indebtedness, material adverse effect and cross default provision — that could cause us to be at risk of default. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make payments when required, would generally result in events of default under such instruments, which could result in the acceleration of a substantial portion of such indebtedness. Acceleration would generally also constitute an event of default under our other outstanding debt instruments, which could result in the acceleration of a substantial portion of such debt instruments. At December 31, 2019, we failed to meet certain covenants under several credit arrangements, including those associated with cross-default provisions, minimum liquidity requirements and minimum asset coverage requirements. In March 2020, these lenders provided permanent waivers to us for breaches of all past covenant violations and cross-default payment failures (discussed below), through March 13, 2020 under the respective credit agreements, and significantly reduced the minimum liquidity requirement and substantially increased the base of eligible assets to calculate the asset coverage requirement.

On January 31, 2020, we failed to pay Total Raffinage Chimie (Total), Nikko Chemicals Co. Ltd (Nikko) and certain affiliates of the Schottenfeld Group LLC (Schottenfeld) an aggregate of $22.5 million of maturing promissory notes, and previously on December 15, 2019 failed to pay Ginkgo $5.2 million of past due interest, past due partnership payments and the first installment of a waiver fee. These failures resulted in an event of default under the respective agreements and triggered cross-defaults under other debt instruments, which permitted the holders of such debt instruments to accelerate the amounts owing under such instruments. We subsequently received waivers from each of the affected cross-default debt holders to waive the right to accelerate due to the event specific cross-defaults. As a result, the indebtedness for which we have obtained such waivers continues to be classified as noncurrent on the Company’s balance sheet in accordance with such debt's terms. The indebtedness of Total and certain Ginkgo, Nikko and Schottenfeld amounts continue to be classified as current liabilities on our balance sheet to the extent that payment due dates are within one year of December 31, 2019.

Subsequent to December 31, 2019, we (i) obtained a waiver and forbearance agreement from Schottenfeld, (ii) amended the credit arrangements with Total and Nikko Notes to extend the maturity date of the original promissory notes, and (iii) entered into a waiver and amendment to the partnership agreement with Ginkgo to waive all past payment defaults under the Ginkgo Note and Ginkgo Partnership Agreement, and to extend the payment due date and modify the periodic partnership payment timing and amount. See Note 15, “Subsequent Events” for further information.

Although we obtained extensions to make these payments, we currently do not have sufficient funds to repay the amounts due under the Total, Nikko, Schottenfeld and Ginkgo credit arrangements, and while we intend to seek equity financing, the proceeds of which would be used to repay Total, Nikko, Schottenfeld and Ginkgo, there can be no assurance that we will be able to obtain such financing on our expected timeline, or on acceptable terms, if at all. Also, while we have been able to cure these defaults to date to avoid additional cross-acceleration, we may not be able to cure such a default promptly in the future. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. See Note 1, Basis of Presentation and Summary of Accounting Policies" in Part II, Item 8 of this Annual Report on Form 10-K for additional information.

Our consolidated financial statements as of and for the year ended December 31, 2019 have been prepared on the basis that we will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. Due to the factors described above, there is substantial doubt about our ability to continue as a going

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concern within one year after the date that the financial statements in this Annual Report on Form 10-K are issued. Our ability to continue as a going concern will depend, in large part, on our ability to raise additional proceeds through financings, achieve positive cash flows from operations during the next 12 months from the date of this filing, and refinance or extend other existing debt maturities occurring later in 2020, which is uncertain. The financial statements do not include any adjustments that might result from the outcome of this uncertainty, which could have a material adverse effect on our financial condition. In addition, if we are unable to continue as a going concern, we may be unable to meet our obligations under our existing debt facilities, which could result in the acceleration of such debt payment obligations, and we may be forced to liquidate our assets. In such a scenario, the values we receive for our assets in liquidation or dissolution could be significantly lower than the values reflected in our consolidated balance sheet.

Our operating plan for 2020 contemplates a significant reduction in our net cash outflows resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and engineering developments, and (iii) cash inflows from collaborations and grants. These factors are expected to improve our liquidity.

If we are unable to generate sufficient cash inflows from product sales and collaboration arrangements, and draw sufficient funds from current or pending financing arrangements, we will need to obtain additional funding from equity or other debt financings, which may not occur timely or on reasonable terms, if at all, and agree to burdensome covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights, or grant licenses on terms that are not favorable.

If we do not achieve our planned operating results, our ability to continue as a going concern will be jeopardized and we may need to take the following actions to support our liquidity needs in 2020:

•Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts;

•Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors;

•Reduce or delay uncommitted capital expenditures, including expenditures related the construction and commissioning of the new production facility in Brazil, nonessential facilities and lab equipment, and information technology projects; and

•Closely monitor our working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could negatively impact our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

•Achieve planned production levels;

•Develop and commercialize products within planned timelines or at planned scales; and

•Continue other core activities.

We expect to fund operations for the foreseeable future with cash currently on hand, cash inflows from collaborations, grants, product sales, licenses and royalties and equity and debt financings, to the extent necessary. Some of our research and development collaborations are subject to the risk that we may not meet milestones. Future equity and debt financings, if needed, are subject to the risk that we may not be able to secure financing in a timely manner or on reasonable terms, if at all. Our planned working capital and capital expenditure needs for 2020 are dependent on significant inflows of cash from renewable product sales, new collaborations, and licenses and royalties from existing collaboration partners.

For details, see the following Notes in Part II, Item 8 of this Annual Report on Form 10-K:

•Note 4, "Debt"

•Note 5, "Mezzanine Equity"

•Note 6, "Stockholders' Deficit"

Cash Flows during the Years Ended December 31, 2019 and 2018

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are for personnel costs and costs related to the production and sales of our products, offset by cash received from sales to customers.

For the year ended December 31, 2019, net cash used in operating activities was $156.9 million, which was primarily comprised of our $242.8 million net loss and an increase of $23.8 million in working capital, partly offset by $109.6 million of

46

non-cash charges. Non-cash charges were primarily comprised of a $44.2 million loss upon extinguishment of debt, a $19.4 million loss from change in fair value of debt, $12.6 million of amortization of right-of-use assets under operating leases, $12.6 million of stock-based compensation expense and $11.7 million of debt discount accretion. The increase in working capital was primarily comprised of an $18.0 million increase in inventories, a $17.1 million decrease in lease liabilities, a $13.2 million increase in deferred cost of products sold, an $8.1 million increase in prepaid expenses and other assets, and a $6.9 million decrease in contract liabilities, mostly offset by a $42.7 million combined increase in accounts payable and accrued and other liabilities.

For the year ended December 31, 2018, net cash used in operating activities was $109.4 million, which was comprised of our $230.2 million net loss, partly offset by $96.3 million of non-cash charges and a $24.6 million decrease in working capital. Non-cash charges consisted primarily of a $30.9 million loss from change in fair value of derivative instruments, $16.6 million of debt discount accretion, $9.2 million of stock-based compensation, $6.8 million of warrants fair value recorded as legal expense, and $4.9 million of depreciation and amortization. The decrease in working capital was primarily comprised of an $11.6 million increase in accounts payable, an $8.1 million decrease in unbilled receivables and a $7.4 million decrease in accounts receivable.

Cash Flows from Investing Activities

For the year ended December 31, 2019, net cash used in investing activities was $13.1 million and was comprised of property, plant and equipment purchases.

For the year ended December 31, 2018, net cash provided by investing activities was $12.5 million and was comprised of property, plant and equipment purchases.

Cash Flows from Financing Activities

For the year ended December 31, 2019, net cash provided by financing activities was $124.9 million, primarily comprised of $189.2 million of net proceeds from debt issued and $53.7 million from the exercises of warrants and sales of common stock, partly offset by $112.4 million of debt principal payments.

For the year ended December 31, 2018, net cash provided by financing activities was $108.0 million, primarily comprised of $57.8 million of proceeds from the exercise of warrants to purchase common stock and $94.4 million from debt issued, partly offset by $41.7 million of debt principal payments.

Off-Balance Sheet Arrangements

None.

Contractual Obligations

The following is a summary of our contractual obligations as of December 31, 2019:

Payable by Year Ended December 31, (In thousands)	Total		2020		2021		2022		2023		2024		Thereafter
Principal payments on debt	$	297,462	$	74,551	$	68,572	$	115,538	$	36,840	$	307	$	1,654
Interest payments on debt	82,095		39,324		28,513		13,457		494		91		216
Financing and operating leases	35,668		12,288		12,106		7,719		3,363		192		—
Manufacturing capacity reservation fee	6,893		6,893		—		—		—		—		—
Partnership payment obligation	11,112		5,556		3,175		2,381		—		—		—
Contract termination fee	3,670		3,670		—		—		—		—		—
Total	$	436,900	$	142,282	$	112,366	$	139,095	$	40,697	$	590	$	1,870

ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Not applicable for smaller reporting companies.

47

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

AMYRIS, INC.

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

	Page
Report of Independent Registered Public Accounting Firm	49
Consolidated Balance Sheets	50
Consolidated Statements of Operations	51
Consolidated Statements of Comprehensive Loss	52
Consolidated Statements of Stockholders' Deficit and Mezzanine Equity	53
Consolidated Statements of Cash Flows	54
Notes to Consolidated Financial Statements	56

48

Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of Amyris, Inc.

Opinion on the Consolidated Financial Statements

We have audited the accompanying consolidated balance sheets of Amyris, Inc. and subsidiaries (the Company) as of December 31, 2019 and 2018, the related consolidated statements of operations, comprehensive loss, stockholders’ deficit and mezzanine equity, and cash flows for each of the two years in the period ended December 31, 2019, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2019 and 2018, and the results of their operations and their cash flows for each of the two years in the period ended December 31, 2019, in conformity with accounting principles generally accepted in the United States of America.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (“PCAOB”), the Company's internal control over financial reporting as of December 31, 2019, based on criteria established in Internal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”) and our report dated March 13, 2020 expressed an adverse opinion thereon.

Going Concern

The accompanying consolidated financial statements have been prepared assuming that the Company will continue as a going concern. As discussed in Note 1 to the consolidated financial statements, the Company has suffered recurring losses from operations, has an accumulated deficit of $1.8 billion and current debt service requirements that raise substantial doubt about its ability to continue as a going concern. Management’s plans in regard to these matters are also described in Note 1. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.

Changes in Accounting Principles

As discussed in Note 1to the consolidated financial statements, the Company has changed its accounting method of accounting for leases on January 1, 2019, due to the adoption of Financial Accounting Standard Board’s Accounting Standards Codification 842, Leases. . The Company also amended the classification of certain equity-linked financial instruments with down round features and the respective disclosure requirements in fiscal year 2019 due to adoption of Accounting Standards Update No. 2017-11.

Basis for Opinion

These consolidated financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on these consolidated financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud.

Our audits included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. We believe that our audits provides a reasonable basis for our opinion.

/s/ Macias Gini & O'Connell LLP

We have served as the Company's auditor since 2019.

San Francisco, California

March 13, 2020

49

AMYRIS, INC.

CONSOLIDATED BALANCE SHEETS

December 31, (In thousands, except shares and per share amounts)	2019		2018
Assets
Current assets:
Cash and cash equivalents	$	270	$	45,353
Restricted cash	469		741
Accounts receivable, net of allowance of $45 and $642, respectively	16,322		16,003
Accounts receivable - related party, net of allowance of $0 and $0, respectively	3,868		1,349
Accounts receivable, unbilled - related party	—		8,021
Contract assets	8,485		—
Inventories	27,770		9,693
Deferred cost of products sold - related party	3,677		489
Prepaid expenses and other current assets	12,750		10,566
Total current assets	73,611		92,215
Property, plant and equipment, net	28,930		19,756
Contract assets, noncurrent - related party	1,203		1,203
Deferred cost of products sold, noncurrent - related party	12,815		2,828
Restricted cash, noncurrent	960		960
Recoverable taxes from Brazilian government entities	7,676		3,005
Right-of-use assets under financing leases, net (Note 2)	12,863		—
Right-of-use assets under operating leases, net (Note 2)	13,203		—
Other assets	9,705		7,958
Total assets	$	160,966	$	127,925
Liabilities, Mezzanine Equity and Stockholders' Deficit
Current liabilities:
Accounts payable	$	51,234	$	26,844
Accrued and other current liabilities	36,655		28,979
Financing lease liabilities (Note 2)	3,465		—
Operating lease liabilities (Note 2)	4,625		—
Contract liabilities	1,353		8,236
Debt, current portion (includes instrument measured at fair value of $24,392 and $57,918, respectively)	45,313		124,010
Related party debt, current portion	18,492		23,667
Total current liabilities	161,137		211,736
Long-term debt, net of current portion (includes instrument measured at fair value of $26,232 and $0, respectively)	48,452		43,331
Related party debt, net of current portion	149,515		18,689
Financing lease liabilities, net of current portion (Note 2)	4,166		—
Operating lease liabilities, net of current portion (Note 2)	15,037		—
Derivative liabilities	9,803		42,796
Other noncurrent liabilities	23,024		23,192
Total liabilities	411,134		339,744
Commitments and contingencies (Note 8)
Mezzanine equity:
Contingently redeemable common stock (Note 5)	5,000		5,000
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of December 31, 2019 and 2018, and 8,280 and 14,656 shares issued and outstanding as of December 31, 2019 and 2018, respectively	—		—
Common stock - $0.0001 par value, 250,000,000 shares authorized as of December 31, 2019 and 2018, respectively; 117,742,677 and 76,564,829 shares issued and outstanding as of December 31, 2019 and 2018, respectively	12		8
Additional paid-in capital	1,543,668		1,346,996
Accumulated other comprehensive loss	(43,804)		(43,343)
Accumulated deficit	(1,755,653)		(1,521,417)
Total Amyris, Inc. stockholders’ deficit	(255,777)		(217,756)
Noncontrolling interest	609		937
Total stockholders' deficit	(255,168)		(216,819)
Total liabilities, mezzanine equity and stockholders' deficit	$	160,966	$	127,925

See accompanying notes to consolidated financial statements.

50

AMYRIS, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

Years Ended December 31, (In thousands, except shares and per share amounts)	2019		2018
Revenue
Renewable products (includes related party revenue of $56 and $360, respectively)	$	59,872	$	33,598
Licenses and royalties, net (includes related party revenue of $49,051 and $5,958, respectively)	54,043		7,658
Grants and collaborations (includes related party revenue of $4,120 and $4,735 respectively)	38,642		22,348
Total revenue (includes related party revenue of $53,227 and $11,053, respectively)	152,557		63,604
Cost and operating expenses
Cost of products sold	76,185		36,698
Research and development	71,460		68,722
Sales, general and administrative	126,586		90,902
Impairment of other assets	216		3,865
Total cost and operating expenses	274,447		200,187
Loss from operations	(121,890)		(136,583)
Other income (expense)
Loss on divestiture	—		(1,778)
Interest expense	(58,665)		(42,703)
Gain (loss) from change in fair value of derivative instruments	2,777		(30,880)
(Loss) gain from change in fair value of debt	(19,369)		2,082
Loss upon extinguishment of debt	(44,208)		(17,424)
Other expense, net	(783)		(2,949)
Total other expense, net	(120,248)		(93,652)
Loss before income taxes	(242,138)		(230,235)
Provision for income taxes	(629)		—
Net loss attributable to Amyris, Inc.	(242,767)		(230,235)
Less deemed dividend to preferred shareholder on issuance and modification of common stock warrants	(34,964)		—
Less deemed dividend related to proceeds discount upon conversion of Series D preferred stock	—		(6,852)
Add: losses allocated to participating securities	7,380		13,991
Net loss attributable to Amyris, Inc. common stockholders	$	(270,351)	$	(223,096)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	101,370,632		60,405,910
Basic loss per share	$	(2.67)	$	(3.69)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted	101,296,575		60,405,910
Diluted loss per share	$	(2.72)	$	(3.69)

See accompanying notes to consolidated financial statements.

51

AMYRIS, INC.

CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

Years Ended December 31, (In thousands)	2019		2018
Comprehensive loss:
Net loss attributable to Amyris, Inc.	$	(242,767)	$	(230,235)
Foreign currency translation adjustment	(461)		(1,187)
Comprehensive loss attributable to Amyris, Inc.	$	(243,228)	$	(231,422)

See accompanying notes to consolidated financial statements.

52

AMYRIS, INC.

CONSOLIDATED STATEMENTS OF STOCKHOLDERS' DEFICIT AND MEZZANINE EQUITY

	Preferred Stock			Common Stock
(In thousands, except number of shares)	Shares	Amount		Shares	Amount		Additional Paid-in Capital		Accumulated Other Comprehensive Loss		Accumulated Deficit		Noncontrolling Interest		Total Stockholders' Deficit		Mezzanine Equity - Common Stock
December 31, 2017	22,171	$	—	45,637,433	$	5	$	1,114,546	$	(42,156)	$	(1,290,420)	$	937	$	(217,088)	$	5,000
Cumulative effect of change in accounting principle for ASC 606 (see "Significant Accounting Policies" in Note 1)	—	—		—	—		—		—		(762)		—		(762)		—
Issuance of common stock upon exercise of warrants	—	—		20,891,038	2		62,152		—		—		—		62,154		—
Settlement of derivatives liability upon exercise of warrants	—	—		—	—		108,670		—		—		—		108,670
Issuance of common stock in private placement, net of issuance costs of $0	—	—		205,168	—		1,415		—		—		—		1,415		—
Issuance of common stock in private placement - related party, net of issuance costs of $0	—	—		1,643,991	—		6,050		—		—		—		6,050		—
Issuance of common stock upon conversion of preferred stock	(7,515)	—		1,548,480	—		—		—		—		—		—		—
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock	—	—		—	—		6,852		—		—		—		6,852		—
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock	—	—		—	—		(6,852)		—		—		—		(6,852)		—
Issuance of common stock upon conversion of convertible notes	—	—		5,674,926	1		42,368		—		—		—		42,369		—
Issuance of common stock for settlement of debt interest payments	—	—		238,898	—		1,800		—		—		—		1,800		—
Issuance of common stock upon exercise of stock options	—	—		70,807	—		288		—		—		—		288		—
Issuance of common stock upon ESPP purchase	—	—		246,230	—		777		—		—		—		777		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		407,858	—		(260)		—		—		—		(260)		—
Stock-based compensation	—	—		—	—		9,190		—		—		—		9,190		—
Foreign currency translation adjustment	—	—		—	—		—		(1,187)		—		—		(1,187)		—
Net loss attributable to Amyris, Inc.	—	—		—	—		—		—		(230,235)		—		(230,235)		—
December 31, 2018	14,656	—		76,564,829	$	8	$	1,346,996	$	(43,343)	$	(1,521,417)	$	937	$	(216,819)	$	5,000
Cumulative effect of change in accounting principle for ASU 2017-11 (see "Significant Accounting Policies" in Note 1)	—	—		—	—		32,512		—		8,531		—		41,043		—
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	—	—		14,107,637	2		62,859		—		—		—		62,861		—
Issuance of common stock in private placement, net of issuance costs - related party	—	—		10,478,338	1		39,499		—		—		—		39,500		—
Issuance and modification of common stock warrants	—	—		—	—		34,964		—		—		—		34,964		—
Deemed dividend to preferred shareholder on issuance and modification of common stock warrants	—	—		—	—		(34,964)		—		—		—		(34,964)		—
Issuance of common stock in private placement	—	—		3,610,944	—		14,221		—		—		—		14,221		—
Issuance of warrants in connection with related party debt issuance	—	—		—	—		20,121		—		—		—		20,121		—
Issuance of warrants in connection with related party debt modification	—	—		—	—		4,932		—		—		—		4,932		—
Issuance of warrants in connection with debt accounted for at fair value	—	—		—	—		5,358		—		—		—		5,358		—
Stock-based compensation	—	—		—	—		12,554		—		—		—		12,554		—
Fair value of pre-delivery shares issued to lenders	—	—		7,500,000	1		4,214		—		—		—		4,215		—
Issuance of common stock upon ESPP purchase	—	—		318,490	—		1,078		—		—		—		1,078		—
Fair value of bifurcated embedded conversion feature in connection with debt modification	—	—		—	—		398		—		—		—		398		—
Issuance of common stock upon exercise of stock options	—	—		3,612	—		27		—		—		—		27		—
Issuance of common stock upon exercise of warrants	—	—		2,515,174	—		1		—		—		—		1		—
Conversion of Series B preferred shares into common shares	(6,376)	—		1,012,071	—		—		—		—		—		—		—
Distribution to non-controlling interests	—	—		—	—		—		—		—		(328)		(328)		—
Foreign currency translation adjustment	—	—		—	—		—		(461)		—		—		(461)		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		1,631,582	—		(1,102)		—		—		—		(1,102)		—
Net loss attributable to Amyris, Inc.	—	—		—	—		—		—		(242,767)		—		(242,767)		—
Balance as of December 31, 2019	8,280	—		117,742,677	$	12	$	1,543,668	$	(43,804)	$	(1,755,653)	$	609	$	(255,168)	$	5,000

See accompanying notes to consolidated financial statements.

53

AMYRIS, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

Years Ended December 31, (In thousands)	2019		2018
Operating activities
Net loss attributable to Amyris, Inc.	$	(242,767)	$	(230,235)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss upon conversion or extinguishment of debt	44,208		17,424
Loss (gain) from change in fair value of debt	19,369		(2,082)
Amortization of right-of-use assets under operating leases	12,597		—
Stock-based compensation	12,554		9,190
Accretion of debt discount	11,665		16,602
Expense for warrants issued for covenant waivers	5,358		—
Depreciation and amortization	4,581		4,921
Impairment of property, plant and equipment	1,354		—
Loss in equity-method investee	297		—
Loss on disposal of property, plant and equipment	212		941
(Gain) loss from change in fair value of derivative instruments	(2,777)		30,880
Gain on foreign currency exchange rates	(22)		(2,223)
Modification of warrants recorded as legal expense	—		6,764
Issuance costs on warrant exercises for cash	—		4,389
Loss on impairment of other assets	216		3,865
Debt issuance costs expensed due to fair value option	—		3,810
Loss on divestiture	—		1,778
Changes in assets and liabilities:
Accounts receivable	(2,818)		7,448
Contract assets	(8,485)		—
Contract assets - related party	8,021		8,056
Inventories	(17,989)		(4,416)
Deferred cost of products sold - related party	(13,175)		(3,317)
Prepaid expenses and other assets	(8,064)		(6,383)
Accounts payable	23,748		11,603
Accrued and other liabilities	18,981		8,461
Lease liabilities	(17,125)		—
Contract liabilities	(6,872)		3,158
Net cash used in operating activities	(156,933)		(109,366)
Investing activities
Purchases of property, plant and equipment	(13,080)		(12,472)
Net cash used in investing activities	(13,080)		(12,472)
Financing activities
Proceeds from issuance of debt, net of issuance costs	189,175		94,371
Proceeds from issuance of common stock in private placements, net of issuance costs - related party	39,500		—
Proceeds from issuance of common stock in private placements, net of issuance costs	14,221		1,415
Proceeds from ESPP purchases	1,078		777
Proceeds from exercises of common stock options	27		288
Proceeds from exercise of warrants, net of issuance costs	1		57,767
Principal payments on debt	(112,393)		(41,668)
Principal payments on financing leases	(5,268)		(981)
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(1,103)		(260)
Capital distribution to noncontrolling interest	(328)		—
Debt issuance costs incurred in connection with debt instrument accounted at fair value	—		(3,752)
Net cash provided by financing activities	124,910		107,957
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(252)		(77)
Net decrease in cash, cash equivalents and restricted cash	(45,355)		(13,958)
Cash, cash equivalents and restricted cash at beginning of year	47,054		61,012
Cash, cash equivalents and restricted cash at end of year	$	1,699	$	47,054
Reconciliation of cash, cash equivalents and restricted cash to the consolidated balance sheets
Cash and cash equivalents	$	270	$	45,353
Restricted cash, current	469		741
Restricted cash, noncurrent	960		960
Total cash, cash equivalents and restricted cash	$	1,699	$	47,054

54

Amyris, Inc.

CONSOLIDATED STATEMENTS OF CASH FLOWS, Continued

Years Ended December 31, (In thousands)	2019		2018
Supplemental disclosures of cash flow information:
Cash paid for interest	$	20,780	$	18,524
Supplemental disclosures of non-cash investing and financing activities:
Cumulative effect of change in accounting principle for ASU 2017-11 (Note 2)	$	41,043	$	—
Lease liabilities recorded upon adoption of ASC 842 (Note 2)	$	33,552	$	—
Right-of-use assets under operating leases recorded upon adoption of ASC 842 (Note 2)	$	29,713	$	—
Cumulative effect adjustment of ASC 606	$	—	$	762
Accrued interest added to debt principal	$	7,292	$	3,664
Acquisition of additional interest in equity-method investee in exchange for payment obligation	$	5,031	$	—
Acquisition of property, plant and equipment under accounts payable, accrued liabilities and notes payable	$	2,576	$	—
Acquisition of right-of-use assets under operating leases	$	3,551	$	—
Debt fair value adjustment in connection with debt issuance	$	11,575	$	—
Derecognition of derivative liabilities upon exercise of warrants	$	—	$	108,670
Fair value of embedded features in connection with debt issuances and modifications	$	237	$	—
Fair value of embedded features in connection with debt issuances and modifications - related party	$	1,954	$	—
Fair value of pre-delivery shares in connection with debt issuance	$	4,215	$	—
Fair value of warrants recorded as debt discount in connection with debt issuances	$	8,965	$	—
Fair value of warrants recorded as debt discount in connection with debt issuances - related party	$	16,155	$	—
Fair value of warrants recorded as debt discount in connection with debt modification	$	398	$	—
Fair value of warrants recorded as debt discount in connection with debt modification - related party	$	2,050	$	—
Financing of equipment under financing leases	$	7,436	$	271
Financing of insurance premium under note payable	$	253	$	495
Issuance of common stock - related party	$	—	$	6,050
Issuance of common stock for settlement of debt principal and interest payments	$	—	$	1,800
Issuance of common stock upon conversion of convertible notes	$	62,860	$	24,970

See accompanying notes to consolidated financial statements.

55

Amyris, Inc.

Notes to Consolidated Financial Statements

1. Basis of Presentation and Summary of Significant Accounting Policies

Business Description

Amyris, Inc. and subsidiaries (collectively, Amyris or the Company) is a leading industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets. The Company's proven technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. The Company's biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. The Company has successfully used its technology to develop and produce many distinct molecules at commercial volumes.

Going Concern

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations for at least the next 12 months following the issuance of the financial statements. As of December 31, 2019, the Company had negative working capital of $86.7 million and an accumulated deficit of $1.8 billion.

As of December 31, 2019, the Company's debt (including related party debt), net of deferred discount and issuance costs of $20.3 million and a fair value adjustment of $15.4 million, totaled $261.8 million, of which $63.8 million is classified as current. However, $75.0 million of debt was converted into equity in January 2020; see Note 15, “Subsequent Events” for more information. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness, material adverse effect and cross default provisions. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding indebtedness. At December 31, 2019, the Company failed to meet certain covenants under several credit arrangements (which are discussed in Note 4, “Debt”), including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. In March 2020, these lenders provided permanent waivers to the Company for breaches of all past covenant violations and cross-default payment failures (discussed below), through March 13, 2020 under the respective credit agreements, and significantly reduced the minimum liquidity requirement and substantially increased the base of eligible assets to calculate the asset coverage requirement..

On January 31, 2020, the Company failed to pay Total Raffinage Chimie (Total), Nikko Chemicals Co. Ltd (Nikko) and certain affiliates of the Schottenfeld Group LLC (Schottenfeld) an aggregate of $17.6 million of maturing promissory notes, and previously on December 15, 2019 failed to pay Ginkgo $5.2 million of past due interest, past due partnership payments and the first installment of a waiver fee. These failures resulted in an event of default under the respective agreements and also triggered cross-defaults under other debt instruments (discussed above) that permitted each of the affected cross-default debt holders of such indebtedness to accelerate the amounts owing under such instruments. The Company subsequently received waivers from each of the affected cross-default debt holders to waive the right to accelerate due to the event specific cross-defaults. As a result, the indebtedness with respect to which the Company has obtained such waivers continues to be classified as long-term on the Company’s balance sheet. The indebtedness reflected by the Total and certain Ginkgo, Nikko and Schottenfeld amounts continues to be classified as a current liability on the Company’s balance sheet as the due date for these amounts was within one year of December 31, 2019.

Subsequent to December 31, 2019, the Company (i) obtained a waiver and forbearance agreement from Schottenfeld, (ii) amended the credit arrangements with Total and Nikko Notes to extend the maturity date of the original promissory notes, and (iii) entered into a waiver and amendment to the partnership agreement with Ginkgo to waive all past payment defaults under the Ginkgo Note and Ginkgo Partnership Agreement, and to extend the payment due date and modify the periodic partnership payment timing and amount. See Note 15, “Subsequent Events” for further information.

Although the Company obtained extensions to make these payments, it currently does not have sufficient funds to repay the amounts due under the Total, Nikko, Schottenfeld and Ginkgo credit arrangements, and while the Company intends to seek equity or debt financing, the proceeds of which would be used to repay Total, Nikko, Schottenfeld and Ginkgo, there can be no assurance that the Company will be able to obtain such financing on our expected timeline, or on acceptable terms, if at all.

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Also, while the Company has been able to cure these defaults to date to avoid additional cross-acceleration, it may not be able to cure such a default promptly in the future.

Further, cash and cash equivalents of $0.3 million as of December 31, 2019 are not sufficient to fund expected future negative cash flows from operations and cash debt service obligations through March 2021. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that these financial statements are issued. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. In addition to repaying the Total, Nikko, Schottenfeld and Ginkgo amounts previously discussed, the Company's ability to continue as a going concern will depend, in large part, on its ability to raise additional proceeds through financings, achieve positive cash flows from operations during the 12 months from the date of this filing, and refinance or extend other existing debt maturities occurring later in 2020, all of which are uncertain and outside the control of the Company. Further, the Company's operating plan for 2020 contemplates a significant reduction in its net operating cash outflows as compared to the year ended December 31, 2019, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) reduced spending in general and administrative areas, and (iv) an increase in cash inflows from collaborations and grants. If the Company is unable to complete these actions, it expects to be unable to meet its operating cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and the Company may be forced to obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all, and/or liquidate its assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these financial statements. The Company has in the past, including in July 2019, had certain of its debt instruments accelerated for failure to make a payment when due. While we have been able to obtain permanent waivers or cure these defaults to date to avoid additional cross-acceleration, we may not be able to obtain waivers or cure such a default promptly in the future.

Basis of Consolidation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States (U.S. GAAP). The consolidated financial statements include the accounts of Amyris, Inc. and its wholly-owned and partially-owned subsidiaries in which the Company has a controlling interest after elimination of all significant intercompany accounts and transactions.

Investments and joint venture arrangements are assessed to determine whether the terms provide economic or other control over the entity requiring consolidation of the entity. Entities controlled by means other than a majority voting interest are referred to as variable-interest entities (VIEs) and are consolidated when Amyris has both the power to direct the activities of the VIE that most significantly impact its economic performance and the obligation to absorb losses or the right to receive benefits that could potentially be significant to the entity. For any investment or joint venture in which (i) the Company does not have a majority ownership interest, (ii) the Company possesses the ability to exert significant influence and (iii) the entity is not a VIE for which the Company is considered the primary beneficiary, the Company accounts for the investment or joint venture using the equity method. Equity investments in which the Company does not exert significant influence and that do not have readily determinable fair values are measured at cost, adjusted for changes from observable market transactions, less impairment (“adjusted cost basis”). The Company evaluates its investments for impairment by considering a variety of factors, including the earnings capacity of the related investments. Fair value measurements for the Company’s equity investments are classified within Level 3 of the fair value hierarchy based on the nature of the fair value inputs. Realized and unrealized gains or losses are recognized in other income or expense.

Raizen Joint Venture Agreement

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into a joint venture agreement relating to the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products. In connection with the formation of the joint venture, among other things, (i) the joint venture will construct a manufacturing facility on land owned by Raizen and leased to the joint venture (the Sweetener Plant), (ii) the Company will grant to the joint venture an exclusive, royalty-free, worldwide license to certain technology owned by the Company relevant to the joint venture’s business, and (iii) the Company and Raizen will enter into a shareholders agreement setting forth the rights and obligations of the parties with respect to, and the management of, the joint venture. The formation of the joint venture is subject to certain conditions, including certain regulatory approvals and the achievement of certain technological and economic milestones relating to the Company’s existing production of its alternative sweetener product. If such conditions are not satisfied by May 2020, the joint venture will automatically terminate. However, the termination date can be extended by mutual agreement of the parties. In addition, notwithstanding the satisfaction of the closing conditions, Raizen may elect not to

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consummate the formation and operation of the joint venture, in which event, the Company will retain the right to construct and operate the Sweetener Plant.

Upon the closing of the joint venture, each party will make an initial capital contribution to the joint venture of 2.5 million Brazilian Real (R$2.5 million) and the joint venture will be owned 50% by the Company and 50% by Raizen. Within 60 days of the formation, the parties will make an aggregate cash contribution to the joint venture of USD $9.0 million to purchase certain fixed assets currently owned by the Company and located at the site of the Company’s former joint venture with Sao Martinho S.A. in Pradopolis, Brazil for USD $3.0 million, as well as to pay for costs related to the removal and transportation of such assets to the site of the Sweetener Plant. In addition, within six months of the formation, the Company will contribute to the joint venture its existing supply agreements related to its alternative sweetener product, subject to certain exceptions, in exchange for shares of dividend-bearing preferred stock in the joint venture, which will be entitled, for a period of 10 years commencing from the initial date of operation of the Sweetener Plant, to certain priority fixed cumulative dividends including, in the event that certain technological and economic milestones are met in any fiscal quarter, a percentage of the operating cash flow of the joint venture in such quarter.

The Company is evaluating the accounting treatment for its future interest in the joint venture under ASC 810, Consolidations and ASC 323, Equity Method and Joint Ventures and will conclude once the corporate governance and economic participation structure is finalized and the formation of the joint venture is consummated.

Use of Estimates and Judgements

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates, and such differences may be material to the consolidated financial statements. Significant estimates and judgements used in these consolidated financial statements are discussed in the relevant accounting policies below or specifically discussed in the Notes to Consolidated Financial Statements where such transactions are disclosed.

Significant Accounting Policies

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with an original or remaining maturity of three months or less at the date of purchase to be cash equivalents. Cash and cash equivalents are maintained with various financial institutions.

Inventories

Inventories, which consist of farnesene-derived products, flavors and fragrances ingredients and clean beauty products, are stated at the lower of actual cost or net realizable value and are categorized as finished goods, work in process or raw material inventories. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds their estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or net realizable value approach that is used to value inventory. Cost for farnesene-derived products and flavors and fragrances ingredients are computed on a weighted-average basis. Cost for clean beauty products are computed on a standard cost basis.

Property, Plant and Equipment, Net

Property, plant and equipment are recorded at cost. Depreciation and amortization are computed straight-line based on the estimated useful lives of the related assets, ranging from 3 to 15 years for machinery, equipment and fixtures, and 15 years for buildings. Leasehold improvements are amortized over their estimated useful lives or the period of the related lease, whichever is shorter.

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The Company expenses costs for maintenance and repairs and capitalizes major replacements, renewals and betterments. For assets retired or otherwise disposed, both cost and accumulated depreciation are eliminated from the asset and accumulated depreciation accounts, and gains or losses related to the disposal are recorded in the statement of operations for the period.

Impairment

Long-lived assets that are held and used by the Company are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. Determination of recoverability of long-lived assets is based on an estimate of the undiscounted future cash flows resulting from the use of the asset and its eventual disposition. Measurement of an impairment loss for long-lived assets that management expects to hold and use is based on the difference between the fair value of the asset and its carrying value. Long-lived assets to be disposed of are reported at the lower of carrying amount or fair value less costs to sell.

Recoverable Taxes from Brazilian Government Entities

Recoverable taxes from Brazilian government entities represent value-added taxes paid on purchases in Brazil, which are reclaimable from the Brazilian tax authorities, net of reserves for amounts estimated not to be recoverable.

Fair Value Measurements

The carrying amounts of certain financial instruments, such as cash equivalents, short-term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities.

The Company measures the following financial assets and liabilities at fair value:

•Freestanding and bifurcated derivatives in connection with certain debt and equity financings; and

•Senior Convertible Notes Due 2022 and 6% Convertible Notes Due 2021 (see Note 3, "Fair Value Measurement" and Note 4, "Debt", for which the Company elected fair value accounting.

Fair value is based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation techniques are applied. These valuation techniques involve some level of management estimation and judgement, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

Changes to the inputs used in these valuation models can have a significant impact on the estimated fair value of the Senior Convertible Notes Due 2022, 6% Convertible Notes Due 2021 and the Company's embedded and freestanding derivatives. For example, a decrease (increase) in the estimated credit spread for the Company results in an increase (decrease) in estimated fair value. Conversely, a decrease (increase) in the stock price results in a decrease (increase) in estimated fair value.

The changes during 2019 and 2018 in the fair values of the bifurcated compound embedded derivatives are primarily related to the change in price of the Company's common stock and are reflected in the consolidated statements of operations as “Gain (loss) from change in fair value of derivative instruments”.

For debt instruments for which the Company has not elected fair value accounting, fair value is based on the present value of expected future cash flows and assumptions about the then-current market interest rates as of the reporting period and the creditworthiness of the Company. Most of the Company's debt is carried on the consolidated balance sheet on a historical cost basis net of unamortized discounts and premiums, because the Company has not elected the fair value option of accounting. However, for the Senior Convertible Notes Due 2022 and the 6% Notes Due 2021, the Company elected fair value accounting, so that balances reported for those debt instruments represent fair value as of the applicable balance sheet date; see Note 3, "Fair Value Measurement", for additional information. Changes in fair value of the Senior Convertible Notes Due 2022 and the 6% Convertible Notes Due 2021 are reflected in the consolidated statements of operations as “Gain (loss) from change in fair value of debt”.

For all debt instruments, including any for which the Company has elected fair value accounting, the Company classifies interest that has been accrued during each period as Interest expense on the consolidated statements of operations.

Derivatives

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Embedded derivatives that are required to be bifurcated from the underlying debt instrument (i.e., host) are accounted for and valued as separate financial instruments. The Company has evaluated the terms and features of its convertible notes payable and convertible preferred stock and identified compound embedded derivatives requiring bifurcation and accounting at fair value, using the valuation techniques mentioned in the Fair Value Measurements section of this Note, because the economic and contractual characteristics of the embedded derivatives met the criteria for bifurcation and separate accounting due to the instruments containing conversion options, certain “make-whole interest” provisions, down-round conversion price adjustment provisions and/or conversion rate adjustments, and mandatory redemption features that are not clearly and closely related to the debt host instrument.

Prior to the adoption of ASU 2017-11, certain previously issued warrants with a fair value of $41 million issued in conjunction with the convertible debt and equity financings were freestanding financial instruments and classified as derivative liabilities as of December 31, 2019. Upon adoption of ASU 2017-11 on January 1, 2019, these freestanding instruments met the criteria to be accounted for within equity and the $41 million derivative liability balance was reclassified to stockholders’ equity.

During the third and fourth quarter of 2019, the Company issued warrants in connection with a debt financing that met the criteria of a freestanding instrument but did not qualify for equity accounting treatment. As a result, these warrants are accounting for at fair value until settled and are classified as derivative liabilities at December 31, 2019. See Note 6 “Stockholders’ Deficit” for further information.

Noncontrolling Interest

Noncontrolling interests represent the portion of net income (loss), net assets and comprehensive income (loss) that is not allocable to the Company, in situations where the Company consolidates its equity investment in a joint venture for which there are other owners. The amount of noncontrolling interest is comprised of the amount of such interests at the date of the Company's original acquisition of an equity interest in a joint venture, plus the other shareholders' share of changes in equity since the date the Company made an investment in the joint venture.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents, short-term investments and accounts receivable. The Company places its cash equivalents and investments (primarily certificates of deposits) with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:

As of December 31,	2019	2018
Customer A (related party)	19%	**
Customer B	21%	24%
Customer C	**	19%
Customer E	**	11%
Customer F	10%	**

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** Less than 10%

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Customers representing 10% or greater of revenue were as follows:

Years Ended December 31,	Year First Customer	2019	2018
Customer A (related party)	2017	35%	17%
Customer B	2014	10%	18%
Customer C	2014	**	13%
Customer D	2014	**	13%
Customer G	2019	12%	*

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* Not a customer

** Less than 10%

Revenue Recognition

The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer, and transaction price is allocated utilizing stand-alone selling price. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does not incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators, among others, when determining if it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does not meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in Note 9, "Revenue Recognition".

The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to receive payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. For most of the Company's renewable products customers, supply agreements between the Company and each customer indicate when transfer of title occurs.

In some cases, the Company may make a payment to a customer. When that occurs, the Company evaluates whether the payment is for a distinct good or service receivable from the customer. If the fair value of the goods or services receivable is greater than or equal to the amount paid to the customer, then the entire payment is treated as a purchase. If, on the other hand, the fair value of goods or services is less than the amount paid, then the difference is treated as a reduction in transaction price of the Company's sales to the customer or a reduction of cumulative to-date revenue recognized from the customer in the period the payment is made or goods or services are received from the customer.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts may contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis.

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The following is a description of the principal goods and services from which the Company generates revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does not have the ability to direct the product to a different customer. It is at this point that the Company has the right to receive payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do not include rights of return, except for direct-to-consumer products, for which the Company estimates sales returns subsequent to sale and reduces revenue accordingly. For renewable products other than direct-to-consumer, returns are accepted only if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception which requires the Company to estimate the revenue that is recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts, using the best evidence available at the time, derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends. Estimates are adjusted to actual or as new information becomes available.

When the Company’s intellectual property license is not the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts.

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services: The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to

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scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaboration partners with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include one or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement, and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Generally, revenue is recognized using an input-based measure of progress towards the satisfaction of the performance obligations which can be labor hours expended or time-based in proportion to the estimated total project effort or total projected time to complete. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Certain performance obligations are associated with milestones agreed between the Company and its customer. Revenue generated from the performance of services in accordance with these milestones is recognized upon confirmation from the customer that the milestone has been achieved. In these cases, amounts recognized are constrained to the amount of consideration received upon achievement of the milestone.

The Company generally invoices its collaboration partners on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Contract liabilities arise from amounts received in advance of performing the research and development activities and are recognized as revenue in future periods as the performance obligations are satisfied.

Grants: The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect grant revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

The Company receives certain consideration from AICEP Portugal Global (AICEP), and entity funded by government of Portugal, under the Consortium Internal Regulatory Agreement and an AICEP Investment Contract (the “Agreements”) entered

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into by Amyris (the “Company”) with Universidade Católica Portuguesa (UCP) Porto Campus. The Company considered this arrangement to be a government grant and accounts for the arrangement under International Accounting Standard 20 “Accounting for Government Grants and Disclosure of Government Assistance”. Grant revenue is recognized when there is reasonable assurance that monies will be received and that conditions attached to the grant have been met.

Cost of Products Sold

Cost of products sold includes the production costs of renewable products, which include the cost of raw materials, in-house manufacturing labor and overhead, amounts paid to contract manufacturers, including amortization of tolling fees, and period costs including inventory write-downs resulting from applying lower of cost or net realizable value inventory adjustments. Cost of products sold also includes certain costs related to the scale-up of production. Shipping and handling costs charged to customers are recorded as revenues. Outbound shipping costs incurred are included in cost of products sold. Such charges were not material for any of the periods presented.

The Company recognizes deferred cost of products sold as an asset on the balance sheet when a cost is incurred in connection with a revenue performance obligation that will not be fulfilled until a future period. The Company also recorded a deferred cost of products asset in 2018 and 2019 for the fair value of amounts paid to DSM under a supply agreement for manufacturing capacity to produce its sweetener product at the Brotas facility in Brazil. The deferred cost of products sold asset is expensed to cost of products sold on a units of production basis over the five-year term of the supply agreement. On a quarterly basis, the Company evaluates its future production volumes for its sweetener product and adjusts the unit cost to be expensed over the remaining estimated production volume. The Company also periodically evaluates the asset for recoverability based on changes business strategy and product demand trends over the term of the supply agreement.

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants, including internal research. Research and development costs consist of direct and indirect internal costs related to specific projects, as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Debt Extinguishment

The Company accounts for the income or loss from extinguishment of debt in accordance with ASC 470, Debt, which indicates that for all extinguishments of debt, including instances where the terms of a debt instrument are modified in a manner that significantly changes the underlying cash flows, the difference between the reacquisition consideration and the net carrying amount of the debt being extinguished should be recognized as gain or loss when the debt is extinguished. Losses from debt extinguishment are shown in the consolidated statements of operations under "Other income (expense)" as "Loss upon extinguishment of debt".

Stock-based Compensation

The Company accounts for stock-based employee compensation plans under the fair value recognition and measurement provisions of U.S. GAAP. Those provisions require all stock-based payments to employees, including grants of stock options and restricted stock units (RSUs), to be measured using the grant-date fair value of each award. The Company recognizes stock-based compensation expense net of expected forfeitures over each award's requisite service period, which is generally the vesting term. Expected forfeiture rates are estimated based on the Company's historical experience. Stock-based compensation plans are described more fully in Note 11, "Stock-based Compensation".

Income Taxes

The Company is subject to income taxes in the United States and foreign jurisdictions and uses estimates to determine its provisions for income taxes. The Company uses the asset and liability method of accounting for income taxes, whereby deferred tax asset or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. The Company recognizes a valuation allowance against its net deferred tax assets unless it is more likely than not that such deferred tax assets will be realized. This assessment requires judgement as to the likelihood and amounts of future taxable income by tax jurisdiction.

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The Company applies the provisions of Financial Accounting Standards Board (FASB) guidance on accounting for uncertainty in income taxes. The Company assesses all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position’s sustainability, and the tax benefit to be recognized is measured at the largest amount of benefit that is greater than 50 percent likely of being realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and the Company will determine whether (i) the factors underlying the sustainability assertion have changed and (ii) the amount of the recognized tax benefit is still appropriate. The recognition and measurement of tax benefits requires significant judgement, and such judgements may change as new information becomes available.

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into U.S. dollars at the rates in effect at each balance sheet date, and revenue and expense amounts are translated at average rates during each period, with resulting foreign currency translation adjustments recorded in other comprehensive loss, net of tax, in the consolidated statements of stockholders’ deficit. As of December 31, 2019 and 2018, cumulative translation adjustment, net of tax, were $43.8 million and $43.3 million, respectively.

Where the U.S. dollar is the functional currency, remeasurement adjustments are recorded in other income (expense), net in the accompanying consolidated statements of operations. Net losses resulting from foreign exchange transactions were $0.2 million and $1.6 million for the years ended December 31, 2019 and 2018, respectively and are recorded in other income (expense), net in the consolidated statements of operations.

New Accounting Standards or Updates Recently Adopted

During the year ended December 31, 2019 the Company adopted the following Accounting Standards Updates (ASUs):

Leases In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) (ASU 2016-02). The standard requires the recognition of lease liabilities and right-of-use (ROU) assets on the balance sheet arising from lease transactions at the lease commencement date and the disclosure of key information about leasing arrangements. In July 2018, the FASB issued ASU 2018-11, Leases (Topic 842): Targeted Improvements, which provided entities the option to use the effective date as the date of initial application on transition to the new guidance. The Company elected this transition method, and as a result, the Company did not adjust comparative information for prior periods. The Company elected certain additional practical expedients permitted by the new guidance allowing the Company to carry forward historical accounting related to lease identification and classification for existing leases upon adoption.

The Company adopted this standard on January 1, 2019 using the modified retrospective approach and elected the package of practical expedients permitted under transition guidance, which allowed the Company to carry forward its historical assessments of: (1) whether contracts are or contain leases, (2) lease classification and (3) initial direct costs, where applicable. The Company did not elect the practical expedient allowing the use-of-hindsight which would require the Company to reassess the lease term of its leases based on all facts and circumstances through the effective date and did not elect the practical expedient pertaining to land easements as this is not applicable to the Company’s current contracts. The Company elected the post-transition practical expedient to not separate lease components from non-lease components for all leases of manufacturing equipment. The Company also elected a policy of not recording leases on its condensed consolidated balance sheets when the leases have a term of 12 months or less and the Company is not reasonably certain to elect an option to purchase the leased asset.

The Company's adoption of this standard had the effect of increasing assets and liabilities by $25.7 million, after considering prepaid and other current and noncurrent assets previously recorded on the condensed consolidated balance sheet but did not have a material impact on the condensed consolidated statements of operations or cash flows. The most significant impact relates to (1) the recognition of new ROU assets and lease liabilities on the balance sheet for the Company's operating leases; and (2) providing significant new disclosures about the Company's leasing activities.

Upon adoption, the Company recognized operating lease liabilities of $33.6 million, based on the present value of the remaining minimum rental payments under current leasing standards for existing operating leases. The Company also recognized ROU assets of $29.7 million, which represents the operating lease liability, adjusted for prepaid expenses and deferred rent. The difference between the operating lease ROU assets and lease liabilities reflects the net of advanced rent payments and deferred rent balances that were derecognized at the time of adoption.

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Financial Instruments with "Down Round" Features In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features. The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update became effective in the first quarter of fiscal year 2019, and the Company adopted the standard using a modified retrospective approach. Since the adoption of ASU 2017-11 would have classified the warrants effected as equity at inception, the cumulative-effect adjustment should (i) record the issuance date value of the warrants as if they had been equity classified at the issuance date, (ii) reverse the effects of changes in the fair value of the warrants that had been recorded in the statement of operations of each period, and (iii) eliminate the derivative liabilities from the balance sheet. Upon adoption, the Company (i) recorded an increase of $32.5 million to additional paid-in capital, (ii) recorded a decrease to accumulated deficit of $8.5 million and (iii) decreased the warrant liability by $41.0 million.

Recent Accounting Standards or Updates Not Yet Effective

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement, which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for fair value measurements by removing, modifying or adding certain disclosures. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative arrangement is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. The ASU provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020 retroactively. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments—Credit Losses (Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to measure all expected credit losses for most financial assets held at the reporting date based on an expected loss model which includes historical experience, current conditions, and reasonable and supportable forecasts. Entities will now use forward-looking information to better form their credit loss estimates. ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand significant estimates and judgments used in estimating credit losses, as well as the credit quality and underwriting standards of an entity's portfolio. ASU 2016-13 will become effective for the Company beginning in the first quarter of fiscal year 2020. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments- Credit Losses. This ASU clarifies and addresses certain items related to amendments in ASU 2016-13. This new guidance is effective for the Company beginning on January 1, 2020. This new guidance is not expected to have a material impact on the Company’s consolidated financial statements.

Income Taxes In December 2019, the FASB issued ASU 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes, which simplifies the accounting for income taxes. This guidance will become effective for the Company in the first quarter of fiscal year 2021 on a prospective basis. The Company is currently evaluating the impact of the new guidance on its consolidated financial statements.

In January 2020, the FASB issued ASU 2020-01, Investments-Equity Securities (Topic 321), Investments-Equity Method and Joint Ventures (Topic 323), and Derivatives and Hedging (Topic 815)-Clarifying the Interactions between Topic 321, Topic 323, and Topic 815. The guidance provides clarification of the interaction of rules for equity securities, the equity method of accounting and forward contracts and purchase options on certain types of securities. This new guidance is effective for the

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Company beginning on January 1, 2021. While the Company is currently assessing the impact of the new guidance, it is not expected to have a material impact on the Company’s consolidated financial statements.

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2. Balance Sheet Details

Allowance for Doubtful Accounts

Allowance for doubtful accounts activity and balances were as follows:

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Year
Allowance for doubtful accounts:
Year Ended December 31, 2019	$	642	$	110	$	(707)	$	45
Year Ended December 31, 2018	$	642	$	—	$	—	$	642

Inventories

December 31, (In thousands)	2019		2018
Raw materials	$	3,255	$	3,901
Work in process	7,204		539
Finished goods	17,311		5,253
Total inventories	$	27,770	$	9,693

Deferred cost of products sold — related party

December 31, (In thousands)	2019		2018
Deferred cost of products sold - related party	$	3,677	$	489
Deferred cost of products sold, noncurrent - related party	12,815		2,828
Total	$	16,492	$	3,317

In November 2018, the Company amended the supply agreement with DSM to secure manufacturing capacity at the Brotas facility for sweetener production through 2022. See Note 9, “Revenue Recognition” for information regarding the November 2018 Supply Agreement Amendment. The supply agreement was included as an element of a combined transaction with DSM, which resulted in a fair value allocation of $24.4 million to the manufacturing capacity fees. See Note 3, “Fair Value Measurement” for information related to this fair value allocation. Of the $24.4 million fair value allocated to the manufacturing capacity fee, $3.3 million was recorded as deferred cost of products sold during 2018. Also, the Company paid an additional $14.1 million in manufacturing capacity fees during 2019, which were recorded as additional deferred cost of products sold. The remaining $7.0 million manufacturing capacity fees will be recorded as deferred cost of products sold in the period the additional payments are made to DSM. The manufacturing capacity deferred cost of products sold asset is expensed to cost of products sold on a units of production basis as the Company's sweetener product is sold over the five-year term of the

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supply agreement. During the years ended December 31, 2019 and 2018, the Company expensed $0.9 million and $0, respectively, of the deferred cost of products sold asset.

Prepaid expenses and other current assets

December 31, (In thousands)	2019		2018
Non-inventory production supplies	$	5,376	$	2,391
Prepayments, advances and deposits	4,726		5,644
Recoverable taxes from Brazilian government entities	79		631
Other	2,569		1,900
Total prepaid expenses and other current assets	$	12,750	$	10,566

Property, plant and equipment, net

December 31, (In thousands)	2019		2018
Machinery and equipment	$	48,041	$	43,713
Leasehold improvements	41,478		39,922
Computers and software	9,822		9,987
Furniture and office equipment, vehicles and land	3,510		3,016
Construction in progress	9,752		1,749
Total property, plant and equipment, gross	112,603		98,387
Less: accumulated depreciation and amortization	(83,673)		(78,631)
Total property, plant and equipment, net	$	28,930	$	19,756

Property, plant and equipment, net at December 31, 2018 includes $5.0 million of machinery and equipment under capital lease. Accumulated amortization of assets under capital lease totaled $2.3 million as of December 31, 2018. For the year ended December 31, 2018, amortization expense in connection with capital lease assets was $0.7 million. Beginning January 1, 2019, capital lease assets are classified as right-of-use assets under financing leases, net; see "Leases" below.

Losses on disposal of property, plant and equipment were $0.2 million and $0.9 million for the years ended December 31, 2019 and 2018, respectively. Such losses or gains were included in the lines captioned "Research and development expense" and "Sales, general and administrative expense" in the consolidated statements of operations.

Leases

Prior to the modified prospective adoption of ASU 2016-02 on January 1, 2019, the Company leased certain facilities and certain laboratory equipment under operating and financing leases, respectively. The Company recognized rent expense for operating leases on a straight-line basis over the noncancelable lease term and recorded the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Where leases contained escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applied them as straight-line rent expense over the lease term. The Company had noncancelable operating lease agreements for office, research and development, and manufacturing space that expired at various dates, with the latest expiration in May 2023. Rent expense under operating leases was $5.8 million for the year ended December 31, 2018. See below for the Company’s account treatment of leases upon adoption of new leasing standard.

Operating Leases

The Company has entered into operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 year to 5 years, and often include one or more options to renew. These renewal terms can extend the lease term from 1 to 5 years and are included in the lease term when it is reasonably certain that the Company will exercise the option. The operating leases are classified as Right-of-use assets under operating leases, net (ROU assets) on the Company's December 31, 2019 consolidated balance sheet, and represent the Company’s right to use the underlying asset for the lease term. The Company’s obligation to make operating lease payments is included in

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"Operating lease liabilities" and "Operating lease liabilities, net of current portion" on the Company's December 31, 2019 consolidated balance sheet. Based on the present value of the lease payments for the remaining lease term of the Company's existing leases, the Company recognized ROU assets of $29.7 million and operating lease liabilities of $33.6 million on January 1, 2019. Operating lease ROU assets and liabilities commencing after January 1, 2019 are recognized at commencement date based on the present value of lease payments over the lease term. As of December 31, 2019, total ROU assets and operating lease liabilities were $13.2 million and $19.7 million, respectively. All operating lease expense is recognized on a straight-line basis over the lease term. In the year ended December 31, 2019, the Company recorded $16.4 million of operating lease amortization that was charged to expense, of which $7.0 million was recorded to cost of products sold.

Because the rate implicit in each lease is not readily determinable, the Company uses its incremental borrowing rate to determine the present value of the lease payments. The Company has certain contracts for real estate and marketing which may contain lease and non-lease components which it has elected to treat as a single lease component.

Information related to the Company's right-of-use assets and related lease liabilities were as follows:

	Year Ended December 31, 2019
Cash paid for operating lease liabilities, in thousands	$	17,809
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$	33,264
Weighted-average remaining lease term	3.35
Weighted-average discount rate	18.1		%

⁽¹⁾ Includes $29.7 million for operating leases existing on January 1, 2019 and $3.6 million for operating leases that commenced during the year ended December 31, 2019. Also, the Company renegotiated one of its operating leases during 2019, which resulted in a new financing lease. Approximately $7.7 million of Right-of-use assets under operating leases, net were reclassified to Right-of-use assets under financing leases, net related to this operating lease modification.

Financing Leases

The Company has entered into financing leases primarily for laboratory and computer equipment. Assets purchased under financing leases are included in Right-of-use assets under financing leases, net on the consolidated balance sheets. For financing leases, the associated assets are depreciated or amortized over the shorter of the relevant useful life of each asset or the lease term. At December 31, 2019, accumulated amortization of assets under financing lease was $1.7 million.

Maturities of Financing and Operating Leases

Maturities of lease liabilities as of December 31, 2019 were as follows:

Years Ending December 31 (In thousands)	Financing Leases		Operating Leases		Total Lease Obligations
2020	$	4,490	$	7,798	$	12,288
2021	4,565		7,541		12,106
2022	—		7,719		7,719
2023	—		3,363		3,363
2024	—		192		192
Thereafter	—		—		—
Total future minimum payments	9,055		26,613		35,668
Less: amount representing interest	(1,424)		(6,951)		(8,375)
Present value of minimum lease payments	7,631		19,662		27,293
Less: current portion	(3,465)		(4,625)		(8,090)
Long-term portion	$	4,166	$	15,037	$	19,203

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Other assets

December 31, (In thousands)	2019		2018
Equity-method investment	$	4,734	$	—
Contingent consideration	3,303		4,286
Deposits	295		2,465
Other	1,373		1,207
Total other assets	$	9,705	$	7,958

In September 2019, the Company was notified by DSM that certain contingent consideration payable to the Company upon the realization of certain NOL tax benefits transferred to DSM with the sale of the Brotas facility in December 2017 would not be realized due to changes in DSM’s Brazilian legal entity structure. The Company considered this information in conjunction with the probability and timing of DSM’s realization of the underlying NOL tax benefits and determined that a portion of the contingent consideration receivable was not recoverable as of December 31, 2018 and recorded a $3.9 million impairment in the statement of operations as Impairment of other assets. The Company reassessed the recoverability of this receivable at December 31, 2019 based on projected utilization of the underlying tax credits by DSM and recorded an additional impairment of $0.2 million for the year ended December 31, 2019.

In October 2019, the Company agreed to purchase the ownership interest previously held by Cosan in Novvi LLC, a joint venture among the Company, Cosan and certain other members, for $10.8 million (Purchase Price). The Company is obligated to pay the Purchase Price through the assignment of certain preferred dividends to be distributed by the proposed joint venture between the Company and Raizen Energia S.A., provided that, if the joint venture is not formed by October 2021, the Purchase Price shall be paid in full by October 31, 2022. The Company measured and recorded the fair value of the investment based on the present value of the unsecured $10.8 million obligation, which was deemed to be more readily determinable than the fair value of the Novvi partnership interest. In accordance with equity-method accounting, the Company records its share of Novvi's earnings or losses for each accounting period and adjusts the investment balance accordingly. However, the Company is not obligated to fund Novvi's potential future losses, so the Company will not record equity-method losses that would result in the investment in Novvi falling to below zero and becoming a liability. For additional information regarding the Company's accounting for equity-method investments, see Note 1, "Basis of Presentation and Summary of Significant Accounting Policies".

Accrued and other current liabilities

December 31, (In thousands)	2019		2018
Accrued interest	$	8,209	$	3,853
Payroll and related expenses	7,296		9,220
Contract termination fees	5,347		4,092
Ginkgo partnership payments obligation	4,319		2,155
Asset retirement obligation(1)	3,184		3,063
Professional services	2,968		1,173
Tax-related liabilities	1,685		2,139
Other	3,647		3,284
Total accrued and other current liabilities	$	36,655	$	28,979

______________

(1) The asset retirement obligation represents liabilities incurred but not yet discharged in connection with our 2013 abandonment of a partially constructed facility in Pradópolis, Brazil.

Other noncurrent liabilities

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December 31, (In thousands)	2019		2018
Liability for unrecognized tax benefit	$	7,204	$	6,582
Liability in connection with acquisition of equity-method investment	5,249		—
Ginkgo partnership payments, net of current portion (See Note 4)	4,492		6,185
Refund liability	3,750		—
Contract liabilities, net of current portion(1)	1,449		1,587
Deferred rent, net of current portion	—		6,440
Contract termination fees, net of current portion	—		1,530
Capital leases, net of current portion	—		195
Other	880		673
Total other noncurrent liabilities	$	23,024	$	23,192

______________

(1) Contract liabilities, net of current portion at December 31, 2019 and 2018 includes $1,204 at each date in connection with DSM, which is a related party.

In relation to the refund liability item above, in April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in variable consideration of $12.5 million in the form of a stand-ready obligation to refund some or all of the $12.5 million consideration if certain criteria are not met by December 2021. The Company periodically updates its estimate of amounts to be retained and reduces the refund liability and records additional license and royalty revenue as the criteria are met. The Company recorded an additional $8.8 million of license and royalty revenue during the year ended December 31, 2019 related to a change in the estimated refund liability, which reduced the balance to $3.8 million.

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3. Fair Value Measurement

Assets and liabilities are measured and reported at fair value based on the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The fair value hierarchy prioritizes the inputs to valuation techniques used to measure fair value. An asset's or liability's classification level is based on the lowest level of input that is significant to the fair value measurement. Assets and liabilities carried at fair value are valued and disclosed in one of the following three levels of the valuation hierarchy:

•Level 1: Quoted market prices in active markets for identical assets or liabilities.

•Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

•Level 3: Unobservable inputs that are not corroborated by market data.

Liabilities Measured and Recorded at Fair Value on a Recurring Basis

As of December 31, 2019 and 2018, the Company’s financial liabilities measured and recorded at fair value on a recurring basis were classified within the fair value hierarchy as follows:

December 31, (In thousands)	2019								2018
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Senior Convertible Notes Due 2022	$	—	$	—	$	50,624	50,624		$	—	$	—	$	—	$	—
6% Convertible Notes Due 2021	—		—		—		—		—		—		57,918		57,918
Embedded derivatives bifurcated from debt instruments	—		—		2,832		2,832		—		—		—		—
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		6,971		6,971		—		—		42,796		42,796
Total liabilities measured and recorded at fair value	$	—	$	—	$	60,427	$	60,427	$	—	$	—	$	100,714	$	100,714

The Company did not hold any financial assets to be measured and recorded at fair value on a recurring basis as of December 31, 2019 and 2018. Also, there were no transfers between the levels during 2019 or 2018.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgements and consider factors specific to the asset or liability. The method of determining the fair value of compound embedded derivative liabilities is described subsequently in this note. Market risk associated with compound embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

At December 31, 2019 and December 31, 2018, the carrying value of certain financial instruments, such as cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable and other current accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable.

Changes in fair value of derivative liabilities are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of derivative instruments".

Changes in the fair value of debt that is accounted for at fair value are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of debt".

Senior Convertible Notes Due 2022

On November 15, 2019, the Company issued $66.0 million of Senior Convertible Notes Due 2022 and elected the fair value option of accounting for this debt instrument (see Note 4, "Debt" for details). At December 31, 2019, the contractual outstanding principal of the Senior Convertible Notes Due 2022 was $66.0 million and the fair value was $50.6 million. The Company measured the fair value using a binomial lattice model (which is discussed in further detail below) with the following inputs: (i) 233% discount yield, (ii) 45% equity volatility, (iii) 25% / 75% probability of principal repayment in cash or stock, respectively and (iv) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year.

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In connection with the issuance of the Senior Convertible Notes Due 2022, the Company was required to pre-deliver 7.5 million shares of common stock (the Pre-Delivery Shares) to the note holders, which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the note holders to sell, trade or hold, subject to certain limitations, for as long as the Senior Convertible Notes Due 2022 are outstanding. However, the Company may elect or be required to apply the value of the pre-delivered shares to satisfy periodic principal and interest payments or other repayment events. Within ten business days following redemption or repayment of in full the Senior Convertible Notes Due 2022 and the satisfaction or discharge by the Company of all outstanding Company obligations under the Senior Convertible Notes Due 2022, the noteholders shall deliver 7.5 million shares of the Company’s common stock to the Company, less any shares used to satisfy any accrued interest or principal amortization payments under such notes.

The Company concluded the Pre-Delivery Shares provision meets the criteria of freestanding instrument that is legally detachable and separately exercisable from the Senior Convertible Notes Due 2022 and should be classified in equity as the common shares issued are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the Pre-Delivery Shares within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the shares to be reclassified to an asset or liability. The Company measured the issue date fair value of the Pre-Delivery Shares under an expected borrowing cost approach using a 9.75% annual borrowing rate over a 19-month estimated repayment term for the Senior Convertible Notes Due 2022. The resulting $4.2 million fair value was recorded in equity as additional paid in capital with an offset to the fair value of the Senior Convertible Notes Due 2022. See Note 6, “Stockholders’ Deficit” for further information regarding the issuance of the common stock.

For the year ended December 31, 2019, the Company recorded a $3.8 million gain from change in fair value of debt in connection with the initial issuance and subsequent fair value remeasurement of the Senior Convertible Notes Due 2022, as follows:

In thousands
Fair value at November 14, 2019	$	54,425
Less: Gain from change in fair value	(3,801)
Fair value at December 31, 2019	$	50,624

A binomial lattice model was used to determine if the Senior Convertible Notes Due 2022 would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible note will be converted early if the conversion value is greater than the holding value and (ii) the convertible note will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible note is called, the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible note. Using this lattice method, the Company valued the Senior Convertible Notes Due 2022 using the "with-and-without method", where the fair value of the Senior Convertible Notes Due 2022 including the embedded and freestanding features is defined as the "with", and the fair value of the Senior Convertible Notes Due 2022 excluding the embedded and freestanding features is defined as the "without". This method estimates the fair value of the Senior Convertible Notes Due 2022 by looking at the difference in the values of Senior Convertible Notes Due 2022 with the embedded and freestanding derivatives and the fair value of Senior Convertible Notes Due 2022 without the embedded and freestanding features. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company remeasures the fair value of the debt instrument and records the change as a gain or loss from change in fair value of debt in the statement of operations for each reporting period.

6% Convertible Notes Due 2021

On December 10, 2018, the Company issued $60.0 million of 6% Convertible Notes Due 2021 (see Note 4, "Debt" for details) and elected the fair value option of accounting for this debt instrument. The notes were extinguished in November 2019. The Company recorded a $23.2 million loss from change in fair value of debt in the year ended December 31, 2019 prior to extinguishing the debt.

Derivative Liabilities Recognized in Connection with the Issuance of Debt and Equity Instruments

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt and equity instruments – either freestanding or compound embedded – measured at fair value using significant unobservable inputs (Level 3):

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(In thousands)	Equity-related Derivative Liability		Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2018	$	41,272	$	1,524	$	42,796
Derecognition upon adoption of ASU 2017-11	(39,513)		(1,524)		(41,037)
Fair value of derivative liabilities issued during the period	—		15,158		15,158
Change in fair value of derivative liabilities	2,039		(4,816)		(2,777)
Derecognition on extinguishment	(3,798)		(539)		(4,337)
Balance at December 31, 2019	$	—	$	9,803	$	9,803

As of December 31, 2019, the $3.8 million derivative liability recorded in connection with the November 2018 Securities Purchase Agreement with DSM was settled and extinguished through a cash payment in April 2019.

During the second half of 2019, the Company issued four debt instruments with an embedded mandatory redemption feature and two freestanding liability classified warrants with conversion rate adjustment and antidilution provisions. See Note 4, “Debt” for a description of the transactions and the initial accounting treatment for these debt related derivatives. There is no current observable market for these types of derivatives and the Company determined the fair value of the embedded mandatory redemption feature using a probability weighted discounted cash flow model measuring the fair value of the debt instrument both with and without the embedded feature, which is discussed in more detail below; and the freestanding liability warrants using a Black-Scholes-Merton option pricing model, which is also discussed in more detail below.

The collective fair value of the four embedded derivatives totaled $2.5 million at issuance date and were recorded as a derivative liability and a debt discount against the underlying debt instruments. In the fourth quarter of 2019, the Company modified certain key terms in two of the four underlying debt instruments, resulting in a debt extinguishment of the two instruments. Consequently, the collective fair value of the two embedded derivative liabilities totaling $0.5 million were written off against the loss on debt extinguishment and the $0.7 million collective fair value of the two new embedded mandatory redemption features were recorded as derivative liabilities at the date of debt modification. The collective fair value of the four embedded derivative liabilities totaled $2.8 million at December 31, 2019.

The freestanding liability warrants issued on September 10, 2019 and November 14, 2019 had an initial fair value of $7.9 million and $4.0 million, respectively and were recorded as a derivative liability and a debt discount. The warrants will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations as a gain or loss on change in fair value of derivative liabilities. At December 31, 2019 the warrants derivative had a fair value of $6.9 million. For the year ended December 31, 2019, the Company recorded a $4.8 million gain from change in fair value of debt-related embedded derivative liabilities.

Valuation Methodology and Approach to Measuring the Derivative Liabilities

The liabilities associated with the Company’s freestanding and compound embedded derivatives outstanding at December 31, 2019 and 2018 represent the fair value of freestanding equity instruments, mandatory redemption features embedded in certain debt instruments and antidilution provisions in some of the Company's debt warrant instruments. See Note 4, "Debt", and Note 6, "Stockholders' Deficit" for further information regarding these host instruments. There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the freestanding instrument or embedded derivatives using the Black-Scholes-Merton option pricing model, a probability weighted discounted cash flow analysis, or a Monte Carlo simulation.

The Company uses the Black-Scholes-Merton option pricing model to determine the fair value of its liability classified warrants issued in 2019. Input assumptions for these freestanding instruments are as follows:

Input assumptions for liability classified warrants:	Range
Fair value of common stock on issue date	$3.09 – $4.76
Expected volatility	94% - 105%
Risk-free interest rate	1.58% - 1.67%
Dividend yield	0.0	%

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The Company uses a probability weighted discounted cash flow model to measure the fair value of the mandatory redemption features embedded in the four debt instruments issued in the second half of 2019. The model is designed to measure and determine if the debt instruments would be called or held at each decision point. Within the model, the following assumption is made: the underlying debt instrument will be called early if the change in control redemption value is greater than the holding value. If the underlying debt instrument is called, the holder will maximize their value by finding the optimal decision between (i) redeeming at the redemption price and (ii) holding the instrument until maturity. Using this assumption, the Company valued the embedded derivatives on a "with-and-without method", where the fair value of each underlying debt instrument including the embedded derivative is defined as the "with", and the fair value of each underlying debt instrument excluding the embedded derivatives is defined as the "without". This method estimates the fair value of the embedded derivatives by comparing the fair value differential between the with and without mandatory redemption feature. The model incorporates the mandatory redemption price, time to maturity, risk-free interest rate, estimated credit spread and estimated probability of a change in control default event.

The Company used a Monte Carlo simulation valuation model to determine the fair value of the May 2017 and August 2017 Cash and Dilution Warrants through December 31, 2018. Upon adoption of ASU 2017-11 on January 1, 2019, the fair value of these warrants was reclassified to equity as they no longer met the criteria for derivative liability accounting. Monte Carlo simulation combines a random number generator based on a probability distribution and additional inputs of volatility, time to expiration to generate a stock price and other uncertainties. The generated stock price at the time of expiration is then used to calculate the value of the option. The model then calculates results tens of thousands of times, each time using a different set of random values from the probability functions. The resulting Monte Carlo simulation valuation is based on the average of all the calculated results.

The market-based assumptions and estimates used in valuing the compound embedded and freestanding derivative liabilities include amounts in the following ranges/amounts:

December 31,	2019	2018
Risk-free interest rate	1.6% - 1.7%	2.5% - 3.0%
Risk-adjusted discount yield	20.0% - 27.0%	17.2% - 27.3%
Stock price volatility	45%	45.0% - 85.0%
Probability of change in control	5.0%	0.0%
Stock price	$3.09	$3.34
Credit spread	18.4% - 25.4%	14.6% - 24.9%
Estimated conversion dates	2022 - 2023	2019 - 2025

Changes in valuation assumptions can have a significant impact on the valuation of the embedded and freestanding derivative liabilities and debt that the Company elects to account for at fair value. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. Certain of the convertible notes, shares of convertible preferred stock and warrants also include conversion or exercise price adjustment features and, for example, certain issuances of common stock by the Company at prices lower than the current conversion or exercise price result in a reduction of the conversion price of such notes or convertible preferred stock, or a reduction in the exercise price of, or an increase in the number of shares subject to, such warrants, which increases the value of the embedded and freestanding derivative liabilities and debt measured at fair value; see Note 4, "Debt" for details.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable and credit facilities are recorded at carrying value, which is representative of fair value at the date of acquisition. The Company estimates the fair value of these instruments using observable market-based inputs (Level 2). The carrying amount (the total amount of net debt presented on the balance sheet) of the Company's debt at December 31, 2019 and at December 31, 2018, excluding the debt instruments recorded at fair value, was $195.8 million and $151.8 million, respectively. The fair value of such debt at December 31, 2019 and at December 31, 2018 was $194.8 million and $149.3 million,

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respectively, and was determined by (i) discounting expected cash flows using current market discount rates estimated for certain of the debt instruments and (ii) using third-party fair value estimates for the remaining debt instruments.

Assets and Liabilities Measured and Recorded at Fair Value on a Non-Recurring Basis

On November 19, 2018, the Company amended its supply agreement with DSM, as discussed in Note 9, “Revenue Recognition” to secure production capacity at the Brotas facility in exchange for future cash payments totaling $22.7 million, the issuance of 1,643,991 shares common stock valued at $6.1 million on the date of issuance and a further cash payment for the difference between the fair value of the common stock and $7.3 million on March 29, 2019. In addition, the Company modified certain warrants held by DSM which resulted in the transfer of $2.9 million of value to DSM and paid $1.8 million to settle certain obligations to DSM related to the 2017 sale of the Brotas facility. The Company also entered into other transactions contemporaneously with the amended supply agreement as discussed in Note 10, “Related Party Transactions”. This series of transactions with DSM in November 2018 was accounted for as a combined transaction in which the Company determined and allocated the fair value of the consideration to each element. The fair value of the consideration transferred to DSM under the combined arrangement totaled $33.3 million and was allocated as follows (in thousands):

Element	Fair Value Allocation
Manufacturing capacity reservation fee	$	24,395
Legal settlement and consent waiver	6,764
Working capital adjustment	2,145
Total fair value of consideration transferred	$	33,304

The fair value of these elements is based on Level 3 inputs, which considered the lowest level of input that is significant to the fair value measurement of these elements. To determine the fair value of the manufacturing capacity reservation fee, the Company used a discounted cash flow model under a cost savings valuation approach based on a competing manufacturing quote for similar capacity, location and timing. The Company used a discount rate of 22.5% and a tax rate of 0% to discount the gross cash flows. The fair value of the legal settlement for failure to obtain consent from DSM prior to executing the August 2018 Vivo Warrant transaction was determined by calculating the difference between the fair values of the warrants held by Vivo prior to and after the August 2018 Vivo Warrant transaction using a combination of a Monte Carlo simulation and the Black-Scholes-Merton option pricing model. The fair value of the working capital adjustment was determined to equal the difference between the preliminary estimate for working capital upon closing the Brotas facility sale and the final working capital amounts transferred.

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4. Debt

	2019								2018
December 31, (In thousands)	Principal		Unaccreted Debt (Discount) Premium		Fair Value Adjustment		Net		Principal		Unaccreted Debt (Discount) Premium		Fair Value Adjustment		Net
Convertible notes payable
Senior convertible notes due 2022	$	66,000	$	—	$	(15,376)	$	50,624	$	—	$	—	$	—	$	—
6% convertible notes due 2021	—		—		—		—		60,000		—		(2,082)		57,918
2015 Rule 144A convertible notes	—		—		—		—		37,887		(2,413)		—		35,474
2014 Rule 144A convertible notes	—		—		—		—		24,004		(867)		—		23,137
August 2013 financing convertible notes	—		—		—		—		4,415		(70)		—		4,345
	66,000		—		(15,376)		50,624		126,306		(3,350)		(2,082)		120,874
Related party convertible notes payable
2014 Rule 144A convertible notes	10,178		—		—		10,178		24,705		(1,038)		—		23,667
	10,178		—		—		10,178		24,705		(1,038)		—		23,667
Loans payable and credit facilities
Schottenfeld notes	20,350		(1,315)		—		19,035		—		—		—		—
Nikko notes	14,318		(901)		—		13,417		4,598		(1,047)		—		3,551
Ginkgo note	12,000		(3,139)		—		8,861		12,000		(4,047)		—		7,953
Other loans payable	1,828		—		—		1,828		312		—		—		312
GACP term loan facility	—		—		—		—		36,000		(1,349)		—		34,651
	48,496		(5,355)		—		43,141		52,910		(6,443)		—		46,467
Related party loans payable
Foris notes	115,351		(9,516)		—		105,835		—		—		—		—
DSM notes	33,000		(4,621)		—		28,379		25,000		(6,311)		—		18,689
Naxyris note	24,437		(822)		—		23,615		—		—		—		—
	172,788		(14,959)		—		157,829		25,000		(6,311)		—		18,689
Total debt	$	297,462	$	(20,314)	$	(15,376)	261,772		$	228,921	$	(17,142)	$	(2,082)	209,697
Less: current portion							(63,805)								(147,677)
Long-term debt, net of current portion							$	197,967							$	62,020

Future minimum payments under the debt agreements as of December 31, 2019 are as follows:

Years ending December 31 (In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020	$	43,384	$	26,324	$	10,437	$	33,730	$	113,875
2021	40,177		3,342		—		53,566		97,085
2022	—		15,177		—		113,818		128,995
2023	—		13,011		—		24,323		37,334
2024	—		398		—		—		398
Thereafter	—		1,870		—		—		1,870
Total future minimum payments	83,561		60,122		10,437		225,437		379,557
Less: amount representing interest(1)	(17,561)		(11,626)		(259)		(52,649)		(82,095)
Less: future conversion of accrued interest to principal	—		—		—		—		—
Present value of minimum debt payments	66,000		48,496		10,178		172,788		297,462
Less: current portion of debt principal	(31,800)		(21,193)		(10,178)		(11,380)		(74,551)
Noncurrent portion of debt principal	$	34,200	$	27,303	$	—	$	161,408	$	222,911

______________

⁽¹⁾ Excluding net debt discount of $20.3 million that will be amortized to interest expense over the term of the debt.

August 2013 Financing Convertible Note

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On January 14, 2019, Wolverine Flagship Fund Trading Limited (Wolverine) agreed to waive payment of the August 2013 Financing Convertible Note held by Wolverine at its January 15, 2019 maturity until July 15, 2019 in exchange for a fee, payable on or prior to July 15, 2019, of $0.6 million. The due date of the waiver fee was extended to October 13, 2019 and was subsequently paid on October 29, 2019. The Company concluded that the maturity date extension represented a debt modification, and the fee was accounted for as additional debt discount to be amortized over the remaining term.

On July 8, 2019, $5.1 million principal balance of the convertible note and unpaid interest was exchanged for 1.8 million shares of common stock with a total fair value of $5.9 million or $3.30 per share and a warrant to purchase 1.1 million shares of common stock with a fair value of $1.9 million. The Company recorded a $2.7 million loss on debt extinguishment for the difference between the carrying value of the debt and the sum of the fair values of the common stock and warrant. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of the common stock and warrant issued in connection with this exchange.

2015 Rule 144A Convertible Notes Extinguishment

On April 16, 2019, the Company repaid in cash the $37.9 million outstanding principal, as well as accrued and unpaid interest, under its 9.50% Convertible Senior Notes due 2019 (the 2015 Rule 144A Convertible Notes). This repayment did not result in an extinguishment gain or loss.

2014 Rule 144A Convertible Notes

In May 2019, the Company exchanged a portion of its 6.50% Convertible Senior Notes (the 2014 Rule 144A Convertible Notes), representing $38.2 million aggregate principal amount of 2014 Rule 144A Convertible Notes, for shares of common stock, warrants to purchase common stock and a new senior convertible note as described below and repaid the remaining $10.5 million of the 2014 Rule 144A Convertible Notes in cash at maturity.

Notes Conversion into Common Stock

On May 10, 2019, the Company exchanged $13.5 million aggregate principal amount of 2014 Rule 144A Convertible Notes held by certain non-affiliated investors, including accrued and unpaid interest thereon, for an aggregate of 3.5 million shares of common stock and warrants to purchase an aggregate of 1.4 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, in a private exchange.

On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of 2014 Rule 144A Convertible Notes held by Foris, including accrued and unpaid interest thereon, for 1.1 million shares of common stock and a warrant to purchase up to 0.4 million shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from issuance, in a private exchange. On August 28, 2019, the Company and Foris agreed to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share in connection with the “August 2019 Foris Credit Agreements” below. Also, see Note 6, “Stockholders’ Deficit” for additional information and Note 15, “Subsequent Events” for information regarding the amendment and exercise of the warrants on January 31, 2020.

On May 15, 2019, the Company exchanged $10.0 million aggregate principal amount of 2014 Rule 144A Convertible Notes held by Maxwell (Mauritius) Pte Ltd for 2.5 million shares of common stock in a private exchange.

The Company evaluated the May 2019 note conversions into common stock discussed above and concluded that the transactions resulted in a debt extinguishment. The Company recorded a $5.9 million loss on debt extinguishment of the 2014 144A Convertible Notes in the three months ended June 30, 2019. The loss represented the difference between the $30.8 million fair value of 7.1 million common shares issued upon exchange, $3.8 million fair value of warrants issued to purchase 1.7 million shares of common stock and $0.4 million of fees incurred, less the $29.1 million carrying value of the debt that was extinguished. See Note 6. "Stockholders’ Deficit" for further information regarding the fair value measurement of the common stock and warrants issued in connection with the May 2019 note conversions discussed above.

Total Note Exchange and Extensions

On May 15, 2019, the Company exchanged $9.7 million aggregate principal amount of 2014 Rule 144A Convertible Notes due May 15, 2019 held by Total Raffinage Chimie (Total) for a new senior convertible note (the New Note) with an equal principal amount and with substantially identical terms, except that the New Note had a maturity date of June 14, 2019.

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Effective June 14, 2019, the Company and Total agreed to extend the maturity date of the New Note from June 14, 2019 to July 18, 2019. Effective July 18, 2019, the Company and Total agreed to (i) further extend the maturity date of the New Note from July 18, 2019 to August 28, 2019 and (ii) increase the interest rate on the New Note to 10.5% per annum, beginning July 18, 2019. Effective August 28, 2019, the Company and Total agreed to (i) further extend the maturity date of the New Note from August 28, 2019 to October 28, 2019 and (ii) increase the interest rate on the New Note to 12% per annum, beginning August 28, 2019. On October 31, 2019, the Company and Total agreed, effective as of October 28, 2019, to (i) extend the maturity date of the New Note from October 28, 2019 to December 16, 2019 and (ii) capitalize all interest accruing under the New Note from May 15, 2019 through and including November 14, 2019, in the amount of $0.5 million, which interest would be added to the principal of the New Note, which would begin accruing interest on such new principal amount on November 15, 2019. Effective December 16, 2019, the Company and Total agreed to extend the maturity date of the New Note from December 16, 2019 to January 31, 2020. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to repay the $10.2 million New Note by January 31, 2020.

The Company accounted for the note exchange and series of extensions with Total as a debt modification; however, no additional fees were paid in connection with the exchange and extensions, and consequently there was no impact on the carrying value of the debt as of December 31, 2019.

Foris Debt Transactions—Related Party

The Company has loans payable to Foris Ventures, LLC (Foris) with a total principal balance of $115.4 million at December 31, 2019. Foris is an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than five percent of the Company’s outstanding common stock. The notes payable to Foris are comprised of the following (amounts in thousands):

Description	Date Issued	Original Loan Amount		Balance at December 31, 2019		Interest Rate per Annum	Maturity Date
Foris $19 Million Note	August 28, 2019	$	19,000	$	19,000	12.0%	January 1, 2023
Foris LSA	April 15, 2019	36,000		96,351		12.5%	For $81.0 million borrowed prior to November 27, 2019, the maturity date is July 1, 2022; for $10.0 million borrowed November 27, 2019, the maturity date is March 31, 2023.
		$	55,000	$	115,351

Foris Credit Agreements

On April 8, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $8.0 million (the April Foris Credit Agreement), which the Company borrowed in full on April 8, 2019 and issued to Foris a promissory note in the principal amount of $8.0 million (the April Foris Note). The April Foris Note has a maturity date of October 14, 2019, which has no stated interest rate. The Company agreed to pay Foris a fee of $1.0 million, payable on or prior to the maturity date; provided, that the fee will be reduced to $0.5 million if the Company repays the April Foris Note in full by July 15, 2019. The Company accrues this fee as interest expense over the six-month term of the note.

On June 11, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $8.5 million, which the Company borrowed in full on June 11, 2019 and issued to Foris a promissory note in the principal amount of $8.5 million (the June Foris Note). The June Foris Note (i) accrues interest at a rate of 12.5% per annum and is payable on the maturity date or the earlier repayment or other satisfaction of the June Foris Note, and (ii) matured on August 28, 2019.

On July 10, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $16.0 million (the July Foris Credit Agreement), of which the Company borrowed $8.0 million on July 10, 2019 and $8.0 million on July 26, 2019 and issued to Foris promissory notes, each in the principal amount of $8.0 million, on such dates (the July Foris Notes). The July Foris Notes (i) accrue interest at a rate of 12.5% per annum, which is payable on the maturity date or the earlier repayment or other satisfaction of the applicable July Foris Note, and (ii) mature on December 31, 2019.

In connection with the entry into the July Foris Credit Agreement, the Company and Foris amended the warrant issued to Foris on August 17, 2018 to reduce the exercise price of such warrant from $7.52 per share to $2.87 per share. The warrant modification resulted in $4.0 million of incremental value which was accounted for as a debt discount to the $16 million July

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Foris Notes. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of the modified warrant.

On August 14, 2019, the April Foris Note, the June Foris Note and the July Foris Notes were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral granted to Foris under the LSA, and such notes were cancelled in connection therewith. See "LSA Assignment, Amendments and Waiver" below for further information.

Foris LSA Assignment, Amendments and Waivers

On April 4, 2019, the Company and GACP Finance Co., LLC (GACP) amended the Loan and Security Agreement, dated June 29, 2018 (as amended, the LSA), to remove, add and modify certain restrictions, covenants and other provisions and to waive breaches of certain covenants under the LSA occurring prior to, as of and after December 31, 2018 through April 8, 2019. In connection with such waiver, the Company agreed to pay GACP fees of $0.8 million, which the Company paid in April 2019. This waiver fee was recorded as interest expense in the statement of operations in the nine months ended September 30, 2019.

On April 15, 2019, the Company, GACP and Foris Ventures, LLC (Foris), an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than 5% of the Company’s outstanding common stock) entered into a Loan Purchase Agreement, pursuant to which Foris agreed to purchase and assume from GACP, the outstanding principal balance under the LSA, which totaled $36.0 million and all documents and assets related thereto. In connection with such purchase and assignment, the Company agreed to repay Foris $2.5 million of the purchase price and accrued interest paid by Foris to GACP (the LSA Obligation). The closing of the loan purchase and assignment occurred on April 16, 2019.

On August 14, 2019, the Company and Foris entered into an Amendment No. 5 and Waiver to the LSA (the LSA Amendment and Waiver), pursuant to which (i) the maturity date of the loans under the LSA was extended from July 1, 2021 to July 1, 2022, (ii) the interest rate for the loans under the LSA was modified to the greater of (A) 12% or (B) the rate of interest payable with respect to any indebtedness of the Company, including, but not limited to, the rate of interest charged pursuant to the Naxyris Loan Agreement, provided, that for such purpose, the rate of interest charged pursuant to the Naxyris Loan Agreement shall be the rate of interest payable by the Borrower pursuant to the Naxyris Loan Agreement, minus 25 basis points (iii) the amortization of the loans under the LSA was delayed until December 16, 2019, (iv) certain accrued and future interest and agency fee payments under the LSA were delayed until December 16, 2019, (v) certain covenants under the LSA, including related definitions, were amended to provide the Company with greater operational and financial flexibility, including, without limitation, to permit the incurrence of the indebtedness under the August 2019 Naxyris Loan (as described below) and the granting of liens with respect thereto, subject to the terms of an intercreditor agreement between Foris and Naxyris S.A. (Naxyris) governing the respective rights of the parties with respect to, among other things, the assets securing the Naxyris Loan Agreement (as defined below) and the LSA (the Intercreditor Agreement), (vi) certain outstanding unsecured promissory notes issued by the Company to Foris on April 8, 2019, June 11, 2019, July 10, 2019 and July 26, 2019 (as described in the “Foris Credit Agreements” section above), in an aggregate principal amount of $32.5 million, as well as the $2.5 million LSA Obligation, were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral granted to Foris under the LSA, and such promissory notes and contractual obligation were canceled in connection therewith, and (vii) Foris agreed to waive certain existing defaults under the LSA, including with respect to covenants related to cross-defaults, minimum liquidity and minimum asset coverage requirements. After giving effect to the LSA Amendment and Waiver, there was $71.0 million aggregate principal amount of loans outstanding under the LSA.

The Company also issued to Foris a warrant (the LSA Warrant) on August 14, 2019 to purchase up to 1.4 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The warrant had a fair value of $2.9 million, which was measured using the Black-Scholes-Merton option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant.

Due to multiple changes in key provisions of the LSA from April 15, 2019 through August 14, 2019, the Company analyzed the before and after cash flows from the prior twelve months of modifications resulting from the increased principal balance, decreased interest rate, extended maturity date, waiver of default interest and the fair value of the new LSA Warrant provided to Foris in order to determine if these changes result in a modification or extinguishment of the original LSA. Based on the combined before and after cash flows of the five separate note balances making up the new principal balance of the LSA and the fair value of the LSA warrant, the change in cash flows was not significantly different. Consequently, the LSA Amendment and Waiver was accounting for as a debt modification with the $2.9 million fair value of the LSA Warrant

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recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA.

Foris LSA Amendments, Additional Loan and Warrant Issuance

On October 10, 2019, the Company and Foris entered into Amendment No. 6 to the LSA (the October 2019 LSA Amendment), pursuant to which the maximum loan commitment of Foris under the LSA was increased by $10.0 million. On October 11, 2019, the Company borrowed an additional $10.0 million from Foris under the LSA (the October 2019 LSA Loan), which is subject to the terms and provisions of the LSA, including the lien on substantially all the assets of the Company. After giving effect to the LSA Loan, there was $81.0 million aggregate principal amount of loans outstanding under the LSA. Also, in connection with the October 2019 LSA Amendment, the Company issued a warrant (the October 2019 Foris LSA Warrant) to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The warrant had a fair value of $4.1 million which was measured using the Black-Scholes-Merton option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant.

On October 28, 2019, the Company and Foris entered into an amended and restated LSA (the A&R LSA), pursuant to which, among other things, certain covenants and related definitions were amended to permit the incurrence of the indebtedness under the October 2019 Naxyris Loan (as defined below), subject to the terms of an amended and restated intercreditor agreement, dated October 28, 2019, between Foris and Naxyris governing the respective rights of the parties with respect to, among other things, the assets securing the A&R Naxyris LSA (as defined below) and the A&R LSA, and additional covenants were added relating to, among other things, maintenance of intellectual property, compliance with laws, delivery of reports and repayment of indebtedness.

On November 27, 2019, the Company borrowed an additional $10.0 million from Foris under the A&R LSA dated October 28, 2019. The new loan has identical terms to the previous loans under the LSA except that the maturity date is March 31, 2023 (as opposed to July 1, 2022 for the other loans under the LSA). In connection with the new loan, the Company issued a warrant to purchase up to 1,000,000 shares of common stock at an exercise price of $3.87 per share, exercisable for a period of two years from issuance (the November 2019 Foris Warrant). The warrant had a fair value of $2.1 million which was measured using the Black-Scholes-Merton option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant. After giving effect to the LSA Loan, there was $91.0 million aggregate principal amount of loans outstanding under the A&R LSA.

Due to multiple changes in key provisions of the LSA through November 27, 2019, the Company analyzed the before and after cash flows from the prior twelve months of modifications resulting from the increased principal balance, decreased interest rate, extended maturity date, waiver of default interest and the fair value of the new LSA Warrant, the October 2019 Foris Warrant and the November 2019 Foris Warrant provided to Foris in order to determine if these changes result in a modification or extinguishment of the original LSA. Based on the combined before and after cash flows of the various note balances making up the new principal balance of the LSA and the fair value of the three warrants, the Company determined that the change in cash flows through and including the October 2019 LSA Amendment were significantly different. Consequently, the October 2019 LSA Amendment was accounting for as a debt extinguishment and a new debt issuance. The Company recorded a $12.8 million loss on extinguishment comprised of (i) $8.7 million unamortized debt discount and (ii) the $4.1 million fair value of the October 2019 Foris LSA Warrant (a non-cash fee paid to the lender).

However, the change in cash flows from the October 2019 LSA Amendment to the November 27, 2019 borrowing under the A&R LSA were not significantly different. As a result, the A&R LSA was accounting for as a debt modification. The Company recorded a new $3.5 million debt discount, comprised of (i) $2.1 million fair value of the November 2019 Warrant, recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the A&R LSA, and (ii) $1.4 million fair value of a bifurcated embedded mandatory redemption feature, recorded as a derivative liability and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the A&R LSA. See Note 3, “Fair Value Measurement” for further information on the valuation and subsequent fair value accounting for the bifurcated embedded derivative.

August 2019 Foris Credit Agreements

On August 28, 2019, the Company and Foris entered into a credit agreement for an unsecured credit facility in an aggregate principal amount of $19.0 million (the August 2019 Foris Credit Agreement), which the Company borrowed in full on August 28, 2019 (the Foris $19 Million Note). The Foris $19 Million Note (i) accrues interest at a rate of 12% per annum, which is payable quarterly in arrears on each March 31, June 30, September 30 and December 31, beginning December 31,

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2019, and (ii) matures on January 1, 2023. The Company may at its option repay the amounts outstanding under the Foris $19 Million Note before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment.

The Foris $19 Million Note also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.5 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Foris $19 Million Note. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

In connection with the entry into the August 2019 Foris Credit Agreement, the Company issued to Foris a warrant (the August 2019 Foris Warrant) to purchase up to 4.9 million shares of Common Stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant. The warrant had a $8.7 million fair value and a $5.2 million relative fair value after allocating the Foris $19 Million Note proceeds to the $0.5 million fair value of the embedded mandatory redemption feature contained in the Foris $19 Million Note, and allocating on a residual basis, to the relative fair values of the Foris $19 Million Note and the August 2019 Foris Warrant. The $5.2 million relative fair value of the August 2019 Foris Warrant was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the term of the Foris $19 Million Note.

Also, on August 28, 2019 in connection with the entry into the August 2019 Foris Credit Agreement, the Company and Foris amended the warrant to purchase up to 3.9 million shares of common stock issued to Foris on April 26, 2019 to reduce the exercise price from $5.12 per share to $3.90 per share, and amended the warrant to purchase up to 0.4 million shares of common stock issued to Foris on May 14, 2019 to reduce the exercise price from $4.56 per share to $3.90 per share. The warrant modifications resulted in $1.1 million of incremental value that was recorded as an increase to additional paid in capital and a debt discount to be amortized to interest expense under the effective interest method over the term of the Foris $19 Million Note. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of these warrant modifications.

In addition to the $5.2 million relative fair value of the August 2019 Foris Warrant, the $0.5 million fair value of the embedded mandatory redemption feature, and $1.1 million incremental value related to the warrant modifications, the Company incurred $0.1 million of legal fees in connection the issuing the Foris $19 Million Note. These amounts totaled $6.8 million and were recorded as a debt discount to be amortized as interest expense under the effective interest method over the term of the Foris $19 Million Note. This note was repaid in full in January 2020; see "Warrant Exercise, Common Stock Purchase and Debt Equitization by Foris – Related Party" in Note 15, "Subsequent Events" for additional information.

Naxyris LSA

On August 14, 2019, the Company, certain of the Company’s subsidiaries (the Subsidiary Guarantors) and, as lender, Naxyris, an existing stockholder of the Company and an investment vehicle owned by Naxos Capital Partners SCA Sicar, which is affiliated with NAXOS S.A.R.L. (Switzerland), for which director Carole Piwnica serves as director, entered into a Loan and Security Agreement (the Naxyris Loan Agreement) to make available to the Company a secured term loan facility in an aggregate principal amount of up to $10.4 million (the August 2019 Naxyris Loan), which the Company borrowed in full on August 14, 2019. In connection with the funding of the August 2019 Naxyris Loan, the Company paid Naxyris an upfront fee of $0.4 million.

Loans under the August 2019 Naxyris Loan have a maturity date of July 1, 2022 and accrue interest at a rate per annum equal to the greater of (i) 12% or (ii) the rate of interest payable with respect to any indebtedness of the Company plus 25 basis points, which interest will be payable monthly in arrears, provided that all interest accruing from and after August 14, 2019 through December 1, 2019 shall be due and payable on December 15, 2019.

The obligations of the Company under the Naxyris Loan Agreement are (i) guaranteed by the Subsidiary Guarantors and (ii) secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors (the Collateral), junior in payment priority to Foris subject to certain limitations and exceptions, as well as the terms of the Intercreditor Agreement.

Mandatory prepayments of the outstanding amounts under the August 2019 Naxyris Loan will be required upon the occurrence of certain events, including asset sales, a change in control, and the incurrence of additional indebtedness, subject

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to certain exceptions and reinvestment rights. Outstanding amounts under the August 2019 Naxyris Loan must also be prepaid to the extent that the borrowing base exceeds the outstanding principal amount of the loans under the August 2019 Naxyris Loan. In addition, the Company may at its option prepay the outstanding principal amount of the loans under the August 2019 Naxyris Loan in full before the maturity date. Any prepayment of the loans under the August 2019 Naxyris Loan prior to the maturity date, whether pursuant to a mandatory or optional prepayment, is subject to a prepayment charge equal to one year’s interest at the then-current interest rate for the August 2019 Naxyris Loan. Upon any repayment of the loans under the August 2019 Naxyris Loan, whether on the maturity date or earlier pursuant to an optional or mandatory prepayment, the Company will pay Naxyris an end of term fee based on a percentage of the aggregate amount borrowed. In addition, (i) the Company will be required to pay a fee equal to 6% of any amount the Company fails to pay within three business days of its due date and (ii) any interest that is not paid when due will be added to principal and will accrue compound interest at the applicable rate.

The August 2019 Naxyris Loan contains customary affirmative and negative covenants and financial covenants, including covenants related to minimum revenue, minimum liquidity and minimum asset coverage requirements.

The August 2019 Naxyris Loan also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.3 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the August 2019 Naxyris Loan. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

In connection with the entry into the August 2019 Naxyris Loan, on August 14, 2019 the Company issued to Naxyris a warrant (the Naxyris LSA Warrant) to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant. The warrant had a $4.0 million fair value and a $3.0 million relative fair value after allocating the August 2019 Naxyris Loan proceeds to the $0.3 million fair value of the embedded mandatory redemption feature contained in the August 2019 Naxyris Loan, and allocating on a residual basis, to the relative fair values of the August 2019 Naxyris Loan and the Naxyris LSA Warrant. The $3.0 million relative fair value of the Naxyris LSA Warrant was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the term of the August 2019 Naxyris Loan.

In addition to the $3.0 million relative fair value of the Naxyris LSA Warrant and the $0.3 million fair value of the embedded mandatory redemption feature, the August 2019 Naxyris Loan contained $0.4 million original issue discount, $0.5 million mandatory end of term fee and $0.3 million of issuances costs, all totaling $4.5 million. All such amounts were recorded as a debt discount to be amortized to interest expense over the term of the August 2019 Naxyris Loan.

Naxyris LSA Amendment

On October 28, 2019, the Company, the Subsidiary Guarantors and Naxyris amended and restated the Naxyris Loan Agreement (the A&R Naxyris LSA), pursuant to which the maximum loan commitment of Naxyris under the Naxyris Loan Agreement was increased by $10.4 million. On October 29, 2019, the Company borrowed an additional $10.4 million (the October 2019 Naxyris Loan) from Naxyris under the A&R Naxyris LSA, which is subject to the terms and provisions of the A&R Naxyris LSA, including the lien on substantially all of the assets of the Company and the Subsidiary Guarantors. Also, under the terms of A&R Naxyris LSA, the Company owes a 5% end of term fee on the October 2019 Naxyris Loan amount and a $2.0 million term loan fee, both of which are due at July 1, 2022 maturity or upon full repayment of the amounts borrowed under the A&R Naxyris LSA. Also, the Company paid Naxyris an upfront fee of $0.4 million at the funding date of the October 2019 Naxyris Loan. After giving effect to the October 2019 Naxyris Loan amount, there is $24.4 million aggregate principal amount of loans outstanding under the A&R Naxyris LSA.

Also, in connection with the entry into the A&R Naxyris LSA, on October 28, 2019 the Company issued to Naxyris a warrant to purchase up to 2.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance (the October 2019 Naxyris Warrant). The warrant had a $3.6 million fair value and a $2.8 million relative fair value after allocating the October 2019 Naxyris Loan proceeds to the $0.5 million fair value of the embedded mandatory redemption feature contained in the October 2019 Naxyris Loan, and allocating on a residual basis, to the relative fair values of the October 2019 Naxyris Loan and the October 2019 Naxyris Warrant. The $2.8 million relative fair value of the October 2019 Naxyris Warrant was recorded as an increase to additional paid in capital and as a loss on debt extinguishment (as discussed below).

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Due to changes in key terms of the Naxyris Loan Agreement through the addition of the October 2019 Naxyris Loan, the Company analyzed the before and after cash flows under the August 2019 Naxyris Loan and October 2019 Naxyris Loan in order to determine if these changes result in a modification or extinguishment of the original Naxyris Loan Agreement. Based on the combined before and after cash flows related to the increased principal balance, increased end of term fees and the fair value of new warrants provided to Naxyris, the Company determined that the change in cash flows were significantly different. Consequently, the October 2019 Naxyris Loan was accounting for as a debt extinguishment and new debt issuance. The Company recorded a $9.7 million loss on extinguishment comprised of (i) $4.0 million of unamortized debt discount, net of the $0.3 million fair value of the bifurcated embedded mandatory redemption feature, (ii) $2.9 million of original issue discount and end of term fees and (iii) the $2.8 million fair value of the October 2019 Naxyris Warrant (a non-cash fee paid to the lender).

The October 2019 Naxyris Loan contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.5 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the new debt issuance. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature. The Company also capitalized $0.4 million of legal fees related to the October 2019 Naxyris Loan as a debt discount.

Schottenfeld September 2019 Credit Agreements

On September 10, 2019, the Company entered into separate credit agreements (the Investor Credit Agreements) with each of Schottenfeld Opportunities Fund II, L.P., Phase Five Partners, LP and Koyote Trading, LLC (the Investors or Schottenfeld Holdings Group LLC) to make available to the Company unsecured credit facilities in an aggregate principal amount of $12.5 million, which the Company borrowed in full on September 10, 2019 and issued to the Investors separate promissory notes in the aggregate principal amount of $12.5 million (the Investor Notes). Each Investor Note (i) accrues interest at a rate of 12% per annum, which is payable quarterly in arrears on each March 31, June 30, September 30 and December 31, beginning December 31, 2019, and (ii) matures on January 1, 2023. The Company may at its option repay the amounts outstanding under the Investor Notes before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment.

The Investor Notes also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.3 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Investor Notes. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

In connection with the September 10, 2019 Investor Credit Agreements, the Company issued to the Investors warrants (the September 2019 Investor Warrants) to purchase up to an aggregate of 3.2 million shares of common stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. The September 2019 Investor Warrants had a $7.9 million fair value which was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Investor Notes. See Note 3, “Fair Value Measures” for information regarding the fair value measurement and accounting of these liability warrants.

Schottenfeld November 2019 Credit and Security Agreement

On November 14, 2019, the Company entered into a credit and security agreement (the Schottenfeld CSA) with Schottenfeld Opportunities Fund II, L.P. and Phase Five Partners, LP (two investors affiliated with Schottenfeld Group Holdings LLC) to borrow an additional $7.9 million, resulting in net proceeds to the Company of $7.5 million after deduction of a 5% original issue discount, and to grant the Investor Notes a security interest in the collateral granted to the Investors under the Schottenfeld CSA (as described below). The loans accrue interest at 12% per annum, mature on the earlier to occur of (i) the closing of a $50 million or greater financing and (ii) January 15, 2020, and are secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors, junior in payment priority to Foris and Naxyris subject to the Subordination Agreement among Foris, Naxyris and the Investors. In connection therewith, the Company issued to such investors warrants to purchase an aggregate of 2.0 million shares of common stock at an exercise price of $3.87 per share, with an exercise term of 2 years from issuance (the November 2019 Schottenfeld CSA Warrants). In connection with the warrant issuance, the Company will be required to pay the November 2019 Schottenfeld CSA Warrants holders and the September 2019 Investor Warrants holders a fee if the Company issues equity securities in connection with the $50 million or greater financing provision that have an issue, conversion or exercise price of less than $3.90 or $3.87 per share, respectively. In such case, the fee will be the difference between the exercise price of such warrants (i.e., $3.90 or

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$3.87) and the issue, conversion or exercise price of the equity securities issued in the $50 million or greater financing, times the total number of warrants issued to such investors in November 2019 and September 2019. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to repay the $7.9 million loan by January 15, 2020.

The November 2019 Schottenfeld CSA Warrants had a $4.0 million fair value which was recorded as a derivative liability and a loss on debt extinguishment (as discussed below). See Note 3, “Fair Value Measures” for information regarding the fair value measurement and accounting of these liability warrants. Also, the Schottenfeld CSA also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.2 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Schottenfeld CSA (as discussed below). See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

Due to multiple changes in key provisions of Investor Credit Agreements and the Schottenfeld CSA, the Company analyzed the before and after cash flows resulting from the increased principal balance and the fair value of the new November 2019 Schottenfeld CSA Warrants to determine whether these changes result in a modification or extinguishment of the original Schottenfeld and Phase Five notes. Based on the combined before and after cash flows of each note, the change in cash flows was significantly different. Consequently, the Schottenfeld CSA was accounted for as a debt extinguishment and a new debt issuance. The Company recorded an $11.2 million loss upon extinguishment of debt, which was comprised of $6.8 million of unaccreted discount and the balance of the derivative liability recorded in connection with the previous debt instrument, the $4.0 million fair value of the November 2019 Schottenfeld CSA Warrant (as a non-cash fee paid to the lender), and a $0.4 million original issue discount that was netted against the Schottenfeld CSA loan proceeds.

In recording the new debt issuance, the Company also capitalized $0.2 million of legal fees related to the Schottenfeld CSA and the initial fair value of the mandatory redemption feature of $0.2 million was as a debt discount to be amortized to interest expense under the effective interest method over the term of the new debt issuance.

DSM Credit Agreements—Related Party

DSM $25 Million Note

In December 2017, the Company and DSM entered into a credit agreement (the DSM Credit Agreement) to make available to the Company an unsecured credit facility of $25.0 million. On December 28, 2017, the Company borrowed $25.0 million under the DSM Credit Agreement, representing the entire amount available thereunder, and issued a promissory note to DSM in an equal principal amount (the DSM Note). The Company used the proceeds of the amounts borrowed under the DSM Credit Agreement to repay all outstanding principal under a promissory note in the principal amount of $25.0 million issued to Guanfu Holding Co., Ltd. in December 2016 (the Guanfu Note). Given multiple elements in the arrangements with DSM, the Company fair valued the DSM Note to determine the arrangement consideration that should be allocated to the DSM Note. The fair value of the DSM Note was discounted using a Company specific weighted average cost of capital rate that resulted in a debt discount of $8.0 million. The debt discount is being amortized over the loan term using the effective interest method.

The DSM Note (i) is an unsecured obligation of the Company, (ii) matures on December 31, 2021 and (iii) accrues interest from and including December 28, 2017 at 10% per annum, payable quarterly. The DSM Note may be prepaid in full or in part at any time without penalty or premium. The DSM Credit Agreement and the DSM Note contain customary terms, covenants and restrictions, including certain events of default after which the DSM Note may become due and payable immediately.

DSM $8 Million Note

On September 17, 2019, the Company and DSM entered into a credit agreement (the 2019 DSM Credit Agreement) to make available to the Company a secured credit facility in an aggregate principal amount of $8.0 million, to be issued in separate installments of $3.0 million, $3.0 million and $2.0 million, respectively, with each installment being subject to certain closing conditions, including the payment of certain existing obligations of the Company to DSM. On September 17, 2019, the Company borrowed the first installment of $3.0 million under the 2019 DSM Credit Agreement, all of which proceeds were used to pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of $3.0 million. On September 19, 2019, the Company borrowed the second installment of $3.0 million under the 2019 DSM Credit Agreement, all of which proceeds were used to pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of $3.0 million. On September 23, 2019, the Company borrowed the final

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installment of $2.0 million under the 2019 DSM Credit Agreement, $1.5 million of which proceeds were used to pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of $2.0 million. The promissory notes issued under the 2019 DSM Credit Agreement (i) mature on August 7, 2022, (ii) accrue interest at a rate of 12.5% per annum from and including the applicable date of issuance, which interest is payable quarterly in arrears on each January 1, April 1, July 1 and October 1, beginning January 1, 2020, and (iii) are secured by a first-priority lien on certain Company intellectual property licensed to DSM. The Company may at its option repay the amounts outstanding under the 2019 DSM Credit Agreement before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment. In addition, the Company is required to repay the amounts outstanding under the 2019 DSM Credit Agreement (i) in an amount equal to the gross cash proceeds, if any, received by the Company upon the exercise by DSM of any of the common stock purchase warrants issued by the Company to DSM on May 11, 2017 or August 7, 2017 (see Note 6, “Stockholders’ Deficit”) and (ii) in full upon the request of DSM at any time following the receipt by the Company of at least $50.0 million of gross cash proceeds from one or more sales of equity securities of the Company on or prior to June 30, 2020. In connection with issuance of the 2019 DSM Credit Agreement, the Company incurred $0.3 million of legal fees which were recorded as a debt discount to be amortized as interest expense under the effective interest method over the term of the 2019 DSM Credit Agreement.

Ginkgo Note, Partnership Agreement and Note Amendment

In November 2017, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a partnership agreement (Ginkgo Partnership Agreement) to replace and supersede the 2016 Ginkgo Collaboration Agreement. Under the Ginkgo Partnership Agreement, the Company and Ginkgo agreed:

•to issue the $12 million November 2017 Ginkgo Note (as defined below), which effectively guarantees Ginkgo $12 million minimum future royalties under the profit margin sharing provisions noted below;

•to pay Ginkgo quarterly fees of $0.8 million (Partnership Payments) for a total of $12.7 million, beginning on December 31, 2018 and ending on September 30, 2022;

•to share profit margins from sales of a certain product to be developed under the Ginkgo Partnership Agreement on a 50/50 basis, subject to certain conditions, provided that net profits will be payable to Ginkgo for any quarterly period to the extent that such net profits exceed the sum of (a) quarterly interest payments due under the November 2017 Ginkgo Note and (b) Partnership Payments due in such quarter;

•to continue to collaborate on limited research and development; and

•to provide each other licenses (with royalties) to specified intellectual property for limited purposes.

The Ginkgo Partnership Agreement provides for an initial term of two years and will automatically renew for successive one-year terms thereafter unless otherwise terminated. The Company does not expect to recognize any future revenue under this arrangement.

The Company recorded the $6.1 million present value of the $12.7 million partnership payments in other liabilities (see Note 2, "Balance Sheet Details"), with the remaining $6.6 million recorded as a debt discount to be recognized as interest expense under the effective interest method over the five-year payment term. The Company also concluded the partnership payment obligation under the Ginkgo Partnership Agreement represents consideration payable to a former customer; and consequently, the present value of the partnership payments should be recorded as a reduction of cumulative revenue recognized to date from Ginkgo in the period the partnership agreement was executed. The Company reached a similar conclusion regarding the $12.0 million Ginkgo Note described below. In total, the Company recorded a $13.1 million reduction in licenses and royalties revenue and $13.1 million in notes payable and other liabilities as of and for the year ended December 31, 2017 upon execution of the Ginkgo Partnership Agreement.

In November 2017, the Company issued an unsecured promissory note in the principal amount of $12.0 million to Ginkgo (the November 2017 Ginkgo Note) in connection with the termination of the Ginkgo Collaboration Agreement and the execution of the Ginkgo Partnership Agreement. The November 2017 Ginkgo Note accrues interest at 10.5% per annum, payable monthly, and has a maturity date of October 19, 2022. The November 2017 Ginkgo Note may be prepaid in full without penalty or premium at any time, provided that certain payments have been made under the Company’s partnership agreement with Ginkgo. The November 2017 Ginkgo Note also contains customary terms, covenants and restrictions, including certain events of default after which the note may become due and payable immediately. The Company recorded the $7.0 million present value of the November 2017 Ginkgo Note as a note payable liability, and the remaining $5.0 million was recorded as a debt discount which is being accreted to interest expense over the loan term using the effective interest method.

On September 29, 2019, in connection with Ginkgo granting certain waivers under the November 2017 Ginkgo Note and the Ginkgo Partnership Agreement, (i) the Company and Ginkgo amended the November 2017 Ginkgo Note to increase the

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interest rate from 10.5% per annum to 12% per annum, beginning October 1, 2019, (ii) Ginkgo agreed to waive default interest, defer past due interest and partnership payments under the November 2017 Ginkgo Note and Ginkgo Partnership Agreement until December 15 and (iii) the Company agreed to pay a cash waiver fee of $1.3 million, payable in installments of $0.5 million on December 15, 2019 and $0.8 million on March 31, 2020. The Company accounted for this amendment as a modification and accrued the $1.3 million waiver fee in other current liabilities and a charge to interest expense during the year ended December 31, 2019. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to pay the $5.2 million past due interest, default interest on past due amounts, partnership payments and the $0.5 million waiver fee installment on December 15, 2019.

6% Convertible Notes Due 2021

In December 2018, the Company issued $60.0 million in aggregate principal amount of senior convertible notes (the 6% Convertible Notes Due 2021) for $56.2 million of net proceeds, after deducting offering expenses and placement agent and advisory fees.

The Company elected to account for the 6% Convertible Notes Due 2021 at fair value as of the issuance date. Management believes that the fair value option better reflects the underlying economics of the 6% Convertible Notes Due 2021, which contain multiple embedded derivatives. Under the fair value election, changes in fair value are reported in the consolidated statements of operations as "(Loss) gain from change in fair value of debt" in each reporting period subsequent to the issuance of the 6% Convertible Notes Due 2021.

In May, June and July 2019, the Company exchanged the 6% Convertible Notes Due 2021 for new senior convertible notes and warrants to purchase common stock. Since the Company elected the fair value accounting option for the 6% Convertible Notes and records all changes in fair value through (Loss) gain from change in fair value of debt in the consolidated statement of operations, this series of exchanges was not required to be evaluated for modification or extinguishment accounting treatment. However, the Company considered the issuance of the warrant in connection with these exchanges as compensation to the noteholders for waiving certain covenant violations during the period, and recorded a $5.3 million increase to additional paid in capital and a charge to interest expense for the fair value of the equity-classified May 15, 2019, June 24, 2019 and July 24, 2019 warrants. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant.

On November 8, 2019, the Company entered into a Securities Exchange Agreement with certain private investors (the Investors), pursuant to which the Investors purchased the 6% Convertible Notes Due 2021 from the original holder and subsequently exchanged the 6% Convertible Notes Due 2021 with the Company for new 5% Senior Convertible Notes (the Senior Convertible Notes Due 2022) having an aggregate principal amount of $66.0 million. See the Senior Convertible Notes Due 2022 section below for further information on the exchange.

The Company evaluated the Investor’s purchase of the 6% Convertible Notes Due 2021 from the original holder and subsequent exchange with the Company for the Senior Convertible Notes Due 2022 and determined the purchase and exchange met the criteria for extinguishment accounting. The Company recorded a $1.9 million loss of debt extinguishment as of December 31, 2019, determined as follows:

In thousands
Fair value at December 31, 2018	$	57,918
Less: principal paid in cash during 2019	(13,395)
Less: principal converted to common stock during 2019	(15,000)
Loss on change in fair value during 2019	18,303
Accrued interest	3,168
Carrying value of registration rights liability	5,757
Net carrying value at extinguishment	56,751
Total reacquisition price	58,640
Loss on debt extinguishment	$	1,889

Senior Convertible Notes Due 2022

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As discussed above under the 6% Convertible Notes Due 2021 section, on November 8, 2019, the Company entered into a securities exchange agreement with certain private investors (the Investors). The Investors completed the purchase of the Second Exchange Note from the current holder, and on November 15, 2019 the Company exchanged the 6% Convertible Notes Due 2021 held by the Investors for the Senior Convertible Notes Due 2022.

The Senior Convertible Notes Due 2022 are general unsecured obligations of the Company and will mature on September 30, 2022 unless earlier converted or redeemed.

The Senior Convertible Notes Due 2022 are payable in fixed monthly installments of $3.0 million from February 1, 2020 through July 1, 2020 and then $3.4 million monthly thereafter in either cash or, at the Company’s option, subject to the satisfaction of certain equity conditions, in shares of common stock at a discount to the then-current market price, subject to a price floor. The holders have the right, upon notice to the Company, to defer all or any portion of any installment amount to a future installment date. Each installment payment will reduce the principal amount under the Senior Convertible Notes Due 2022 by 90% of the amount of such installment payment.

The Senior Convertible Notes Due 2022 accrue interest at a rate of 5% per annum, and is payable on each installment date. Interest on the Senior Convertible Notes Due 2022 may be paid in either cash or, at the Company’s option, subject to the satisfaction of the equity conditions, shares of common stock at the installment conversion price. Upon the occurrence and during the continuation of an event of default, interest on the Senior Convertible Notes Due 2022 will accrue at a rate of 15% per annum.

The Company may at its option redeem the Senior Convertible Notes Due 2022, in full, at a price equal to 115% of the greater of (A) the principal amount of the Senior Convertible Notes Due 2022 being redeemed and (B) the intrinsic value of the shares of common stock underlying the principal amount of the Senior Convertible Notes Due 2022 being redeemed. In addition, the Company is required to (i) redeem the Senior Convertible Notes Due 2022 in an aggregate amount of $10.0 million following the receipt by the Company of at least $75.0 million of aggregate net cash proceeds from one or more financing transactions, at a price equal to 110% of the amount being redeemed and (ii) redeem the Senior Convertible Notes Due 2022 in an aggregate amount of $10.0 million on December 31, 2019, at a price equal to 110% of the amount being redeemed, in each case unless such redemption is deferred by the holder, and (iii) raise aggregate net cash proceeds of $30 million by December 31, 2019 and an additional $75 million by March 15, 2020 from one or more financing transactions by January 31, 2020. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to redeem $10 million of the Senior Convertible Notes Due 2022 and raise aggregate cash proceeds of $30 million on or by December 31, 2019 and a description of an amendment to certain other redemption provisions in the Senior Convertible Notes Due 2022.

The Senior Convertible Notes Due 2022 are convertible from time to time, at the election of the holders, into shares of common stock at an initial conversion price of $5.00 per share. The conversion price is subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

The Senior Convertible Notes Due 2022 contain customary terms and covenants, including (i) a restriction on the Company’s ability to incur additional indebtedness, (ii) covenants related to minimum revenue, minimum liquidity, financing activity and the conversion or exchange of existing indebtedness into equity, (iii) certain events of default, after which the holders may (A) require the Company to redeem all or any portion of their Senior Convertible Notes Due 2022 in cash at a price equal to 115% of the amount being redeemed and (B) convert all or any portion of their Senior Convertible Notes Due 2022 at a discount to the Installment conversion price and (iv) certain other events, after which the holders may convert all or any portion of their Senior Convertible Notes Due 2022 at a discount to the conversion price. See Note 15, “Subsequent Events” for further information regarding the amendment to certain conversion provisions in the Senior Convertible Notes Due 2022.

Notwithstanding the foregoing, the holders do not have the right to convert any portion of a New Note, and the Company does not have the option to pay any amount under the Senior Convertible Notes Due 2022 in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding immediately after giving effect to such conversion or payment, as applicable (the Ownership Limitation) or (b) the aggregate number of shares issued with respect to the Senior Convertible Notes Due 2022 (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed the limitation imposed by Nasdaq Listing Standard Rule 5635(d) (the Exchange Cap), unless Stockholder Approval (as defined below) has been obtained. In the event that (i) the Company is prohibited from issuing any shares of common stock under the Senior Convertible Notes Due 2022 as a result of the Ownership Limitation (other than in connection with a conversion of Senior Convertible Notes Due 2022), the related principal amount of the Senior Convertible Notes Due 2022 shall be deferred to a future installment date as determined by the holder, and (ii) after January 31, 2020, the Company is prohibited from issuing

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any shares of common stock under the Senior Convertible Notes Due 2022 as a result of the Exchange Cap, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Exchange Cap.

Pursuant to the Senior Convertible Notes Due 2022, the Company agreed to use commercially reasonable efforts to obtain from the Company’s stockholders the approval contemplated by Nasdaq Listing Standard Rule 5635(d) with respect to the issuance of shares of common stock upon conversion of, or otherwise pursuant to, the Senior Convertible Notes Due 2022 in excess of the limitation imposed by such rule, including without limitation the issuance of shares of common stock upon conversion of, or otherwise pursuant to, the Senior Convertible Notes Due 2022 in excess of the Exchange Cap (the Stockholder Approval), at an annual or special meeting of stockholders to be held on or prior to January 31, 2020. Pursuant to the Senior Convertible Notes Due 2022, if the Company does not obtain the Stockholder Approval by January 31, 2020, the Company will use best efforts to obtain the Stockholder Approval thereafter. See Note 15, “Subsequent Events” for further information regarding the amendment, forbearance and waiver to certain provisions in the Senior Convertible Notes Due 2022, including the deadline for the Company to seek the Stockholder Approval.

The Company has elected to account for the Senior Convertible Notes Due 2022 at fair value, as of the issuance date. Management believes that the fair value option better reflects the underlying economics of the Senior Convertible Notes Due 2022, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the Senior Convertible Notes Due 2022. For the year ended December 31, 2019, the Company recorded a gain of $3.8 million, which is shown as Fair Value Adjustment in the table at the beginning of this Note 4. See Note 3, "Fair Value Measurement" for information about the assumptions that the Company used to measure the fair value of the Senior Convertible Notes Due 2022.

Nikko Loan Agreements and Notes

The loans payable to Nikko Chemicals Co., Ltd. at December 31, 2019 are comprised of the following (amounts in thousands):

Description	Date Issued	Original Loan Amount		Balance at December 31, 2019		Interest Rate per Annum	Maturity Date
Nikko $5.0M Note	July 29, 2019	$	5,000	$	5,000	5.00%	December 18, 2020
Nikko $4.5M Note	December 19, 2019	4,500		4,500		2.75%	January 31, 2020
Nikko $3.9M Note	December 19, 2016	3,900		2,862		5.00%	December 1, 2029
Nikko $1.5M Note B	August 3, 2017	1,500		900		2.75%	August 1, 2020
Nikko $450K Note	December 9, 2019	450		450		2.75%	March 31, 2020
Nikko $350K Note	November 20, 2019	350		350		2.75%	January 31, 2020
Nikko $200K Capex Loan	February 1, 2019	200		171		5.00%	January 1, 2026
Nikko $500K Note	October 31, 2019	500		84		2.75%	January 10, 2020
		$	16,400	$	14,317

Nikko Loan Agreements

On July 29, 2019, the Company and Nikko entered into a loan agreement (the Nikko Loan Agreement) to make available to the Company secured loans in an aggregate principal amount of $5.0 million, to be issued in separate installments of $3.0 million and $2.0 million, respectively. On July 30, 2019, the Company borrowed the first installment of $3.0 million under the Nikko Loan Agreement and received net cash proceeds of $2.8 million, with the remaining $0.2 million being withheld by Nikko as prepayment of the interest payable on such loan through the maturity date. On August 8, 2019, the Company borrowed the remaining $2.0 million available under the Nikko Loan Agreement and received net cash proceeds of $1.9 million, with the remaining $0.1 million being withheld by Nikko as prepayment of the interest payable on such loan through the maturity date. The loans (i) mature on December 18, 2020, (ii) accrue interest at a rate of 5% per annum from and including the applicable loan date through the maturity date, which interest is required to be prepaid in full on the date of the applicable loan, and (iii) are secured by a first-priority lien on 12.8% of the Aprinnova JV interests owned by the Company.

On December 19, 2019, the Company borrowed $4.5 million from Nikko under a second secured loan agreement. The loan (i) matures on January 31, 2020, (ii) accrues interest at a rate of 2.75% per annum, and (iii) is secured by a first-priority lien on 27.2% of the Aprinnova JV interests owned by the Company. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to pay the $4.5 million loan on January 31, 2020.

Nikko Notes

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Facility Note: In December 2016, in connection with the Company's formation of its cosmetics joint venture (the Aprinnova JV) with Nikko Chemicals Co., Ltd. (Nikko), Nikko made a loan to the Company in the principal amount of $3.9 million and the Company issued a promissory note (the Nikko Note) to Nikko in an equal principal amount. The proceeds of the Nikko Note were used to satisfy the Company's remaining liabilities related to the Company's purchase of a manufacturing facility in Leland, North Carolina and related assets in December 2016, including liabilities under a promissory note in the principal amount of $3.5 million issued in connection therewith. The Nikko Note (i) accrues interest at 5% per year, (ii) has a term of 13 years, (iii) is payable in equal monthly installments of principal and interest beginning on January 1, 2017 and (iv) is secured by a first-priority lien on 10% of the Aprinnova JV interests owned by the Company. In addition, the Company is required to repay the Nikko Note with any profits distributed to the Company by the Aprinnova JV, beginning with the distributions for the fourth fiscal year of the Aprinnova JV, until the Nikko Note is fully repaid. The Nikko Note may be prepaid in full or in part at any time without penalty or premium. The Nikko Note contains customary terms and provisions, including certain events of default after which the Nikko Note may become due and payable immediately.

Aprinnova JV Working Capital Notes: In February 2017, in connection with the formation of the Aprinnova JV in December 2016, Nikko made a working capital loan to the Aprinnova JV in the principal amount of $1.5 million (the First Aprinnova Note). The First Aprinnova Note was fully repaid in January 2018. In August 2017, Nikko made a second working capital loan to the Aprinnova JV in the principal amount of $1.5 million (the Second Aprinnova Note). The Second Aprinnova Note was payable in full on August 1, 2019, with interest payable quarterly. Both notes accrue interest at 2.75% per annum. Effective July 31, 2019, the Company repaid $500,000 and agreed with Nikko to extend the term of the Second Aprinnova Note to August 1, 2020. Under the terms of the extension, the Company is required to make four quarterly principal payments of $100,000 each beginning November 1, 2019 through May 1, 2020 and a final payment of $700,000 at August 1, 2020 maturity.

Aprinnova JV Palladium Notes: In October, November and December 2019, Nikko advanced Aprinnova JV a total of $1.3 million under three separate promissory notes to purchase a palladium catalyst used in the manufacturing process at the Leland facility. These short-term notes accrue interest at 2.75% per annum and mature between January 10, 2020 and March 31, 2020. As of February 28, 2020, the total $1.3 million of note balances has been fully repaid in cash and are no longer outstanding.

Aprinnova JV CapEx Note: On February 1, 2019, the Aprinnova JV and Nikko agreed to fund Nikko’s $0.2 million share of the joint venture’s 2018 capital expenditures through an unsecured seven-year promissory note (the 2018 CapEx Note). The 2018 CapEx note (i) requires quarterly principal payments of $7,200 beginning April 1, 2019, (ii) accrues 5% simple interest per annum, and (iii) matures on January 1, 2026.

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.0 million of restricted cash, noncurrent in connection with this arrangement as of December 31, 2019 and 2018.

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5. Mezzanine Equity

Mezzanine equity at December 31, 2019 and 2018 is comprised of proceeds from common shares sold on May 10, 2016 to the Bill & Melinda Gates Foundation (the Gates Foundation). On April 8, 2016, the Company entered into a Securities Purchase Agreement with the Gates Foundation, pursuant to which the Company agreed to sell and issue 292,398 shares of its common stock to the Gates Foundation in a private placement at a purchase price per share of $17.10, the average of the daily closing price per share of the Company’s common stock on the Nasdaq Stock Market for the twenty consecutive trading days ending on April 7, 2016, for aggregate proceeds to the Company of approximately $5.0 million (the Gates Foundation Investment). The Securities Purchase Agreement includes customary representations, warranties and covenants of the parties.

In connection with the entry into the Securities Purchase Agreement, on April 8, 2016, the Company and the Gates Foundation entered into a Charitable Purposes Letter Agreement, pursuant to which the Company agreed to expend an aggregate amount not less than the amount of the Gates Foundation Investment to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria commencing in 2017. The Company is currently conducting the project. If the Company defaults in its obligation to use the proceeds from the Gates Foundation Investment as set forth above or defaults under certain other commitments in the Charitable Purposes Letter Agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party of, the Gates Foundation Investment shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, or (ii) an amount equal to $17.10 plus a compounded annual return of 10%. As of December 31, 2019, the Company's remaining research and development obligation under this arrangement was $0.4 million.

6. Stockholders’ Deficit

Shares Issuable under Convertible Notes and Convertible Preferred Stock

In connection with various debt transactions (see Note 4, "Debt"), the Company issued certain convertible notes and preferred shares that are convertible into shares of common stock as follows as of December 31, 2019, at any time at the election of each debtholder:

	Number of Shares Instrument Is Convertible into as of December 31, 2019
Senior convertible notes due 2022	13,200,000
2014 Rule 144A convertible notes	181,238
Series D preferred stock (8,280 shares outstanding at December 31, 2019)	1,943,661
	15,324,899

2014 Rule 144A Convertible Notes Exchanges

On May 10, 2019, the Company exchanged $13.5 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by certain non-affiliated investors, including accrued and unpaid interest thereon, for an aggregate of 3.5 million shares of common stock and warrants to purchase an aggregate of 1.4 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, in a private exchange.

On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Foris, including accrued and unpaid interest thereon, for 1.1 million shares of common stock and a warrant to purchase up to 0.4 million shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from issuance, in a private exchange. On August 28, 2019, the Company and Foris agreed to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share. See “August 2019 Foris Warrant Issuance” below for additional information and Note 15, “Subsequent Events” for information regarding the amendment and exercise of the warrants on January 31, 2020.

On May 15, 2019, the Company exchanged $10.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Maxwell (Mauritius) Pte Ltd for 2.5 million shares of common stock in a private exchange.

The Company issued 7.1 million shares of common stock with a fair value totaling $30.8 million based on the Company's closing stock price at the date of each exchange upon exchange of the 2014 Rule 144A Convertible Notes described above. The Company also issued warrants (collectively, the May 2019 6.50% Note Exchange warrant) to purchase a total of 1.7 million

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shares of common stock with a fair value of $3.8 million. The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the convertible notes and will be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrants were measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $4.27 - $4.54, strike price $4.56 - $5.02, volatility 96%, risk-free interest rate 2.20% - 2.26%, and expected dividend yield 0%. The warrant had a fair value of $5.9 million that was recorded as a loss of debt extinguishment. See Note 4, "Debt" for information about the accounting treatment for this debt exchange and related fair value of the warrant.

The exercise price of the warrants issued in the foregoing exchanges is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of the exercisability of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, (i) the exercisability of the warrant issued to Foris is subject to stockholder approval in accordance with Nasdaq rules and regulations, which the Company is seeking at its 2019 annual meeting of stockholders, and (ii) each other warrant provides that the Company may not affect any exercise of such warrant to the extent that, after giving effect to such exercise, the applicable holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding after giving effect to such exercise.

August 2013 Financing Convertible Note Conversion into Equity

On July 8, 2019, Wolverine exchanged $5.1 million principal and accrued and unpaid interest related to its August 2013 Financing Convertible Note for 1.8 million shares of common stock and a warrant (the July 2019 Wolverine Warrant) to purchase 1.1 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The common stock had a fair value of $5.9 million or $3.30 per share and the warrant had a fair value of $1.9 million. The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the convertible note and will be classified in equity, as the warrant is both indexed to the Company’s own stock and meets the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrant to be reclassified to an asset or liability. The fair value of the warrant was measured using the Black-Scholes-Merton option pricing model, with the following parameters: stock price $3.33, strike price $2.87, volatility 94%, risk-free interest rate 1.88%, and expected dividend yield 0%. The resulting $1.9 million fair value was recorded as a loss of debt extinguishment. See Note 4, “Debt” for additional information regarding the loss on debt extinguishment.

Pre-Delivery Shares Issued with Senior Convertible Notes Due 2022

In connection with the issuance of the Senior Convertible Notes Due 2022 on November 15, 2019, the Company issued 7.5 million shares of common stock (the Pre-Delivery Shares) to the note holders which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the note holders to sell, trade or hold, subject to certain limitations, for as long as the Senior Convertible Notes Due 2022 are outstanding. The issuance of these shares resulted in no cash proceeds to the Company. However, the Company may elect or be required to apply some or all of the value of the pre-delivered shares to satisfy periodic principal and interest payments or other repayment events. If the Pre-Delivery Shares are used in satisfaction of a payment(s) due under the Senior Convertible Notes Due 2022, the Company must provide additional shares of common stock to the note holders in order to maintain a 7.5 million share balance on deposit with the holder. The Holder will not (A) loan any Pre-Delivery shares to any third party, (B) prior to February 1, 2020 sell or otherwise transfer or dispose of any Pre-Delivery Shares to any unaffiliated third party and (C) on or after February 1, 2020 sell or otherwise transfer or dispose of any Pre-Delivery Shares to any unaffiliated third party if the amount of such sales, transfers or dispositions on any day would exceed 10% of the composite trading volume (as reported on Bloomberg) of the Common Stock on such day. Within ten business days following redemption or repayment of in full the Senior Convertible Notes Due 2022 and the satisfaction or discharge by the Company of all outstanding Company obligations hereunder, the Holder shall deliver 7.5 million shares of the Company’s common stock to the Company.

The Company concluded the Pre-Delivery Shares provision is a freestanding instrument that is legally detachable and separately exercisable from the Senior Convertible Notes Due 2022 and will be classified in equity as the common shares issued is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the Pre-Delivery Shares within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the shares to be reclassified to an asset or liability. The Company measured the issue date fair value of the Pre-Delivery Shares under an expected borrowing cost approach using a 9.75% annual

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borrowing rate over an 18-month estimated repayment term for the Senior Convertible Notes Due 2022. The resulting $4.2 million fair value was recorded in equity as additional paid in capital with an offset to the fair value of the Senior Convertible Notes Due 2022. See Note 3, “Fair Value Measurements” for further information regarding the fair value measurement and accounting for this freestanding instrument.

Series B Preferred Stock Beneficial Ownership Limitation

On October 24, 2019, the Company filed a certificate of amendment (the Certificate of Amendment) to the Certificate of Designation (the Certificate of Designation) relating to the Company’s Series B 17.38% Convertible Preferred Stock, par value $0.0001 per share (the Series B Preferred Stock), with the Secretary of State of Delaware. The Company had originally filed the Certificate of Designation on May 8, 2017, pursuant to which the conversion of the Series B Preferred Stock was subject to a beneficial ownership limitation of 4.99%, or such other percentage as determined by the holder, not to exceed 9.99% of the number of shares of the Company’s common stock outstanding after giving effect to such conversion (the Beneficial Ownership Limitation). In addition, pursuant to the Certificate of Designation, each share of Series B Preferred Stock automatically converted on October 9, 2017, subject to the Beneficial Ownership Limitation.

Pursuant to the Certificate of Amendment, the Beneficial Ownership Limitation was eliminated, permitting the conversion of any outstanding shares of Series B Preferred Stock, the conversion of which was previously prevented by the Beneficial Ownership Limitation. As such, on October 24, 2019, the remaining 6,376.28 shares of Series B Preferred Stock, which were all held by Foris, automatically converted into 1.0 million shares of the Company’s common stock.

April 2019 Private Placements

On April 16, 2019, the Company sold and issued to Foris 6.7 million shares of common stock at a price of $2.87 per share, for aggregate proceeds to the Company of $20.0 million (the Foris Investment), as well as a warrant (the April 2019 Foris Warrant) to purchase up to 5.4 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance, in a private placement, for aggregate cash proceeds to the Company of $20.0 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

On April 26, 2019, the Company sold and issued (i) 2.8 million shares of common stock at a price of $5.12 per share, as well as a warrant (the April 2019 PIPE Warrants) to purchase up to 4.0 million shares of common stock at an exercise price of $5.12 per share, with an exercise term of two years from issuance, to Foris and (ii) an aggregate of 2.0 million shares of common stock at a price of $4.02 per share, as well as warrants (the April 2019 PIPE Warrants) to purchase up to an aggregate of 1.6 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to certain other non-affiliated investors, in each case in private, for aggregate cash proceeds to the Company of $15.0 million from Foris and $8.2 million from non-affiliated investors, for a total of $23.2 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

On April 29, 2019, the Company sold and issued (i) 0.9 million shares of common stock at a price of $4.76 per share, as well as warrants (the April 2019 PIPE Warrants) to purchase up to an aggregate of 1.2 million shares of common stock at an exercise price of $4.76 per share, with an exercise term of two years from issuance, to affiliates of Vivo Capital LLC (Vivo), an entity affiliated with director Frank Kung and which owns greater than five percent of our outstanding common stock and has the right to designate one member of the Company’s Board of Directors) and (ii) an aggregate of 0.3 million shares of common stock at a price of $4.02 per share, as well as warrants (the April 2019 PIPE Warrants) to purchase up to an aggregate of 0.3 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to certain other non-affiliated investors, in each case in private placements, for aggregate cash proceeds to the Company of $4.5 million from Vivo and $1.3 million from non-affiliated investors, for a total of $5.8 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

On May 3, 2019, the Company sold and issued 1.2 million shares of common stock at a price of $4.02 per share, as well as a warrant (the April 2019 PIPE Warrants) to purchase up to 1.0 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to a non-affiliated investor in a private placement, for aggregate cash proceeds to the Company of $5.0 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

The exercise price of the warrants issued in the foregoing private placements is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month

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anniversary of issuance of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, in connection with the foregoing private placements, the Company agreed not to effect any exercise or conversion of any Company security, and the investors agreed not to exercise or convert any portion of any Company security, to the extent that after giving effect to such exercise or conversion, the applicable investor, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding immediately after giving effect to such exercise or conversion, and the warrant contained a similar limitation. The Company obtained stockholder approval for Foris to exceed such limitation in accordance with Nasdaq rules and regulations at its annual meeting of stockholders on November 19, 2019.

See Note 15, “Subsequent Events” for information regarding the amendment and exercise of certain April 2019 PIPE Warrants on January 31, 2020.

November 2018 DSM Securities Purchase Agreement – Related Party

On November 20, 2018, the Company issued 1,643,991 shares of common stock (the DSM Shares) at $3.68 per share to DSM in a private placement pursuant to a securities purchase agreement, dated November 19, 2018, between the Company and DSM (the DSM SPA), in consideration of certain agreements of DSM set forth in the Supply Agreement Amendment described in Note 9, "Revenue Recognition". The Company also agreed to pay DSM the difference between the DSM SPA purchase price of $4.41 and the closing share price of the Company's common stock on March 28, 2019, multiplied by 1,643,991 million. At inception, the Company recorded a $1.2 million derivative liability for the difference between $4.41 and the Company’s closing stock price on November 20, 2018. At December 31, 2018 fair value based on the Company’s closing stock price was $1.8 million, resulting in a $0.6 million loss from change in fair value of derivative instruments for the year ended December 31, 2018. At March 28, 2019, the Company's stock price was $2.10, and the Company owed DSM $3.8 million in connection with this agreement. Pursuant to the DSM SPA, the Company agreed to file a registration statement providing for the resale by DSM of the DSM Shares and to use commercially reasonable efforts to (i) cause such registration statement to become effective within 181 days following the date of the DSM SPA and (ii) keep such registration statement effective until DSM does not own any DSM Shares or the DSM Shares are eligible for resale under Rule 144 without regard to volume limitations. See Note 10, "Related Party Transactions" for additional information about the accounting for this transaction and other November 2018 transactions with DSM. In April 2019, in connection with the assignment by the Company of its rights under the Value Sharing Agreement (see Note 9, "Revenue Recognition"), the Company satisfied its obligation under the Supply Agreement Amendment relating to the difference between $4.41 and the price of the Company’s common stock on March 28, 2019.

Warrants

The Company issues warrants in certain debt and equity transactions in order to facilitate raising equity capital or reduce borrowing costs. In connection with various debt and equity transactions (see Note 4, "Debt" and below), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrant activity for the year ended December 31, 2019:

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Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2018	Additional Warrants Issued	Exercises	Expiration	Exercise Price per Share of Warrants Exercised		Number Outstanding as of December 31, 2019	Exercise Price per Share as of December 31, 2019
Foris LSA warrants	2019	August 14, 2021	—	3,438,829	—	—	$	—	3,438,829	$2.87
November 2019 Foris warrant	2019	November 27, 2021	—	1,000,000	—	—	$	—	1,000,000	$3.87
August 2019 Foris warrant	2019	August 28, 2021	—	4,871,795	—	—	$	—	4,871,795	$3.90
April 2019 PIPE warrants	2019	April 6, 2021, April 29, 2021 and May 3, 2021	—	8,084,770	—	—	$	—	8,084,770	$3.90/$4.76/$5.02
April 2019 Foris warrant	2019	April 16, 2021	—	5,424,804	—	—	$	—	5,424,804	$2.87
September and November 2019 Investor Credit Agreement warrants	2019	September 10, 2021 and November 14, 2021	—	5,233,551	—	—	$	—	5,233,551	$3.87/$3.90
Naxyris LSA warrants	2019	October 28, 2021	—	2,000,000	—	—	$	—	2,000,000	$2.87
October 2019 Naxyris warrant	2019	October 28, 2021	—	2,000,000	—	—	$	—	2,000,000	$3.87
May-June 2019 6% Note Exchange warrants	2019	May 15, 2021 and June 24, 2021	—	2,181,818	—	—	$	—	2,181,818	$2.87/$5.12
May 2019 6.50% Note Exchange warrants	2019	May 10, 2021 and May 14, 2021	—	1,744,241	—	—	$	—	1,744,241	$3.90/$5.02
July 2019 Wolverine warrant	2019	July 8, 2021	—	1,080,000	—	—	$	—	1,080,000	$2.87
August 2018 warrant exercise agreements	2018	May 17, 2020 and May 20, 2020	12,097,164	—	—	—	$	—	12,097,164	$2.87/$7.52
April 2018 warrant exercise agreements	2018	July 12, 2019	3,616,174	—	—	(3,616,174)	$	—	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,244,820	—	(166,664)	—	$	2.87000	6,078,156	$2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	0.00015	3,968,116	$2.87
May 2017 dilution warrants	2017	July 10, 2022	47,978	4,795,924	(1,758,009)	—	$	0.00015	3,085,893	$0.0015
August 2017 dilution warrants	2017	May 23, 2023	—	3,028,983	—	—	$	—	3,028,983	$0.0001
February 2016 related party private placement	2016	February 12, 2021	171,429	—	—	—	$	—	171,429	$0.15
July 2015 related party debt exchange	2015	July 29, 2020 and July 29, 2025	133,334	—	—	—	$	—	133,334	$0.15
July 2015 private placement	2015	July 29, 2020	81,197	—	(8,547)	—	$	0.15000	72,650	$0.15
July 2015 related party debt exchange	2015	July 29, 2020	58,690	—	—	—	$	—	58,690	$0.15
July 2015 related party debt exchange	2015	July 29, 2020	471,204	245,558	(716,762)	—	$	0.15000	—	$	—
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$160.05
			26,891,512	45,130,273	(2,649,982)	(3,616,174)	$	0.22166	65,755,629

For information regarding warrants issued or exercised subsequent to December 31, 2019, see Note 15, “Subsequent Events”.

Due to certain down-round adjustments to other equity-related instruments during the year ended December 31, 2019, approximately 8.1 million shares became available under the May 2017 and August 2017 dilution warrants and the Temasek Funding Warrant (July 2015 related party debt exchange warrant in the table above). Approximately 2.6 million shares were exercised under the May 2017 cash and dilution warrants and the Temasek Funding Warrant during the year ended December 31, 2019 and resulted in zero proceeds to the Company. Also, a portion of the warrant exercises occurring during 2019 was net share settled, and as a result only 2.5 million shares were legally issued upon exercise of warrants during the year ended December 31, 2019.

Warrant Issuances, Exercises and Modifications in the Year Ended December 31, 2019

July 2019 Foris Credit Agreement Warrant Modification

In connection with the entry into the July Foris Credit Agreement on July 10, 2019 (see Note 4, “Debt”), the Company and Foris amended a warrant to purchase up to 4.9 million shares of common stock issued to Foris on August 17, 2018 to reduce the exercise price of such warrant from $7.52 per share to $2.87 per share. The warrant modification was measured on a before and after modification basis using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.21, strike price $2.87, volatility 124%, risk-free interest rate 1.82%, term 0.9 years, and expected dividend yield 0%. The warrant had an incremental fair value of $4.0 million, which was accounted for as an increase to additional paid in capital and a debt discount to the $16 million July Foris Notes. See Note 4, “Debt” for additional information regarding the debt discount recorded in connection with the modification of the warrant.

6% Convertible Note Exchange Warrants and Modification

In connection with the May 15, 2019 and June 24, 2019 6% Convertible Note Exchanges (see Note 4, “Debt”), the Company issued warrants (the May-June 2019 6% Note Exchange Warrants) to purchase up to 2.0 million and 0.2 million shares of common stock, respectively, at an exercise price of $5.12 per share, with an exercise term of two years from issuance.

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The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. The holders may not exercise the warrants, and the Company may not affect any exercise of the warrants, to the extent that, after giving effect to such exercise, the applicable holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding after giving effect to such exercise.

The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the convertible notes and should be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The fair value of the warrants totaled $4.4 million and were measured using the Black-Scholes-Merton option pricing model with the following parameters: 94% - 96% volatility, 1.72% - 2.16% risk-free interest rate, $3.55 - $4.39 issuance-date stock price, term 2.0 years, and 0% expected dividend yield. The Company concluded that the $4.4 million fair value of the equity-classified May 15, 2019 and June 24, 2019 warrants should be recorded as an increase to additional paid in capital and a charge to interest expense in the statement of operations at the date of issuance. See Note 4, “Debt” for additional information regarding the accounting for the fair value of these warrants.

Further, on July 24, 2019, Company exchanged the May 15, 2019 warrant to purchase up to 2.0 million shares of common stock, for a new warrant to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from May 15, 2019. The exchange warrant has substantially identical terms as the original warrant issued on May 15, 2019, except that the exercise price was reduced from $5.12 to $2.87 per share. The warrant modification was measured on a before and after modification basis using the Black-Scholes-Merton option pricing model with the following parameters: strike price $2.87, volatility 93%, risk-free interest rate 1.86%, term 1.8 years, and expected dividend yield 0%; and resulted in $0.9 million of incremental fair value. The Company concluded that the increase in the fair value of the exchange warrant should be recorded as an increase to additional paid in capital and a charge to interest expense in the statement of operations at the date of modification. See Note 4, “Debt” for additional information regarding the charge to interest expense in connection with the fair value of this warrant.

Foris LSA Warrant Issuances

In connection with the entry into the LSA Amendment and Waiver (see Note 4, “Debt”), on August 14, 2019 the Company issued to Foris a warrant (the Foris LSA Warrant) to purchase up to 1.4 million shares of Common Stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. Pursuant to the terms of the warrant, Foris may not exercise the LSA Warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company obtained at its 2019 annual meeting of stockholders on November 19, 2019.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the LSA Amendment and Waiver and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.59, strike price $2.87, volatility 94%, risk-free interest rate 1.58%, term 2.0 years, and expected dividend yield 0%. The warrant had a fair value of $2.9 million which was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the fair value of this warrant.

In connection with October 2019 LSA Amendment (see Note 4, “Debt”), on October 10, 2019, the Company issued a warrant (the October 2019 Foris LSA Warrant) to purchase 2.0 million shares of common stock, at an exercise price of $2.87 per share, with an exercise term of two years from issuance. Also, in connection with additional borrowings under the October 28, 2019 A&R LSA, on November 27, 2019, the Company issued a warrant (the November 2019 Foris Warrant) to purchase 1.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance. The exercise price of the warrants are subject to standard adjustments but do not contain any anti-dilution protection, and the

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warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrants. In addition, Foris may not exercise the warrants to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company obtained at its 2019 annual meeting of stockholders on November 19, 2019.

The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the October 2019 LSA Amendment and A&R LSA and will be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrants were measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.65 and $4.00, strike price $2.87 and $3.87, volatility 94%, risk-free interest rate 1.63% and expected dividend yield 0%. The October 2019 Foris LSA Warrant had a fair value of $4.1 million and was recorded as an increase to additional paid in capital and as a loss on debt extinguishment as a non-cash fee paid to the lender. The November 2019 Foris Warrant had a fair value of $2.1 million and was recorded as an increase to additional paid in capital and additional debt discount to be amortized over the remaining term of the A&R LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the fair value of each warrant. See Note 15, “Subsequent Events” for information regarding the amendment and exercise of the October 2019 Foris LSA Warrant on January 31, 2020.

Naxyris LSA Warrant Issuances

In connection with the entry into the Naxyris Loan Agreement (see Note 4, “Debt”), on August 14, 2019 the Company issued to Naxyris a warrant (the Naxyris LSA Warrant) to purchase up to 2.0 million shares of the Company’s common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments and permits “cashless” or “net” exercise any time after issuance.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Naxyris Loan Facility and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.59, strike price $2.87, volatility 94%, risk-free interest rate 1.58%, term 2.0 years, and expected dividend yield 0%. The warrant had a $4.0 million fair value and a $3.0 million relative fair value after allocating the Naxyris Loan Facility proceeds to the fair value of an embedded mandatory redemption feature contained in the Naxyris Loan Facility. The $3.0 million relative fair value of the Naxyris LSA Warrant was recorded as an increase to additional paid in capital and a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the relative fair value of this warrant.

Also, in connection with the entry into the A&R Naxyris LSA, on October 28, 2019 the Company issued to Naxyris a warrant (the October 2019 Naxyris Warrant) to purchase up to 2.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments and permits “cashless” or “net” exercise any time after issuance.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Naxyris Loan Facility and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.69, strike price $3.87, volatility 94%, risk-free interest rate 1.64%, term 2.0 years, and expected dividend yield 0%. The warrant had a $3.6 million fair value and a $2.8 million relative fair value after allocating the October 2019 Naxyris Loan proceeds to the fair value of the embedded mandatory redemption feature contained in the October 2019 Naxyris Loan. The $2.8 million relative fair value of the October 2019 Naxyris Warrant was recorded as an increase to additional paid in capital and as a loss on debt extinguishment as a non-cash fee paid to the lender. See Note 4, “Debt” for further information regarding the accounting treatment for the relative fair value of this warrant.

August 2019 Foris Warrant Issuance

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In connection with the entry into the August 2019 Foris Credit Agreement (see Note 4, “Debt”), on August 28, 2019 the Company issued to Foris a warrant (the August 2019 Foris Warrant) to purchase up to 4.9 million shares of Common Stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permits “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. In addition, Foris may not exercise the warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company obtained at its 2019 annual meeting of stockholders on November 19, 2019.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Foris $19 Million Note and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.67, strike price $3.90, volatility 94%, risk-free interest rate 1.50%, term 2.0 years, and expected dividend yield 0%. The warrant had a $8.7 million fair value and a $5.2 million relative fair value after allocating the Foris $19 Million Note proceeds to the fair value of an embedded mandatory redemption feature contained in the Foris $19 Million Note. See Note 4, “Debt” for further information regarding the accounting treatment for the relative fair value of this warrant.

Also, on August 28, 2019 in connection with the entry into the August 2019 Foris Credit Agreement, the Company and Foris amended the warrant to purchase up to 3.9 million shares of common stock issued to Foris on April 26, 2019 to reduce the exercise price of such warrant from $5.12 per share to $3.90 per share, and amended the warrant to purchase up to 0.4 million shares of common stock issued to Foris on May 14, 2019 to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share (see above under “Private Placements” for more information regarding these warrants). The warrant modifications were measured on a before and after modification basis using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.67, strike price $3.90, volatility 98% - 100%, risk-free interest rate 1.50%, term 1.7 years, and expected dividend yield 0%, resulting in $1.1 million of incremental fair value, which was accounted for as an increase to additional paid in capital and a debt discount to the Foris $19 Million Note. See Note 4, “Debt” for additional information regarding the debt discount recorded in connection with the modification of these warrants. See Note 15, “Subsequent Events” for information regarding the amendment and exercise of the August 2019 Foris Warrant on January 31, 2020.

September and November 2019 Investor Credit Agreements Warrants Issuances

In connection with the entry into the Investor Credit Agreements (see Note 4, “Debt”), on September 10, 2019, the Company issued to the Investors warrants (the Investor Warrants) to purchase up to an aggregate of 3.2 million shares of common stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. The exercise price of the warrants is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, no Investor may exercise its warrant to the extent that, after giving effect to such exercise, such Investor, together with its affiliates, would beneficially own in excess of 9.99% of the number of shares of common stock outstanding after giving effect to such exercise. In addition, the Company agreed to file a registration statement providing for the resale by the Investors of the shares of common stock underlying the warrants with the SEC within 60 days following the date of the issuance of the warrants and to use commercially reasonable efforts to (i) cause such registration statement to become effective within 120 days following the date of the issuance of the warrants and (ii) keep such registration statement effective until the Investors no longer beneficially own any such shares of common stock or such shares of common stock are eligible for resale under Rule 144 under the Securities Act without regard to volume limitations. If the Company fails to file the registration statement by the filing deadline or the registration statement is not declared effective by the effectiveness deadline, or the Company fails to maintain the effectiveness of the registration statement as required by the warrants, then the exercise price of the warrants will be reduced by 10%, and by an additional 5% if such failure continues for longer than 90 days, subject to an exercise price floor of $3.31 per share, provided that upon the cure by the Company of such failure, the exercise price of the warrants will revert to $3.90 per share.

In connection with the November 2019 Schottenfeld CSA, on November 14, 2019, the Company warrants (the November 2019 Schottenfeld CSA Warrants) to purchase an aggregate of 2.0 million shares of common stock at an exercise price of $3.87 per share, with an exercise term of 2 years from issuance. In connection with the warrant issuance, the Company will be

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required to pay the November 2019 Schottenfeld CSA Warrants holders and the Investor Warrants holders a fee if the Company issues equity securities in connection with the $50 million or greater financing provision that have an issue, conversion or exercise price of less than $3.90 or $3.87 per share, respectively. In such case, the fee will be the difference between the exercise price of such warrants (i.e., $3.90 or $3.87) and the issue, conversion or exercise price of the equity securities issued in the $50 million or greater financing, times the total number of warrants issued to such investors in November 2019 and September 2019. See Note 15, “Subsequent Events” for information regarding the amendment of the Investor Warrants and the November 2019 Schottenfeld CSA Warrants on February 28, 2020.

The Company concluded the Investor Warrants and the November 2019 Schottenfeld CSA Warrants are freestanding instruments that are legally detachable and separately exercisable from the underlying debt host instruments and should be classified and accounted for as a liability as the warrants contain certain price and share count adjustment protection, and other modification protection provisions that cause the warrants to fail the fixed-for-fixed criterion, and thus, are not considered indexed to the Company’s stock. Accordingly, the Company has accounted for the Investor Warrants and November 2019 Schottenfeld CSA Warrants as a liability and will subsequently remeasure to fair value at each reporting period with changes in fair value recorded in the statement of operations. The warrants were measured using the Black-Scholes-Merton option pricing model with the following parameters as of the September 10, 2019 and November 14, 2019 issuance dates: stock price $4.56 and $3.89, strike price $3.90 and $3.87, volatility 94% and 95%, risk-free interest rate 1.67% and 1.58%, term 2 years, and expected dividend yield 0%. The warrants had an initial fair value of $7.9 million and $4.0 million, respectively and were recorded as derivative liabilities with an offset to either debt discount or loss on debt extinguishment (as a non-cash fee paid to the lender). See Note 3, “Fair Value Measurements” for information regarding the subsequent fair value measurement for this liability classified warrant and see Note 4, “Debt” for further information regarding the initial accounting treatment of the offsetting debt discount or loss on debt extinguishment.

Standstill Agreement

In connection with the September 10, 2019 entry into the Investor Credit Agreements discussed in Note 4, “Debt” and the issuance of the Investor Warrants discussed in the "September and November 2019 Investor Credit Agreements Warrants Issuances " section above, the Company and the Investors entered into a Standstill Agreement (the Investor Standstill Agreement), pursuant to which the Investors agreed that, until the earliest to occur of (i) the Investors no longer beneficially owning any shares underlying the warrants, (ii) the Company entering into a definitive agreement involving the direct or indirect acquisition of all or a majority of the Company’s equity securities or all or substantially all of the Company’s assets or (iii) a person or group, with the prior approval of the Company’s Board of Directors (the Board), commencing a tender offer for all or a majority of the Company's equity securities, neither the Investors nor any of their respective affiliates (together, the Investor Group) will (without the prior written consent of the Board), among other things, (a) acquire any loans, debt securities, equity securities, or assets of the Company or any of its subsidiaries, or rights or options with respect thereto, except that the Investor Group shall be permitted to (y) purchase the shares underlying the warrants pursuant to the exercise of the warrants and (z) acquire beneficial ownership of up to 6.99% of the Company's common stock, or (b) make any proposal, public announcement, solicitation or offer with respect to, or otherwise solicit, seek or offer to effect, or instigate, encourage, or assist any third party with respect to: (1) any business combination, merger, tender offer, exchange offer, or similar transaction involving the Company or any of its subsidiaries; (2) any restructuring, recapitalization, liquidation, or similar transaction involving the Company or any of its subsidiaries; (3) any acquisition of any of the Company’s loans, debt securities, equity securities or assets, or rights or options with respect thereto; or (4) any proposal to seek representation on the Board or otherwise seek to control or influence the management, Board, or policies of the Company, in each case subject to certain exceptions.

May 2017 Warrants

In May 2017, the Company issued 14,768,380 shares of common stock in the aggregate to certain investors (collectively, the May 2017 Cash Warrants). The exercise price of the May 2017 Cash Warrants is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following the issuance of such warrants at a per share price less than the then-current exercise price of the May 2017 Cash Warrants, subject to certain exceptions. As of December 31, 2019, the exercise prices of the May 2017 Cash Warrants were $2.87 per share, and 6,078,156 of May 2017 Cash Warrants were unexercised.

In addition to the May 2017 Cash Warrants, the Company issued to each investor a warrant, with an exercise price of $0.0015 per share (collectively, the May 2017 Dilution Warrants), to purchase a number of shares of common stock sufficient to provide the investor with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the May 2017 Dilution Period at a per share price less than $2.87. As of December 31, 2019, the May 2017 Dilution Warrants were exercisable for an aggregate of 3,085,893 shares.

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The May 2017 Warrants each have a term of five years from the date such warrants initially became exercisable on July 10, 2017. The May 2017 Cash Warrants are freestanding financial instruments and upon adoption of ASU 2017-11 on January 1, 2019 are no longer accounted for as derivative liabilities, but are classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company reclassified the derivative balance at December 31, 2018 to equity at the January 1, 2019 adoption date.

August 2017 DSM Offering – Related Party

On August 7, 2017, the Company issued and sold the following securities to DSM in a private placement (August 2017 DSM Offering):

•25,000 shares of Series B Preferred Stock (August 2017 DSM Series B Preferred Stock) at a price of $1,000 per share;

•a warrant to purchase 3,968,116 shares of common stock at an initial exercise price of $6.30 per share expiring in five years (August 2017 DSM Cash Warrant); and

•the August 2017 DSM Dilution Warrant (as described below).

Net proceeds to the Company were $25.9 million after payment of offering expenses and the allocation of total fair value received to the elements in the arrangement.

The exercise price of the August 2017 DSM Cash Warrant is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following August 7, 2017 (DSM Dilution Period) at a per share price less than the then-current exercise price of the August 2017 DSM Cash Warrant, subject to certain exceptions. As of December 31, 2019, the exercise price of the August 2017 DSM Cash Warrant was $2.87 per share, and 3,968,116 of May 2017 Cash Warrants were unexercised. The August 2017 DSM Dilution Warrants are freestanding financial instruments and upon adoption of ASU 2017-11 on January 1, 2019 are no longer accounted for as derivative liabilities, but are classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company reclassified the derivative balance at December 31, 2018 to equity at the January 1, 2019 adoption date.

The August 2017 DSM Dilution Warrant allows DSM to purchase a number of shares of common stock sufficient to provide DSM with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the DSM Dilution Period at a per share price less than $2.87. The August 2017 DSM Dilution Warrant expires five years from the date it is initially exercisable.

In connection with the August 2017 DSM Offering, the Company and DSM also entered into an amendment to the stockholder agreement dated May 11, 2017 (DSM Stockholder Agreement) between the Company and DSM (Amended and Restated DSM Stockholder Agreement). Under the DSM Stockholder Agreement, DSM was granted the right to designate one director selected by DSM, subject to certain restrictions and a minimum beneficial ownership level of 4.5%, to the Board. Furthermore, DSM has the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. Pursuant to the DSM Stockholder Agreement, DSM agreed not to sell or transfer any of the Series B Preferred Stock or warrants purchased by DSM, or any shares of common stock issuable upon conversion or exercise thereof, other than to its affiliates, without the consent of the Company through May 2018 and to any competitor of the Company thereafter. DSM also agreed that, subject to certain exceptions, until three months after there is no DSM director on the Board, DSM will not, without the prior consent of the Board, acquire common stock or rights to acquire common stock that would result in DSM beneficially owning more than 33% of the Company’s outstanding voting securities at the time of acquisition. The Amended and Restated DSM Stockholder Agreement provides that (i) DSM has the right to designate a second director to the Board, subject to certain restrictions and a minimum beneficial ownership level of 10%, and (ii) the shares of common stock issuable upon conversion or exercise of the securities purchased by DSM in the August 2017 DSM Offering are (a) entitled to the registration rights provided for in the DSM Stockholder Agreement and (b) subject to the transfer restrictions set forth in the DSM Stockholder Agreement.

August 2017 Vivo Offering – Related Party

On August 3, 2017, the Company issued and sold 12,958 shares of Series D Preferred Stock at a price of $1,000 per share along with other securities to Vivo in a private placement (August 2017 Vivo Offering), resulting in net proceeds to the Company of $24.8 million after payment of offering expenses. In the third quarter of 2018 Vivo converted 4,678 shares of August 2017 Offerings Series D Preferred Stock and the Company recognized a $6.8 million deemed dividend for the

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unamortized discounts created from the allocation of proceeds, as a reduction to Additional Paid in Capital and increasing net loss attributable to Amyris, Inc. common stockholders. At December 31, 2019 and 2018, 8,280 shares of Series D Preferred Stock were outstanding. The conversion of the Series D Preferred Stock is subject to a beneficial ownership limitation of 9.99% (August 2017 Vivo Offering Beneficial Ownership Limitation), which limitation may be waived by the holders on 61 days’ prior notice.

Each share of Series D Preferred Stock has a stated value of $1,000 and, subject to the August 2017 Vivo Offering Beneficial Ownership Limitation, is convertible at any time, at the option of the holders, into common stock at a conversion price of $4.26 per share. The Series D Conversion Rate is subject to adjustment in the event of any dividends or distributions of the common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

Prior to declaring any dividend or other distribution of its assets to holders of common stock, the Company shall first declare a dividend per share on the Series D Preferred Stock equal to $0.0001 per share. In addition, the Series D Preferred Stock will be entitled to participate with the common stock on an as-converted basis with respect to any dividends or other distributions to holders of common stock. There were no dividends declared as of December 31, 2019 or 2018.

Unless and until converted into common stock in accordance with its terms, the Series D Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Series D Preferred Stock. The Series D Preferred Stock is classified as permanent equity, as the Company controls all actions or events required to settle the optional conversion feature in shares.

In the event of a Fundamental Transaction, the holders of the Series D Preferred Stock will have the right to receive the consideration receivable as a result of such Fundamental Transaction by a holder of the number of shares of common stock for which the Series D Preferred Stock is convertible immediately prior to such Fundamental Transaction (without regard to whether such Series D Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock. A Fundamental Transaction is defined in the Certificate of Designation of Preferences, Rights and Limitations relating to the Series D Preferred Stock as any of the following: (i) merger with or consolidation into another legal entity; (ii) sale, lease, license, assignment, transfer or other disposition of all or substantially all of the Company’s assets in one or a series of related transactions; (iii) purchase offer, tender offer or exchange offer of the Company’s common stock pursuant to which holders of the Company’s common stock are permitted to sell, tender or exchange their shares for other securities, cash or property and has been accepted by the holders of 50% or more of the outstanding common stock; (iv) reclassification, reorganization or recapitalization of the Company’s stock; or (v) stock or share purchase agreement that results in another party acquiring more than 50% of the Company’s outstanding shares of common stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series D Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder of common stock would receive if the Series D Preferred Stock were fully converted to common stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series D Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock.

In connection with the August 2017 Vivo Offering, the Company and Vivo also entered into a Stockholder Agreement (Vivo Stockholder Agreement) setting forth certain rights and obligations of Vivo and the Company. Pursuant to the Vivo Stockholder Agreement, Vivo will have the right, subject to certain restrictions and a minimum beneficial ownership level of 4.5%, to (i) designate one director selected by Vivo to the Board and (ii) appoint a representative to attend all Board meetings in a nonvoting observer capacity and to receive copies of all materials provided to directors, subject to certain exceptions. Furthermore, Vivo will have the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. Vivo agreed not to sell or transfer any of the shares of common stock, Series D Preferred Stock or warrants purchased by Vivo in the August 2017 Vivo Offering, or any shares of common stock issuable upon conversion or exercise thereof, other than to its affiliates, without the consent of the Company through August 2018 and to any competitor of the Company thereafter. Vivo also agreed that, subject to certain exceptions, until the later of (i) three years from the closing of the August 2017 Vivo Offering and (ii) three months after there is no Vivo director on the Board, Vivo will not, without the prior consent of the Board, acquire common stock or rights to acquire common stock that would result in Vivo beneficially owning more than 33% of the Company’s outstanding voting securities at the time of acquisition. Under the Vivo Stockholder Agreement, the Company agreed to use its commercially reasonable efforts to register, via one or more registration statements filed with the SEC under the Securities Act, the shares of common stock purchased in the August 2017 Vivo Offering as well as the shares of common stock issuable upon conversion or exercise of the Series D Preferred Stock and warrants purchased by Vivo in the August 2017 Vivo Offering.

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For information regarding issuances of equity securities subsequent to December 31, 2019, see Note 15, “Subsequent Events”.

Right of First Investment to Certain Investors

In connection with investments in the Company has granted certain investors, including Vivo and DSM, a right of first investment if the Company proposes to sell securities in certain financing transactions. With these rights, such investors may subscribe for a portion of any such new financing and require the Company to comply with certain notice periods, which could discourage other investors from participating in, or cause delays in its ability to close, such a financing.

7. Net Loss per Share Attributable to Common Stockholders

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, convertible preferred stock, convertible promissory notes and common stock warrants, using the treasury stock method or the as converted method, as applicable. For the year ended December 31, 2018, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss were the same for those years.

The Company follows the two-class method when computing net loss per common share when shares are issued that meet the definition of participating securities. The two-class method requires income available to common stockholders for the period to be allocated between common stock and participating securities based upon their respective rights to receive dividends as if all income for the period had been distributed. The two-class method also requires losses for the period to be allocated between common stock and participating securities based on their respective rights if the participating security contractually participates in losses. The Company’s convertible preferred stock are participating securities as they contractually entitle the holders of such shares to participate in dividends and contractually require the holders of such shares to participate in the Company’s losses.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders:

Years Ended December 31, (In thousands, except shares and per share amounts)	2019		2018
Numerator:
Net loss attributable to Amyris, Inc.	$	(242,767)	$	(230,235)
Less deemed dividend to preferred shareholder on issuance and modification of common stock warrants	(34,964)		—
Less deemed dividend related to proceeds discount upon conversion of Series D preferred stock	—		(6,852)
Add: losses allocated to participating securities	7,380		13,991
Net loss attributable to Amyris, Inc. common stockholders, basic	(270,351)		(223,096)
Adjustment to losses allocated to participating securities	137		—
Gain from change in fair value of derivative instruments	(4,963)		—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(275,177)	$	(223,096)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	101,370,632		60,405,910
Basic loss per share	$	(2.67)	$	(3.69)
Weighted-average shares of common stock outstanding	101,370,632		60,405,910
Effect of dilutive common stock warrants	(74,057)		—
Weighted-average common stock equivalents used in computing net income (loss) per share of common stock, diluted	101,296,575		60,405,910
Diluted loss per share	$	(2.72)	$	(3.69)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

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Years Ended December 31,	2019	2018
Period-end common stock warrants	59,204,650	25,986,370
Convertible promissory notes(1)	13,381,238	13,703,162
Period-end stock options to purchase common stock	5,620,419	5,392,269
Period-end restricted stock units	5,782,651	5,294,848
Period-end preferred shares on an as-converted basis	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted net loss per share	85,932,619	53,332,381

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⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect at the respective year-end. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

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8. Commitments and Contingencies

Guarantor Arrangements

The Company has agreements whereby it indemnifies its executive officers and directors for certain events or occurrences while the executive officer or director is serving in his or her official capacity. The indemnification period remains enforceable for the executive officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of December 31, 2019 and 2018.

The Foris LSA debt facility (see Note 4, "Debt") is collateralized by first-priority liens on substantially all of the Company's assets, including Company intellectual property, other than certain Company intellectual property licensed to DSM and the Company's shares of Aprinnova. Certain of the Company’s subsidiaries have guaranteed the Company’s obligations under the Foris LSA.

The obligations of the Company under the Naxyris note (see Note 4, "Debt") are (i) guaranteed by the Subsidiary Guarantors and (ii) secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors (the Collateral), junior in payment priority to Foris subject to certain limitations and exceptions, as well as the terms of the Intercreditor Agreement.

The Nikko debt instruments are collateralized as follows:

•Nikko $3.9 million note: first-priority lien on 10.0% of the Aprinnova JV interests owned by the Company

•Nikko $5.0 million note: first-priority lien on 12.8% of shares of Aprinnova

•Nikko $4.5 million note: first-priority lien on 27.2% of shares of Aprinnova

The promissory notes issued under the 2019 DSM Credit Agreement (see Note 4, "Debt") are secured by a first-priority lien on certain Company intellectual property licensed to DSM.

The obligations of the Company under the Investor Notes and the Schottenfeld CSA (see Note 4, "Debt" and Note 15, “Subsequent Events”) are secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors, junior in payment priority to Foris and Naxyris subject to the Subordination Agreement among Foris, Naxyris and the Investors.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgement. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all persons and entities that purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The complaint, which was amended by the lead plaintiff on September 13, 2019, alleges securities law violations based on statements and omissions made by the Company during such period. On October 25, 2019, the defendants filed a motion to dismiss the securities class action

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complaint. The hearing on such motion to dismiss was held on February 18, 2020 and we are awaiting a ruling from the Court. Subsequent to the filing of the securities class action complaint described above, on June 21, 2019 and October 1, 2019, respectively, two separate purported shareholder derivative complaints were filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr, et al., and Carlson v. Doerr, et al.) based on similar allegations to those made in the securities class action complaint described above and named the Company and certain of the Company’s current and former officers and directors as defendants. The derivative lawsuits sought to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and omissions made in connection with the Company’s securities filings. The derivative lawsuits were dismissed on October 18, 2019 (Bonner) and December 10, 2019 (Carlson), without prejudice. We believe the securities class action complaint lacks merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

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9. Revenue Recognition

Disaggregation of Revenue

The following tables present revenue by primary geographical market, based on the location of the customer, as well as by major product and service:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Europe	$	10,092	$	54,043	$	6,674	$	70,809	$	7,576	$	7,658	$	14,172	$	29,406
United States	34,295		—		24,376		58,671		16,292		—		9,948		26,240
Asia	11,503		—		7,477		18,980		8,664		—		(2,333)		6,331
Brazil	3,612		—		115		3,727		381		—		561		942
Other	370		—		—		370		685		—		—		685
	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Significant Revenue Agreements

For the years ended December 31, 2019 and 2018, the Company recognized revenue in connection with significant revenue agreements and from all other customers as follows:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Revenue from significant revenue agreements with:
DSM (related party)	$	10	$	49,051	$	4,120	$	53,181	$	18	$	5,958	$	4,735	$	10,711
Firmenich	8,591		4,992		1,413		14,996		3,727		1,700		5,717		11,144
Lavvan	—		—		18,342		18,342		—		—		—		—
Givaudan	7,477		—		1,500		8,977		4,078		—		4,358		8,436
DARPA	—		—		5,504		5,504		—		—		8,436		8,436
Subtotal revenue from significant revenue agreements	16,078		54,043		30,879		101,000		7,823		7,658		23,246		38,727
Revenue from all other customers	43,794		—		7,763		51,557		25,775		—		(898)		24,877
Total revenue from all customers	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Cannabinoid Agreement

On May 2, 2019, the Company consummated a research, collaboration and license agreement (the Cannabinoid Agreement) with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids, subject to certain closing conditions. Under the agreement, the Company would perform research and development activities and Lavvan would be responsible for the manufacturing and commercialization of the cannabinoids developed under the agreement. The Cannabinoid Agreement is being principally funded on a milestone basis, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. The Company could receive aggregate funding of up to $300 million over the term of the Cannabinoid Agreement if all of the milestones are achieved. Additionally, the Cannabinoid Agreement provides for profit share to the Company on Lavvan's gross profit margin once products are commercialized; these payments will be due for the next 20 years. On May 2, 2019, the parties consummated the transactions contemplated by the Cannabinoid Agreement, including the formation of a special purpose entity to hold certain intellectual property created during the collaboration (the Cannabinoid Collaboration IP), the licensing of certain Company intellectual property to Lavvan, the licensing of the Cannabinoid Collaboration IP to the Company and Lavvan, and the granting by the Company to Lavvan of a lien on the Company background intellectual property being licensed to Lavvan under the Cannabinoid Agreement, which lien would be subordinated to the lien on such intellectual property under the Foris LSA (see Note 4, “Debt”).

The Cannabinoid Agreement is accounted for as a revenue contract under ASC 606, with the total transaction price estimated and updated on a quarterly basis, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligations. The Company concluded the agreement contained a single performance obligation of research and development services provided

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continuously over time. The Company estimated the total unconstrained transaction price to be $145 million, based on a high probability of achieving certain underlying milestones. As of December 31, 2019, the Company has constrained $181.0 million of variable consideration related to milestones that have not met the criteria under ASC 606 necessary to be included in the transaction price. The Company concluded that the performance obligation is delivered over time and that revenue recognition is based on an input measure of progress of hours incurred compared to total estimated hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, with cumulative adjustments to revenue recorded as necessary. The Company recognized $18.3 million of collaboration revenue under the Cannabinoid Agreement for the year ended December 31, 2019 based on proportional performance delivered to date. At December 31, 2019, $8.3 million of the collaboration revenues recognized in the year ended December 31, 2019 were recorded as a contract asset. See the "Contract Assets and Liabilities" section below for further information regarding this contract asset.

Firmenich Agreements

In July 2017, the Company and Firmenich entered into the Firmenich Collaboration Agreement Agreement (for the development and commercialization of multiple renewable flavors and fragrances molecules), pursuant to which the parties agreed to exclude certain molecules from the scope of the agreement and to amend certain terms connected with the supply and use of such molecules when commercially produced. In addition, the parties agreed to (i) fix at a 70/30 basis (70% for Firmenich) the ratio at which the parties will share profit margins from sales of two molecules; (ii) set at a 70/30 basis (70% for Firmenich) the ratio at which the parties will share profit margins from sales of a distinct form of compound until Firmenich receives $15.0 million more than the Company in the aggregate from such sales, after which time the parties will share the profit margins 50/50 and (iii) a maximum Company cost of a compound where a specified purchase volume is satisfied, and alternative production and margin share arrangements in the event such Company cost cap is not achieved.

In August 2018, the Company and Firmenich entered into the Firmenich Amended and Restated Supply Agreement, which incorporates all previous amendments and new changes and supersedes the September 2014 supply agreement. With this Amended and Restated Supply Agreement, the parties agreed on the molecules to be supplied under the agreement and the commercial specifications of these products, and made some adjustments to the pricing of the molecules.

Pursuant to the Firmenich Collaboration Agreement, the Company agreed to pay a one-time success bonus to Firmenich of up to $2.5 million if certain commercialization targets are met. Such targets have not yet been met as of December 31, 2019. The one-time success bonus will expire upon termination of the Firmenich Collaboration Agreement, which has an initial term of 10 years and will automatically renew at the end of such term (and at the end of any extension) for an additional 3-year term unless otherwise terminated. At December 31, 2019, the Company had a $0.7 million liability associated with this one-time success bonus that has been recorded as a reduction to the associated collaboration revenue.

Givaudan Agreements

In September 2018, Amyris and Givaudan, entered into a Collaboration Agreement for the development and commercialization of molecules for use and sale in the cosmetics and flavors markets (collectively the “Collaboration Markets”). Under Collaboration Agreement, the parties will collaborate to develop, produce and commercialize. Under the agreement, the Company granted Givaudan exclusive access to specified intellectual property for the development and commercialization of such molecules in the Collaboration Markets in exchange for research and development funding. Funding, including payment terms, will be based on milestones and milestone-based payments, to be mutually agreed upon by the parties on a project by project basis. The Company is currently working on development and commercialization of two significant molecules. The Company also manufactures and supplies a certain compound that was developed by the Company under a prior (expired) collaboration agreement with Givaudan. The supply agreement was entered into in September 2018 and has a five-year term with successive one-year renewals until terminated by either party.

Following the research and development phase of a project, if Givaudan elects to proceed with commercialization, a supply agreement will be negotiated for each compound. The significant terms for each supply agreement are set forth in the Collaboration Agreement including the price at which the molecules are to be supplied. The price for each compound will be negotiated and agreed upon by both parties at a future time. Under the Collaboration Agreement, following commercial development of the agreed upon compound, the Company will manufacture the compound and Givaudan will perform any required downstream polishing, distribution, sales and marketing. The collaboration work and supply of the molecules is exclusively limited to the Cosmetics Actives Market and the Flavors Market.

DSM July and September 2017 Collaboration and Licensing Agreements

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In July and September 2017, the Company entered into three separate collaboration agreements with DSM (DSM Collaboration Agreements) to jointly develop three new molecules in the Health & Wellness (DSM Ingredients) market using the Company’s technology, which the Company would produce and DSM would commercialize. Pursuant to the DSM Collaboration Agreements, DSM will, subject to certain conditions, provide funding for the development of the DSM Ingredients and, upon commercialization, the parties would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredients from the Company at prices agreed by the parties. The development services will be directed by a joint steering committee with equal representation by DSM and the Company. In addition, the parties will share profit margin from DSM’s sales of products that incorporate the DSM Ingredients subject to the DSM Collaboration Agreements.

In connection with the entry into the DSM Collaboration Agreements, the Company and DSM also entered into certain license arrangements (DSM License Agreements) providing DSM with certain rights to use the technology underlying the development of the DSM Ingredients to produce and sell products incorporating the DSM Ingredients. Under the DSM License Agreements, DSM paid the Company $9.0 million for a worldwide, exclusive, perpetual, royalty-free license to produce and sell products incorporating one of the DSM Ingredients in the Health & Wellness field.

December 2017 DSM Agreements

In December 2017, the Company entered into a series of agreements with DSM (December 2017 DSM Agreements) which are described below. The December 2017 DSM Agreements were evaluated as a combined transaction for accounting purposes in conjunction with the sales of the Brotas 1 facility discussed more fully in Note 10, "Related Party Transactions" and Note 12, "Divestiture".

DSM November 2017 Intellectual Property License Agreement

In November 2017, in connection with the Company's divestiture of its Brotas, Brazil production facility (see Note 12, "Divestiture"), the Company and DSM entered into a license agreement covering certain intellectual property of the Company useful in the performance of certain commercial supply agreements assigned by the Company to DSM relating to products currently manufactured at the Brotas facility (DSM November 2017 Intellectual Property License Agreement). In December 2017, DSM paid the Company an upfront license fee of $27.5 million. In accounting for the Divestiture with DSM, a multiple-element arrangement, the license of intellectual property to DSM was identified as revenue deliverable with standalone value and qualified as a separate unit of accounting. The Company performed an analysis to determine the fair value for of the license, and allocated the non-contingent consideration based on the relative fair value. The Company determined that the license had been fully delivered, and, as such, license revenue of $54.6 million was recognized for the period ended December 31. 2017.

On November 19, 2018, the Company and DSM entered into a letter agreement (November 2018 DSM Letter Agreement), pursuant to which the Company agreed (i) to cause the removal of certain existing liens on intellectual property owned by the Company and licensed to DSM and (ii) if such liens were not removed prior to December 15, 2018, to issue to DSM shares of the Company’s common stock with a value equal to $5.0 million. On December 14, 2018, the Company entered into an amendment to the GACP Term Loan Facility to remove such lien, and the November 2018 DSM Letter Agreement was thereby terminated.

DSM Value Sharing Agreement

In December 2017, in conjunction with the Company's divestiture of its Brotas, Brazil production facility (see Note 12, "Divestiture" and Note 10, "Related Party Transactions"), the Company and DSM entered into a value sharing agreement (Value Sharing Agreement), pursuant to which DSM agreed to make certain royalty payments to the Company representing a portion of the profit on the sale of products produced using farnesene purchased under the Nenter Supply Agreement realized by Nenter and paid to DSM in accordance with the Nenter Supply Agreement. In addition, pursuant to the Value Sharing Agreement, DSM agreed to guarantee certain minimum annual royalty payments totaling $33.1 million over the first three calendar years of the Value Sharing Agreement, subject to future offsets in the event that the royalty payments to which the Company would otherwise have been entitled under the Value Sharing Agreement for such years fall below certain milestones. The nonrefundable minimum annual royalty payments were determined to be fixed and determinable and were included as part of the total arrangement consideration subject to allocation in the December 2017 multiple-element divestiture transaction with DSM. At closing, DSM paid the Company a nonrefundable royalty payment of $15.0 million under the Value Sharing Agreement and paid two additional future nonrefundable minimum annual royalty payments totaling $18.1 million related to 2019 and 2020 royalties. In June 2018, the Company received the 2019 non-refundable minimum royalty payment of $9.3 million (net of a $0.7 million early payment discount) and in March 2019, the Company received the 2020 payment of

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$7.4 million (net of a $0.7 million early payment discount). During 2018, the Company and DSM amended the Value Sharing Agreement to (i) provide for the use of estimates in calculating quarterly royalty payments (subject to true-up), (ii) modify how the guaranteed minimum annual royalty payment for 2018 will be offset against value payments accruing during 2018 and (iii) accelerate the minimum annual royalty payment for 2019 from December 31, 2018 to June 30, 2018 in exchange for a fee of $750,000. For the year ended December 31, 2018, the Company recognized $7.9 million of revenue in connection with the DSM Value Sharing Agreement.

In April 2019, the Company assigned to DSM, and DSM assumed, all of the Company’s rights and obligations under the December 2017 DSM Value Sharing Agreement, as amended, for aggregate consideration to the Company of $57.0 million, which included $7.4 million received on March 29, 2019 for the third and final annual royalty payment due under the original agreement. On April 16, 2019, the Company received net cash of $21.7 million, with the remaining $27.9 million used by the Company to offset past due trade payables (including interest) under the 2017 Supply Agreement (discussed below), the obligation under the November 2018 Securities Purchase Agreement, and manufacturing capacity fees under the provisions of Amendment No. 1 to the 2017 Supply Agreement (see Note 10, "Related Party Transactions" for a description of these agreements).

The original Value Sharing Agreement was accounted for as a single performance obligation in connection with a license with fixed and determinable consideration and variable consideration that was accounted for pursuant to the sales-based royalty scope exception. The April 16, 2019 assignment of the December 2017 DSM Value Sharing Agreement was accounted for as a contract modification under ASC 606, resulting in additional fixed and determinable consideration of $37.1 million and variable consideration of $12.5 million in the form of a stand-ready obligation to refund some or all of the $12.5 million consideration if certain criteria outlined in the assignment agreement are not met by December 2021. The Company periodically updates its estimate of amounts to be retained and reduces the refund liability and records additional license and royalty revenue as the criteria are met. The effect of the contract modification on the transaction price, and on the Company’s measure of progress toward complete satisfaction of the performance obligation was recognized as an adjustment to revenue at the date of the contract modification on a cumulative catch-up basis. As a result, the Company recognized $37.1 million of license and royalty in the second quarter of 2019, due to fully satisfying the performance obligation at the modification date.The Company also recognized an additional $3.6 million of previously deferred royalty revenue under the December 2017 DSM Value Sharing Agreement, as the remaining underlying performance obligation was fully satisfied through the April 16, 2019 assignment of the agreement to DSM. The Company recorded an additional $8.8 million of license and royalty revenue in the fourth quarter of 2019 related to a change in the estimated refund liability.

DSM Performance Agreement

In December 2017, in connection with the Company's divestiture of its Brotas, Brazil production facility (see Note 12, "Divestiture"), the Company and DSM entered into a performance agreement (Performance Agreement), pursuant to which the Company will provide certain research and development services to DSM relating to the development of the technology underlying the farnesene-related products to be manufactured at the Brotas facility in exchange for related funding, including certain bonus payments in the event that specific performance metrics are achieved. The Company will record the bonus payments as earned revenue upon the transfer of the developed technology to DSM. If the Company does not meet the established metrics under the Performance Agreement, the Company will be required to pay $1.8 million to DSM. The Performance Agreement will expire in December 2020, subject to the right of each of the parties to terminate for uncured material breach by the other party or in the event the other party is subject to bankruptcy proceedings, liquidation, dissolution or similar proceedings or other specified events.

DSM December 2017 Supply Agreement and November 2018 Supply Agreement Amendment

On November 19, 2018, the Company and DSM entered into an amendment (Supply Agreement Amendment) to the supply agreement, dated December 28, 2017 (Supply Agreement), by and between the Company and DSM. Under the Supply Agreement, DSM agreed to manufacture and supply to the Company certain products useful in the Company’s business, at prices and on production and delivery terms and specifications set forth in the Supply Agreement, which prices are based upon DSM’s manufacturing cost plus an agreed margin. The Supply Agreement originally provided that it would expire (i) with respect to non-farnesene related products, on the date that the Company’s planned new specialty ingredients manufacturing facility in Brazil is fully operational and meets its production targets, but in any event no later than December 31, 2021 and (ii) with respect to farnesene related products, on December 28, 2037, subject in each case to earlier termination in certain circumstances. Pursuant to the Supply Agreement Amendment, (i) the outside expiration date of the Supply Agreement with respect to non-farnesene related products was extended to December 31, 2022, with specified pricing terms added for products manufactured during 2022, (ii) DSM committed to produce certain non-farnesene related products for the Company for two months of each calendar year during the term of the Supply Agreement and (iii) the Company agreed to (A) pay DSM a cash

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fee totaling $15.5 million, payable in installments during 2018 and 2019, (B) issue 1,643,991 shares of the Company's common stock to DSM, and (C) pay DSM a cash fee of $7.3 million, payable on or before March 29, 2019, plus, if the closing price of the Common Stock on the trading day immediately preceding the date of such payment is less than $4.41 per share, an amount equal to such deficiency multiplied by 1,643,991.

In addition, on April 16, 2019 the Company and DSM entered into amendments to the 2017 Supply Agreement and the 2017 Performance Agreement, as well as the Quota Purchase Agreement relating to the December 2017 sale of Amyris Brasil to DSM (see Note 12, “Divestiture”), pursuant to which (i) DSM agreed to reduce certain manufacturing costs and fees paid by the Company related to the production of farnesene under the Supply Agreement through 2021, as well as remove the priority of certain customers over the Company with respect to production capacity at the Brotas, Brazil facility, (ii) the Company agreed to provide DSM rights to conduct certain process and downstream recovery improvements under the Performance Agreement at facilities other than the Brotas, Brazil facility in exchange for DSM providing the Company with a license to such improvements and (iii) the Company released DSM from its obligation to provide manufacturing and support services under the Quota Purchase Agreement in connection with the Company’s planned new manufacturing facility, which is no longer to be located at the Brotas, Brazil location.

DARPA Technology Investment Agreement

In September 2015, the Company entered into a technology investment agreement (TIA) with The Defense Advanced Research Projects Agency (DARPA), under which the Company, with the assistance of specialized subcontractors, is working to create new research and development tools and technologies for strain engineering and scale-up activities. The agreement is being funded by DARPA on a milestone basis. Under the TIA, the Company and its subcontractors could collectively receive DARPA funding of up to $35.0 million over the program’s four year term if all of the program’s milestones are achieved. In conjunction with DARPA’s funding, the Company and its subcontractors are obligated to collectively contribute approximately $15.5 million toward the program over its four year term (primarily by providing specified labor and/or purchasing certain equipment). For the DARPA agreement, the Company recognizes revenue using an output-based measure of progress of the milestones completed relative to remaining milestones, once acknowledged by DARPA.

Contract Assets and Liabilities

When a contract results in revenue being recognized in excess of the amount the Company has invoiced or has the right to invoice to the customer, a contract asset is recognized. Contract assets are transferred to accounts receivable, net when the rights to the consideration become unconditional.

Contract liabilities consist of payments received from customers, or such consideration that is contractually due, in advance of providing the product or performing services such that control has not passed to the customer.

Trade receivables related to revenue from contracts with customers are included in accounts receivable on the consolidated balance sheets, net of the allowance for doubtful accounts. Trade receivables are recorded at the point of renewable product sale or in accordance with the contractual payment terms for licenses and royalties, and grants and collaborative research and development services for the amount payable by the customer to the Company for sale of goods or the performance of services, and for which the Company has the unconditional right to receive payment.

Contract Balances

The following table provides information about accounts receivable and contract liabilities from contracts with customers:

December 31, (In thousands)	2019		2018
Accounts receivable, net	$	16,322	$	16,003
Accounts receivable - related party, net	$	3,868	$	1,349
Accounts receivable, unbilled - related party	$	—	$	8,021
Contract assets	$	8,485	$	—
Contract assets, noncurrent - related party	$	1,203	$	1,203
Contract liabilities	$	1,353	$	8,236
Contract liabilities, noncurrent(1)	$	1,449	$	1,587

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______________

⁽¹⁾The balances in contract liabilities, noncurrent are included in other noncurrent liabilities on the consolidated balance sheets.

Unbilled receivables relate to the Company’s right to consideration from DSM for (i) minimum future royalties and (ii) a material right arising from a customer option for a future transfer of technology. The Company’s right to cash receipt for these minimum royalty amounts occurs on or before December 31, 2019, and the right to cash receipt for the customer option occurs on or before December 31, 2020.

Contract liabilities, current decreased by $6.9 million at December 31, 2019 resulting from collaboration and royalty amounts recognized as revenue during the year ended December 31, 2019 that was included in contract liabilities at the beginning of the period.

Remaining Performance Obligations

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of December 31, 2019.

(In thousands)	As of December 31, 2019
2020	$	56,719
2021	52,313
2022	30,483
2023 and thereafter	—
Total from all customers	$	139,515

In accordance with the disclosure provisions of ASC 606, the table above excludes estimated future revenues for performance obligations that are part of a contract that has an original expected duration of one year or less or a performance obligation with variable consideration that is recognized using the sales-based royalty exception for licenses of intellectual property. Additionally, $181.0 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

10. Related Party Transactions

Related Party Equity

See Note 6, "Stockholders' Deficit" for details of these related party equity transactions:

•November 2018 DSM Securities Purchase Agreement

•August 2017 DSM Offering

Related Party Debt

See Note 4, "Debt" for details of these related party debt transactions:

•DSM Note (also see Note 12, "Divestiture")

•2014 Rule 144A Convertible Notes

•August 2013 Financing Convertible Notes

•Foris LSA

•Foris $19 million Note

•Naxyris LSA

Related party debt was as follows:

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	2019						2018
December 31, (in thousands)	Principal		Unaccreted Debt Discount		Net		Principal		Unaccreted Debt Discount		Net
DSM notes	$	33,000	$	(4,621)	$	28,379	$	25,000	$	(6,311)	$	18,689
Foris
Foris notes	115,351		(9,516)		105,835		—		—		—
2014 Rule 144A convertible notes	—		—		—		5,000		(181)		4,819
	115,351		(9,516)		105,835		5,000		(181)		4,819
Naxyris note	24,437		(822)		23,615		—		—		—
Temasek 2014 Rule 144A convertible note	—		—		—		10,000		(435)		9,565
Total 2014 Rule 144A convertible note	10,178		—		10,178		9,705		(422)		9,283
	$	182,966	$	(14,959)	$	168,007	$	49,705	$	(7,349)	$	42,356

The fair value of the derivative liabilities related to the related party Foris $19 million note, Foris LSA and Naxyris note as of December 31, 2019 and 2018 was $2.6 million and $0.0 million, respectively. The Company recognized losses from change in the fair value of these and previous debt-related derivative liabilities of $0.1 million and $8.5 million for the years ended December 31, 2019 and 2018, respectively; see Note 3, "Fair Value Measurement".

At December 31, 2018, Temasek was no longer a related party. However, the Company and Temasek were related parties when they entered into the 2014 Rule 144A convertible notes transaction, for which terms remained unchanged since the borrowing date.

Related Party Revenue

The Company recognized revenue from related parties and from all other customers as follows:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Revenue from related parties:
DSM	$	10	$	49,051	$	4,120	$	53,181	$	18	$	5,958	$	4,735	$	10,711
Total	46		—		—		46		342		—		—		342
Novvi	—		—		—		—		—		—		—		—
Subtotal revenue from related parties	56		49,051		4,120		53,227		360		5,958		4,735		11,053
Revenue from all other customers	59,816		4,992		34,522		99,330		33,238		1,700		17,613		52,551
Total revenue from all customers	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

See Note 9, "Revenue Recognition" for details of the Company's revenue agreements with DSM.

Related Party Accounts Receivable

Related party accounts receivable was as follows:

December 31, (In thousands)	2019		2018
DSM	$	3,868	$	1,071
Novvi	—		188
Total	—		90
Related party accounts receivable, net	$	3,868	$	1,349

In addition to the amounts shown above, there were the following amounts on the consolidated balance sheet at December 31, 2019 and December 31, 2018, respectively:

•$0 and $8.0 million of unbilled receivables from DSM, in Accounts receivable, unbilled - related party;

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•$1.2 million of unbilled receivables from DSM in Contract assets, noncurrent - related party; and

•$3.3 million and $4.3 million of contingent consideration receivable from DSM in Other assets.

Related Party Accounts Payable and Accrued Liabilities

Amounts due to DSM were as follows:

•Accounts payable and accrued and other current liabilities of $14.0 million and $2.1 million at December 31, 2019 and 2018, respectively; and

•Other noncurrent liabilities of $3.8 million and $3.6 million at December 31, 2019 and 2018, respectively.

Related Party DSM Transactions

The Company is party to the following significant agreements (and related amendments) with related party DSM:

Related to	Agreement	For Additional Information, See the Note Indicated
Debt	DSM Credit Agreement	4. Debt
Debt	2019 DSM Credit Agreement	4. Debt
Divestiture	November 2017 Quota Purchase Agreement	12. Divestiture
Divestiture	December 2017 DSM Transition Services Agreement	12. Divestiture
Equity	August 2017 DSM Offering	6. Stockholders' Deficit
Equity	November 2018 DSM Securities Purchase Agreement	6. Stockholders' Deficit
Revenue	July and September 2017 Collaboration and Licensing Agreements	9. Revenue Recognition
Revenue	December 2017 DSM Supply Agreement	9. Revenue Recognition
Revenue	December 2017 DSM Value Sharing Agreement, as amended	9. Revenue Recognition
Revenue	December 2017 DSM Performance Agreement	9. Revenue Recognition
Revenue	November 2017 Intellectual Property License Agreement	9. Revenue Recognition
Revenue	November 2018 Supply Agreement Amendment	9. Revenue Recognition

Concurrent with the sale of Amyris Brasil in December 2017, the Company and DSM entered into a series of commercial agreements including (i) a license agreement to DSM of its farnesene product for DSM to use in the Vitamin E and lubricant markets; (ii) a royalty agreement that DSM will pay the Company specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene under the Nenter Supply Agreement assigned to DSM; (iii) a performance agreement, which provides an option for DSM to elect a technology transfer upon the achievement of certain development milestones associated with the optimization of farnesene strains; and (iv) a transition services agreement for the Company to provide finance, legal, logistics, and human resource services to support the Brotas facility under DSM ownership for a six-month period with a DSM option to extend for six additional months. See Note 12, “Divestiture” for further information regarding the sale of Amyris Brasil and the related commercial agreements. In addition, the Company entered into a credit agreement with DSM under which the Company borrowed $25 million; see Note 4, "Debt" for additional information.

In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for production of its alternative sweetener product through 2022. See Note 9, “Revenue Recognition” for information regarding the November 2018 Supply Agreement Amendment and the November 2018 DSM Securities Purchase Agreement. The Company also entered into other transactions with DSM in November 2018 which resulted in the Company (i) evaluating this series of November 2018 transactions and considering other certain transactions with DSM in 2018 as a combined arrangement, and (ii) determining and allocating the fair value to each element. The other transactions entered into concurrently with the November 2018 Supply Agreement Amendment and November 2018 DSM Securities Purchase Agreement included an agreement to finalize the working capital adjustments related to the Brotas 1 facility sale in December 2017 and an amendment to reduce the exercise price of the Cash Warrant issued to DSM in the August 2017 DSM Offering and to provide a waiver for any potential claims arising from failure to obtain consent prior to amending the exercise price of the August 2017 Vivo Cash Warrant in the August 2017 Warrant transaction.

The contractual consideration transferred to DSM under the combined arrangement was $34.7 million. The Company performed an analysis to determine the fair value of the elements and allocated the resulting $33.3 million total fair value as follows: (i) $24.4 million to the manufacturing capacity, (ii) $6.8 million to the legal settlement and related consent waiver and (iii) $2.1 million to the working capital adjustment. See Note 3, “Fair Value Measurement” for information related to this fair

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value allocation. The $1.4 million excess consideration transferred above the combined arrangement’s fair value was recorded as a reduction of royalty revenues in the year ended December 31, 2018. Of the $24.4 million fair value allocated to the manufacturing capacity, $3.3 million was recorded as deferred cost of products sold during 2018. Also, the Company paid an additional $14.1 million in manufacturing capacity fees during 2019, which were recorded as additional deferred cost of products sold. The remaining $7.0 million manufacturing capacity fees will be recorded as deferred cost of products sold in the period the additional payments are made to DSM. The deferred cost of products sold asset will be expensed on a units of production basis as products are sold over the five-year term of the supply agreement. On a quarterly basis, the Company evaluates its future production volumes for its sweetener product and adjusts the unit cost to be expensed over the remaining estimated production volume. The $6.8 million of fair value allocated to the legal settlement and related consent waiver was recorded as legal settlement expense for the year ended December 31, 2018. The $2.1 million of fair value allocated to the working capital adjustment was recorded as a loss on divestiture for the year ended December 31, 2018. The contractual consideration transferred to DSM exceeded the fair value of the elements received by $1.4 million and this excess was recorded as a reduction of licenses and royalties revenues in the three months ended December 31, 2018.

Related Party Joint Venture

In December 2016, the Company, Nikko Chemicals Co., Ltd. an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko (collectively, Nikko) entered into a joint venture (the Aprinnova JV Agreement) pursuant to which the Company contributed certain assets, including certain intellectual property and other commercial assets relating to its business-to-business cosmetic ingredients business (the Aprinnova JV Business), as well as its Leland production facility. The Company also agreed to provide the Aprinnova JV with exclusive (to the extent not already granted to a third party), royalty-free licenses to certain of the Company's intellectual property necessary to make and sell products associated with the Aprinnova JV Business (the Aprinnova JV Products). Nikko purchased their 50% interest in the Aprinnova JV in exchange for the following payments to the Company: (i) an initial payment of $10.0 million and (ii) the profits, if any, distributed to Nikko in cash as members of the Aprinnova JV during the three-year period from 2017 to 2019, up to a maximum of $10.0 million.

The Aprinnova JV operates in accordance with the Aprinnova Operating Agreement under which the Aprinnova JV is managed by a Board of Directors consisting of four directors: two appointed by the Company and two appointed by Nikko. In addition, Nikko has the right to designate the Chief Executive Officer of the Aprinnova JV from among the directors and the Company has the right to designate the Chief Financial Officer. The Company determined that it has the power to direct the activities of the Aprinnova JV that most significantly impact its economic performance because of its (i) significant control and ongoing involvement in operational decision making, (ii) guarantee of production costs for certain Aprinnova JV products, as discussed below, and (iii) control over key supply agreements, operational and administrative personnel and other production inputs. The Company has concluded that the Aprinnova JV is a variable-interest entity (VIE) under the provisions of ASC 810, Consolidation, and that the Company has a controlling financial interest and is the VIE's primary beneficiary. As a result, the Company accounts for its investment in the Aprinnova JV on a consolidation basis in accordance with ASC 810.

Under the Aprinnova Operating Agreement, profits from the operations of the Aprinnova JV, if any, are distributed as follows: (i) first, to the Company and Nikko (the Members) in proportion to their respective unreturned capital contribution balances, until each Member’s unreturned capital contribution balance equals zero and (ii) second, to the Members in proportion to their respective interests. In addition, any future capital contributions will be made by the Company and Nikko on an equal (50%/50%) basis each time, unless otherwise mutually agreed. For the year ended December 31, 2019, a $0.3 million distribution was made to Nikko and was recorded as a decrease in noncontrolling interest.

Pursuant to the Aprinnova JV Agreement, the Company and Nikko agreed to make initial working capital loans to the Aprinnova JV in the amounts of $0.5 million and $1.5 million, respectively, and again in 2019 with additional loans of $0.2 million each. Also in 2019, Nikko provided the Aprinnova JV with $1.2 million of short-term loans to purchase certain manufacturing supplies. These loans are described in more detail in Note 4, “Debt”. In addition, the Company agreed to guarantee a maximum production cost for squalane and hemisqualane to be produced by the Aprinnova JV and to bear any cost of production above such guaranteed costs.

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In connection with the contribution of the Leland Facility by the Company to the Aprinnova JV, at the closing of the formation of the Aprinnova JV, Nikko made a loan to the Company in the principal amount of $3.9 million, and the Company in consideration therefore issued a promissory note to Nikko in an equal principal amount, as described in more detail in Note 4, “Debt” under “Nikko Note.”

The following presents the carrying amounts of the Aprinnova JV’s assets and liabilities included in the accompanying consolidated balance sheets. Assets presented below are restricted for settlement of the Aprinnova JV's obligations and all liabilities presented below can only be settled using the Aprinnova JV resources.

December 31, (In thousands)	2019		2018
Assets	$	17,390	$	12,904
Liabilities	$	3,690	$	2,364

The Aprinnova JV's assets and liabilities are primarily comprised of inventory, property, plant and equipment, accounts payable and debt, which are classified in the same categories in the Company's consolidated balance sheets.

Office Sublease

The Company subleases certain office space to Novvi, for which the Company charged Novvi $0.6 million and $0.6 million for the years ended December 31, 2019 and 2018, respectively.

See Note 15, “Subsequent Events” for information regarding related party transactions subsequent to December 31, 2019.

11. Stock-based Compensation

Stock-based Compensation Expense Related to All Plans

Stock-based compensation expense related to all employee stock compensation plans, including options, restricted stock units and ESPP, was as follows:

Years Ended December 31, (In thousands)	2019		2018
Research and development	$	2,900	$	1,797
Sales, general and administrative	9,654		7,393
Total stock-based compensation expense	$	12,554	$	9,190

Plans

2010 Equity Incentive Plan

The Company's 2010 Equity Incentive Plan (2010 Equity Plan) became effective on September 27, 2010 and will terminate in 2020. The 2010 Equity Plan provides for the granting of common stock options, restricted stock awards, stock bonuses, stock appreciation rights, restricted stock units (RSUs) and performance awards. It allows for time-based or performance-based vesting for the awards. Options granted under the 2010 Equity Plan may be either incentive stock options (ISOs) or non-statutory stock options (NSOs). ISOs may be granted only to Company employees (including officers and directors who are also employees). NSOs may be granted to Company employees, non-employee directors and consultants. The Company will be able to issue no more than 2,000,000 shares pursuant to the grant of ISOs under the 2010 Equity Plan. Options under the 2010 Equity Plan may be granted for periods of up to ten years. All options issued to date have had a ten-year life. Under the plan, the exercise price of any ISOs and NSOs may not be less than 100% of the fair market value of the shares on the date of grant. The exercise price of any ISOs and NSOs granted to a 10% stockholder may not be less than 110% of the fair value of the underlying stock on the date of grant. The options and RSUs granted to-date generally vest over three to five years.

As of December 31, 2019 and 2018, options were outstanding to purchase 5,589,315 and 5,339,214 shares, respectively, of the Company's common stock granted under the 2010 Equity Plan, with weighted-average exercise prices per share of $8.89 and $9.62, respectively. In addition, as of December 31, 2019 and 2018, restricted stock units representing the right to receive 5,782,651 and 5,294,803 shares, respectively, of the Company's common stock granted under the 2010 Equity Plan were

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outstanding. As of December 31, 2019 and 2018, 3,815,625 and 2,359,750 shares, respectively, of the Company’s common stock remained available for future awards that may be granted under the 2010 Equity Plan.

The number of shares reserved for issuance under the 2010 Equity Plan increases automatically on January 1 of each year starting with January 1, 2011, by a number of shares equal to 5% of the Company’s total outstanding shares as of the immediately preceding December 31. However, the Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors retains the discretion to reduce the amount of the increase in any particular year.

In May 2018, shareholders approved amendments to the 2010 Equity Plan to (i) increase the number of shares of common stock available for grant and issuance thereunder by 9.0 million shares and (ii) increase the annual per-participant award limit thereunder to 4.0 million shares. Subsequent to the amendments, the total number of shares available for grant was 9,280,000, not including the annual evergreen increases.

2005 Stock Option/Stock Issuance Plan

In 2005, the Company established its 2005 Stock Option/Stock Issuance Plan (2005 Plan) which provided for the granting of common stock options, restricted stock units, restricted stock and stock purchase rights awards to employees and consultants of the Company. The 2005 Plan allowed for time-based or performance-based vesting for the awards. Options granted under the 2005 Plan were ISOs or NSOs. ISOs were granted only to Company employees (including officers and directors who are also employees). NSOs were granted to Company employees, non-employee directors, and consultants.

All options issued under the 2005 Plan had a ten-year life. The exercise prices of ISOs and NSOs granted under the 2005 Plan were not less than 100% of the estimated fair value of the shares on the date of grant, as determined by the Board of Directors. The exercise price of an ISO and NSO granted to a 10% stockholder could not be less than 110% of the estimated fair value of the underlying stock on the date of grant as determined by the Board. The options generally vested over 5 years.

As of December 31, 2019 and 2018, options to purchase 31,104 and 52,389 shares, respectively, of the Company’s common stock granted under the 2005 Plan remained outstanding, and as a result of the adoption of the 2010 Equity Plan discussed above, zero shares of the Company’s common stock remained available for future awards issuance under the 2005 Plan. The options outstanding under the 2005 Plan as of December 31, 2019 and 2018 had a weighted-average exercise price per share of $259.19 and $185.93, respectively.

2010 Employee Stock Purchase Plan

The 2010 Employee Stock Purchase Plan (2010 ESPP) became effective on September 27, 2010. The 2010 ESPP is designed to enable eligible employees to purchase shares of the Company’s common stock at a discount. Offering periods under the 2010 ESPP generally commence on each May 16 and November 16, with each offering period lasting for one year and consisting of two six-month purchase periods. The purchase price for shares of common stock under the 2010 ESPP is the lesser of 85% of the fair market value of the Company’s common stock on the first day of the applicable offering period or the last day of each purchase period. During the life of the 2010 ESPP, the number of shares reserved for issuance increases automatically on January 1 of each year, starting with January 1, 2011, by a number of shares equal to 1% of the Company’s total outstanding shares as of the immediately preceding December 31. However, the Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors retains the discretion to reduce the amount of the increase in any particular year. In May 2018, shareholders approved an amendment to the 2010 ESPP to increase the maximum number of shares of common stock that may be issued over the term of the ESPP by 1 million shares. No more than 1,666,666 shares of the Company’s common stock may be issued under the 2010 ESPP and no other shares may be added to this plan without the approval of the Company’s stockholders.

2018 CEO Performance-based Stock Options

In May 2018, the Company granted its chief executive officer performance-based stock options (PSOs) to purchase 3,250,000 shares. PSOs are equity awards with the final number of PSOs that may vest determined based on the Company’s performance against pre-established EBITDA milestones and Amyris stock price milestones. The EBITDA milestones are measured from the grant date through December 31, 2021, and the stock price milestones are measured from the grant date through December 31, 2022. The PSOs vest in four tranches contingent upon the achievement of both the EBITDA milestones and stock price milestones for each respective tranche, and the chief executive officer’s continued employment with the Company. Over the measurement periods, the number of PSOs that may be issued and the related stock-based compensation expense that is recognized is adjusted upward or downward based upon the probability of achieving the EBITDA milestones.

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Depending on the probability of achieving the EBITDA milestones and stock price milestones and certification of achievement of those milestones for each vesting tranche by the Company’s Board of Directors or Compensation Committee, the PSOs issued could be from zero to 3,250,000 stock options, with an exercise price of $5.08 per share.

Stock-based compensation expense for this award is recognized using a graded-vesting approach over the service period beginning at the grant date through December 31, 2022, as the Company’s management has determined that certain EBITDA milestones are probable of achievement over the next four years as of December 31, 2019, The Company utilized a Monte Carlo simulation to estimate the grant date fair value of each tranche of the award which totaled $5.1 million. For the years ended December 31, 2019 and 2018, the Company recognized $0 and $0.7 million, respectively, of compensation expense for this award. The assumptions used to estimate the fair value of this award with performance and market vesting conditions were as follows:

Stock Option Award with Performance and Market Vesting Conditions:
Fair value of the Company’s common stock on grant date	$	5.08
Expected volatility	70		%
Risk-free interest rate	2.75		%
Dividend yield	0.0		%

Stock Option Activity

Stock option activity is summarized as follows:

Year ended December 31,	2019		2018
Options granted	530,140		4,337,119
Weighted-average grant-date fair value per share	$	3.83	$	5.18
Compensation expense related to stock options (in millions)	$	2.0	$	2.6
Unrecognized compensation costs as of December 31 (in millions)	$	4.5	$	8.5

The Company expects to recognize the December 31, 2019 balance of unrecognized costs over a weighted-average period of 3.8 years. Future option grants will increase the amount of compensation expense to be recorded in these periods.

Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes-Merton option pricing model. The fair value of employee stock options is amortized on a ratable basis over the requisite service period of the awards. The fair value of employee stock options and employee stock purchase plan rights was estimated using the following weighted-average assumptions:

Years Ended December 31,	2019	2018
Expected dividend yield	—%	—%
Risk-free interest rate	1.8%	2.8%
Expected term (in years)	6.9	6.9
Expected volatility	84%	80%

The expected life of options is based primarily on historical share option exercise experience of the employees for options granted by the Company. All options are treated as a single group in the determination of expected life, as the Company does not currently expect substantially different exercise or post-vesting termination behavior among the employee population. The risk-free interest rate is based on the U.S. Treasury yield for a term consistent with the expected life of the awards in effect at the time of grant. Expected volatility is based on the historical volatility of the Company's common stock. The Company has no history or expectation of paying dividends on common stock.

Stock-based compensation expense associated with options is based on awards ultimately expected to vest. At the time of an option grant, the Company estimates the expected future rate of forfeitures based on historical experience. These estimates are revised, if necessary, in subsequent periods if actual forfeiture rates differ from those estimates. If the actual forfeiture rate

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is lower than estimated the Company will record additional expense and if the actual forfeiture is higher than estimated the Company will record a recovery of prior expense.

The Company’s stock option activity and related information for the year ended December 31, 2019 was as follows:

	Number of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding - December 31, 2018	5,390,270	$	11.55	8.5	$	29
Options granted	530,140	$	3.83
Options exercised	(7,445)	$	3.60
Options forfeited or expired	(292,546)	$	17.18
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Vested or expected to vest after December 31, 2019	5,037,260	$	10.88	7.7	$	23
Exercisable at December 31, 2019	1,314,113	$	27.46	6.1	$	10

The aggregate intrinsic value of options exercised under all option plans was $0 and $0.2 million for the years ended December 31, 2019 and 2018, respectively, determined as of the date of option exercise.

Restricted Stock Units Activity and Expense

During the years ended December 31, 2019 and 2018, 2,996,660 and 5,452,664 RSUs, respectively, were granted with weighted-average service-inception date fair value per unit of $3.96 and $5.36, respectively. The Company recognized RSU-related stock-based compensation expense of $10.2 million and $6.4 million, respectively, for the years ended December 31, 2019 and 2018. As of December 31, 2019 and 2018, unrecognized RSU-related compensation costs totaled $22.3 million and $23.8 million, respectively.

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant.

The Company’s RSU and restricted stock activity and related information for the year ended December 31, 2019 was as follows:

	Number of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life (in years)
Outstanding - December 31, 2018	5,294,803	$	5.50	1.4
Awarded	2,996,660	$	3.96
Vested	(1,891,931)	$	5.51
Forfeited	(616,881)	$	4.84
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Vested or expected to vest after December 31, 2019	5,338,558	$	4.78	1.6

ESPP Activity and Expense

During the years ended December 31, 2019 and 2018, 318,490 and 246,230 shares, respectively, of the Company's common stock were purchased under the 2010 ESPP. At December 31, 2019 and 2018, 263,797 and 199,463 shares, respectively, of the Company’s common stock remained reserved for issuance under the 2010 ESPP.

During the years ended December 31, 2019 and 2018, the Company also recognized ESPP-related stock-based compensation expense of $0.4 million and $0.2 million, respectively.

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12. Divestiture

On December 28, 2017, the Company completed the sale of its subsidiary Amyris Brasil Ltda. (Amyris Brasil), which operated the Company’s production facility located in Brotas, Brazil, to DSM and concurrently entered into a series of commercial agreements and a credit agreement with DSM. At closing, the Company received $33.0 million in contractual cash consideration for the capital stock of Amyris Brasil, which was subject to certain post-closing working capital adjustments; and reimbursements contingent upon DSM’s utilization of certain Brazilian tax benefits it acquired with its purchase of Amyris Brasil. The Company used $12.6 million of the cash proceeds received to repay certain indebtedness of Amyris Brasil. The total fair value of the contractual consideration received by the Company for Amyris Brasil was $56.9 million and resulted in a pretax gain of $5.7 million from continuing operations. In November 2018, the Company paid DSM $1.8 million related to the final post-closing working capital adjustment. In connection with the payment, $1.8 million was recorded as a loss on divestiture in the 2018 consolidated statement of operations, in the line captioned "(Loss) gain on divestiture".

Concurrent with the sale of Amyris Brasil, the Company and DSM entered into a series of commercial agreements including (i) a license agreement to DSM of its farnesene product for DSM to use in the Vitamin E and lubricant markets; (ii) a royalty agreement, pursuant to which DSM agreed to pay the Company specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene sold under the Nenter Supply Agreement assigned to DSM; (iii) a performance agreement for the Company to perform research and development to optimize farnesene for production and sale of farnesene products; and (iv) a transition services agreement for the Company to provide finance, legal, logistics, and human resource services to support the Brotas facility under DSM ownership for a six-month period with a DSM option to extend for six additional months (see Note 9, “Revenue Recognition” for additional information). At closing, DSM paid the Company a $27.5 million nonrefundable license fee and a $15.0 million nonrefundable royalty payment, and agreed to pay two additional future nonrefundable minimum annual royalty payments totaling $18.1 million for 2019 and 2020 royalties. These future payments were determined to be fixed and determinable with a fair value of $17.8 million and were included as part of the total consideration subject to allocation in the December 2017 multiple-element divestiture transaction with DSM. In June 2018, the Company received the 2019 non-refundable minimum royalty payment of $9.3 million (net of a $0.7 million early payment discount) and in March 2019, the Company received the 2020 payment of $7.4 million (net of a $0.7 million early payment discount). See Note 9, “Revenue Recognition” and Note 10, "Related Party Transactions" for a full listing and details of agreements entered into with DSM. Additionally, the Company and DSM entered into a $25.0 million credit agreement that the Company used to repay all outstanding amounts under the Guanfu Note; see Note 4, “Debt” for additional information.

The Company accounted for the sale of Amyris Brasil as a sale of a business for proceeds of $54.8 million. The agreements entered into concurrently with the sale of Amyris Brasil including the license agreement, royalty agreement, performance agreement, transition services agreement, and credit agreement contain various elements and, as such, are deemed to be an arrangement with multiple deliverables as defined under U.S. GAAP. The Company performed an analysis to determine the fair value for all elements in the agreements with DSM and separated the elements between the non-revenue and revenue elements. After allocating the total fair value of the non-revenue elements from the fixed and determinable consideration received, the Company allocated the remaining fixed and determinable consideration to the revenue elements based on relative fair value. As such, the Company recognized $54.7 million of license revenue and $2.1 million of deferred revenue related to the performance option and transition services agreements with DSM as of December 31, 2017.

13. Income Taxes

The components of loss before income taxes are as follows:

Years Ended December 31, (In thousands)	2019		2018
United States	$	(227,614)	$	(218,109)
Foreign	(14,524)		(12,125)
Loss before income taxes	$	(242,138)	$	(230,234)

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The components of the provision for income taxes are as follows:

Years Ended December 31, (In thousands)	2019		2018
Current:
Federal	$	621	$	—
State	—		—
Foreign	8		—
Total current provision	629		—
Deferred:
Federal	—		—
State	—		—
Foreign	—		—
Total deferred benefit	—		—
Total provision for income taxes	$	629	$	—

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:

Years Ended December 31,	2019		2018
Statutory tax rate	(21.0)	%	(21.0)	%
Federal R&D credit	(0.7)	%	(0.6)	%
Derivative liability	4.7	%	4.3	%
Nondeductible interest	1.0	%	1.0	%
Other	2.4	%	(0.1)	%
Foreign losses	0.9	%	0.9	%
Change in valuation allowance	13.0	%	15.5	%
Effective income tax rate	0.3	%	—	%

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows:

December 31, (In thousands)	2019		2018
Net operating loss carryforwards	$	88,513	$	57,921
Property, plant and equipment	8,239		9,269
Research and development credits	15,002		12,046
Foreign tax credit	—		—
Accruals and reserves	13,934		8,526
Stock-based compensation	6,164		6,496
Disallowed interest carryforward	7,072		2,359
Capitalized research and development costs	21,723		27,888
Intangible and others	2,503		3,114
Equity investments	304		156
Total deferred tax assets	163,454		127,775
Operating leases right-of-use assets	(2,643)		—
Debt discount and derivatives	(7,176)		(3,750)
Total deferred tax liabilities	(9,819)		(3,750)
Net deferred tax assets prior to valuation allowance	153,635		124,025
Less: valuation allowance	(153,635)		(124,025)
Net deferred tax assets	$	—	$	—

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Activity in the deferred tax assets valuation allowance is summarized as follows:

(In thousands)	Balance at Beginning of Year		Additions		Reductions / Charges		Balance at End of Year
Deferred tax assets valuation allowance:
Year ended December 31, 2019	$	124,025	$	29,610	$	—	$	153,635
Year ended December 31, 2018	$	81,086	$	42,939	$	—	$	124,025

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. Based on the weight of available evidence, especially the uncertainties surrounding the realization of deferred tax assets through future taxable income, the Company believes that it is more likely than not that the net deferred tax assets will not be fully realizable. Accordingly, the Company has provided a full valuation allowance against its net deferred tax assets as of December 31, 2019 and 2018. The valuation allowance increased by $42.9 million during the year ended December 31, 2018 and increased by $29.6 million during the year ended December 31, 2019.

As of December 31, 2019, the Company had federal net operating loss carryforwards of approximately $411.3 million and state net operating loss carryforwards $158.1 million, available to reduce future taxable income, if any. The Internal Revenue Code of 1986, as amended, imposes restrictions on the utilization of net operating losses in the event of an “ownership change” of a corporation. Accordingly, a company’s ability to use net operating losses may be limited as prescribed under Internal Revenue Code Section 382 (IRC Section 382). Events that may cause limitations in the amount of the net operating losses that the Company may use in any one year include, but are not limited to, a cumulative ownership change of more than 50% over a three-year period. During the year ended December 31, 2019, the Company experienced a cumulative ownership change of greater than 50%. As such, net operating losses generated prior to that change are subject to an annual limitation on their use. Due to the limitations imposed, the Company wrote-off $396.5 million of federal NOL carryover and $90.6 million of state NOL carryover that is expected to expire before it can be utilized. Additionally, the Company wrote-off $14.4 million of its historical federal research and development credit carryovers as a result of the limitations. As of December 31, 2019, the Company had foreign net operating loss carryovers of approximately $22.0 million.

As of December 31, 2019, the Company had federal research and development credit carryforwards of $3.3 million and California research and development credit carryforwards of $15.2 million.

If not utilized, the federal net operating loss carryforward will begin expiring in 2034, and the California net operating loss carryforward will begin expiring in 2031. The federal research and development credit carryforwards will expire starting in 2037 if not utilized. The California research and development credit carryforwards can be carried forward indefinitely.

A reconciliation of the beginning and ending amounts of unrecognized tax benefits is as follows:

(In thousands)
Balance at December 31, 2017	$	28,833
Increases in tax positions for prior period	55
Increases in tax positions during current period	1,239
Balance at December 31, 2018	30,127
Increases in tax positions for prior period	—
Increases in tax positions during current period	1,411
Balance at December 31, 2019	$	31,538

The Company’s policy is to include interest and penalties related to unrecognized tax benefits within the provision for taxes. The Company accrued $0.6 million and $0 for interest as of December 31, 2019 and 2018, respectively.

None of the unrecognized tax benefits, if recognized, would affect the effective income tax rate for any of the above years due to the valuation allowance that currently offsets deferred tax assets. The Company does not anticipate that the total amount of unrecognized income tax benefits will significantly increase or decrease in the next 12 months.

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The Company’s primary tax jurisdiction is the United States. For United States federal and state tax purposes, returns for tax years 2006 and forward remain open and subject to tax examination by the appropriate federal or state taxing authorities. Brazil tax years 2011 and forward remain open and subject to examination.

As of December 31, 2019, the U.S. Internal Revenue Service (the IRS) has completed its audit of the Company for tax year 2008 and concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the U.S. federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

14. Geographical Information

The chief operating decision maker is the Company's Chief Executive Officer, who makes resource allocation decisions and assesses performance based on financial information presented on a consolidated basis. There are no segment managers who are held accountable by the chief operating decision maker, or anyone else, for operations, operating results, and planning for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

Revenue

Revenue by geography, based on each customer's location, is shown in Note 9, "Revenue Recognition".

Property, Plant and Equipment

December 31, (In thousands)	2019		2018
United States	$	13,799	$	10,404
Brazil	14,277		6,447
Europe	854		198
	$	28,930	$	17,049

15. Subsequent Events

Warrants Exercises for Cash

On January 13, 2020 Foris Ventures, LLC (Foris), an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock, delivered to the Company an irrevocable notice of cash exercise with respect to a warrant to purchase 4,877,386 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to a warrant issued by the Company on August 17, 2018. On January 14, 2020, the Company received approximately $14.0 million from Foris in connection with the warrant exercise representing 4,877,386 shares of common stock.

On March 11, 2020 Foris provided to the Company a notice of cash exercise to purchase 5,226,481 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to the PIPE Rights (discussed in the January 2020 Private Placement section below) issued by the Company on January 31, 2020. On March 12, 2020, the Company received approximately $15.0 million from Foris in connection with the PIPE Rights exercise.

Exchange of Senior Convertible Notes Due 2022

On January 14, 2020, the Company completed the exchange, pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), of the Company’s Senior Convertible Notes Due 2022 (or the Prior Notes) for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes due 2022), (ii) an aggregate of 2,742,160 shares of Common Stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of Common Stock, (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of Common Stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, (v) accrued and unpaid interest on the Senior Convertible Notes Due 2022 (payable on or prior to January 31, 2020) and (vi) cash fees in an aggregate amount of $1.0 million (payable on or prior to January 31, 2020).

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The New Notes have substantially similar terms as the Prior Notes, except that (i) the Company would not be required to redeem the New Notes in an aggregate principal amount of $10 million on December 31, 2019, (ii) the Company would only be required to redeem the New Notes in an aggregate amount of $10 million following the receipt by the Company of at least $80 million of aggregate net cash proceeds from one or more financing transactions, and at a price of 107% of the amount being redeemed, (iii) the financing activity requirement was reduced such that the Company would only be required to raise aggregate net cash proceeds of $50 million from one or more financing transactions by January 31, 2020, (iv) the Company would have until January 31, 2020 to comply with certain covenants related to the repayment, conversion or exchange into equity or amendment of certain outstanding indebtedness of the Company, and (v) the deadline for the Company to seek the Stockholder Approval would be extended from January 31, 2020 to March 15, 2020.

On February 18, 2020, the Company and the Holders entered into separate waiver and forbearance agreements, (the W&F Agreements), pursuant to which the Holders agreed to, for 60 days following the date of the W&F Agreement, except in case of early termination of the W&F Agreement or, solely with respect to the Stockholder Approval if the other defaults described below have been cured on or prior to the date that is 60 days following the date of the W&F Agreement, until May 31, 2020 (the W&F Period), and in each case subject to certain conditions to effectiveness contained in the W&F Agreement, (i) forbear from exercising certain of their rights and remedies with respect to certain defaults by the Company, including, but not limited to, the Company's failure, on or before January 31, 2020, (A) to receive aggregated net cash proceeds of not less than $50 million from one or more financing transactions, (B) to repay in full or convert into equity all indebtedness outstanding under the Schottenfeld September Credit Agreement and the Schottenfeld November Credit and Security Agreement or amend all such indebtedness outstanding to fit within the definition of permitted indebtedness of the New Notes, and certain other events of default, and (ii) waive any event of default for (A) violations of the minimum liquidity covenant since December 31, 2019 and (B) failure to obtain the Stockholder Approval prior to March 15, 2020.

In addition, pursuant to the W&F Agreements, the Company and the Holders agreed that (i) the New Note amortization payment due on March 1, 2020 (the Amortization Payment) shall be in the aggregate amount of $10.0 million (split proportionally among the Holders) and that the Company shall elect to pay such amortization payment in shares of Common Stock in accordance with the terms of the New Note, provided however, that: (A) the Amortization Stock Payment Price (as defined in the New Note) shall be $3.00, (B) the Amortization Share Payment Period (as defined in the New Note) with respect to the Amortization Payment will end on April 30, 2020 rather than March 31, 2020; and (C) in the event that Holder does not elect to receive the full Amortization Share Amount (as defined in the New Note) during such Amortization Share Payment Period, then the Amortization Payment shall be automatically reduced by the portion of such Amortization Payment not received by the Holder, (ii) there shall be no amortization payment due on April 1, 2020, and (iii) the amortization payment due on May 1, 2020 shall be in the aggregate amount of $8.9 million (split proportionally among the Holders).

On February 24, 2020, a Holder of the Rights notified the Company about the exercise of the Rights for the issuance of an aggregate of 2,484,321 shares of common stock, which were issued by the Company according to the terms of the Senior Convertible Notes Due 2022.

January 2020 Warrant Amendments and Exercises, Debt Equitization and PIPE

As described below in further detail, on January 31, 2020, the Company completed a series of transactions that resulted in the Company (i) receiving $28.3 million in cash, (ii) reducing its aggregate debt principal by $60.0 million and accrued interest by approximately $10.0 million, (iii) issuing an aggregate of (A) 25,326,095 shares of common stock as a result of the exercise of outstanding warrants, and (B) 13,989,973 new shares of common stock in private placements, and (iv) issuing rights to purchase an aggregate of 18,649,961 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months.

Warrant Amendments

On January 31, 2020, the Company entered into separate warrant amendment agreements (the Warrant Amendments) with Foris and certain other holders (the Warrant Holders) of the Company’s outstanding warrants to purchase shares of the Company’s common stock, pursuant to which the exercise price of certain warrants (the Amended Warrants) held by the Warrant Holders totaling 1.2 million shares and Foris totaling 10.2 million shares was reduced to $2.87 per share upon the exercise of the Amended Warrant.

Warrant Exercises by Certain Holders

In connection with the entry into the Warrant Amendments, on January 31, 2020 the Warrant Holders delivered to the Company irrevocable notices of cash exercise with respect to their Amended Warrants, representing an aggregate of 1,160,929 shares of Common Stock (the Warrant Amendment Shares), and the Company issued to the Holders rights to purchase an aggregate of 1,160,929 shares of Common Stock, at an exercise price of $2.87 per share, for an exercise term of twelve months

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from the January 31, 2020 issuance (the Rights). The Company received net proceeds of $3.3 million from the exercise of the Amended Warrants and issued to the Holders the Warrant Amendment Shares.

Warrant Exercise, Common Stock Purchase and Debt Equitization by Foris – Related Party

On January 31, 2020, the Company and Foris entered into a warrant exercise agreement (the Exercise Agreement) pursuant to which (i) Foris (A) exercised all of its then outstanding common stock purchase warrants (the Foris Warrants), totaling 19,287,780 shares of Common Stock (the Foris Warrant Shares), at a weighted average exercise price of approximately $2.84 per share (following the Warrant Amendments noted above) for an aggregate exercise price of $54.8 million (the Exercise Price), and (B) purchased 5,279,171 shares of Common Stock (the Foris Shares), at $2.87 per share for a total purchase price of $15.2 million (Purchase Price), (ii) Foris paid the Exercise Price and the Purchase Price through the cancellation of $70 million of principal and accrued interest owed by the Company to Foris under the Foris $19 million Note and the Foris LSA (as discussed in Note 4, "Debt") and (iii) the Company issued to Foris the Foris Shares and an additional right to purchase 8,778,230 shares of Common Stock at a purchase price of $2.87 per share, for a period of 12 months from the Exercise Agreement.

January 2020 Private Placement

On January 31, 2020 the Company entered into separate Security Purchase Agreements (the Purchase Agreements) with certain accredited investors (the Investors), including Foris, for the issuance and sale of an aggregate of 8,710,802 shares of Common Stock (the PIPE Shares) and rights to purchase an aggregate of 8,710,802 shares of Common Stock (the PIPE Rights) at a purchase price of $2.87 per share, for a period of 12 months for an aggregate purchase price of $25 million.

Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan

In February 2020, the Company's Board of Directors (the Board) approved increases to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (the Equity Plan) and 2010 Employee Stock Purchase Plan (the Purchase Plan). These shares in connection with the Equity Plan represented an automatic annual increase in the number of shares available for grant and issuance under the Equity Plan of 5,887,133 shares and under the Purchase Plan of 588,713 shares. These increases correspond to approximately 5.0% and 0.5%, respectively, of the total outstanding shares of the Company’s common stock as of December 31, 2019. These automatic increases are effective as of January 1, 2020.

Schottenfeld Forbearance Agreement

The Company and Schottenfeld Opportunities Fund II, L.P. (Schottenfeld) and certain of its affiliates (collectively, the Lenders) are parties (i) to certain Credit Agreements, each dated September 10, 2019 (collectively, the September Credit Agreements) and (ii) to a Credit and Security Agreement, dated November 14, 2019 (the CSA, and collectively with the September Credit Agreements, the Credit Agreements), pursuant to which the Company issued to the Lenders certain notes (the September Notes and the November Notes, respectively, and collectively, the Schottenfeld Notes) and warrants (the September Warrants and the November Warrants, respectively, and collectively, the Shottenfeld Warrants) to purchase shares (the Warrant Shares) of the Company’s common stock. See Not 4, “Debt” for further information.

On February 28, 2020, the Company entered into a forbearance agreement with the Lenders, pursuant to which the Lenders would forbear, for 60 days from the date of the Forbearance Agreement, unless terminated earlier (the Forbearance Period), to exercise certain rights under the Credit Agreement as a result of the Company’s defaults under the Credit Agreements and related Schottenfeld Notes, including the failure of the Company to (i) to pay all principal and accrued interest on the November Notes at the maturity date, (ii) the failure to pay on or before December 31, 2019, all accrued and unpaid interest through December 31, 2019 on the September Notes, and (iii) the failure, on or before December 15, 2019, to convert or exchange at least $60 million, but not less than 100%, of certain junior outstanding indebtedness into equity in the Company, and certain other events of default. Under the forbearance agreement the Company agreed to (i) pay a late fee of 5% on any obligations under the November Notes not paid in full on or before the last day of the Forbearance Period; (ii) pay on or prior to the earliest to occur of April 19, 2020 or the last day of the Forbearance Period, (A) all interest due pursuant to the November Notes and the September Notes, plus all interest accruing on such unpaid interest, plus all interest accrued on account of the November Notes and the September Notes from the date of the Forbearance Agreement through the date of such payment, and (B) a forbearance fee in the amount of $150,000; (iii) pay, upon signature of the Forbearance Agreement, $150,000 as a partial payment of the interest that has accrued pursuant to the November Notes and the September Notes as of the date of the Forbearance Agreement; (iv) amended the Schottenfeld Warrants to (A) reduce the exercise price of each Schottenfeld Warrant to $2.87 per share, and (B) with respect to the November Warrants, extend the deadline to register the Warrant Shares for resale by the holders thereof.

Ginkgo Waiver Agreement

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On March 11, 2020, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Waiver Agreement and Amendment to Partnership Agreement (the Ginkgo Waiver), pursuant to the terms of (i) the Ginkgo promissory note dated October 20, 2017, issued by the Company to Ginkgo (as amended, the Ginkgo Note), (ii) the Ginkgo Partnership Agreement, dated October 20, 2017, by and between the Company and Ginkgo, and (iii) the Waiver Agreement and Amendment to Ginkgo Note, dated September 29, 2019, by and between the Company and Ginkgo.

Ginkgo agreed to (i) waive the Company’s failure (a) to pay past due interest and partnership payments, including interest thereon of $6.7 million, and (b) to comply with a reporting covenant prior to March 31, 2020, (iii) to make a prior waiver fee payment of $0.5 million on December 15, 2019, (ii) waive any cross defaults due to events of default under other debt obligations by the Company, and (iii) amend payments on the Ginkgo Partnership Agreement beginning on March 31, 2020 to a monthly payment of $0.5 million through and including October 31, 2021.

Total Note Extension Agreement

On March 11, 2020, the Company and Total Raffinage Chimie (Total) entered into a Senior Convertible Note Maturity Extension Agreement that resulted in the reissuance of the December 20, 2019 promissory note under which the Company owed Total $10.2 million plus accrued interest. Under the terms of the Senior Convertible Note Maturity Extension Agreement, the Company paid Total $1.5 million to satisfy all accrued but unpaid interest and to reduce the principal balance of the reissued note by $1.1 million. The reissued note has (i) a maturity date of March 31, 2020, (ii) a $9.1 million principal amount due, (iii) accrues interest at a rate of 12.0% per annum maturity date and (iv) terms substantially identical to the December 20, 2019 promissory note.

Nikko Amendment to Loan Agreement

On March 12, 2020, the Company and Nikko Chemicals Co. Ltd. (Nikko), entered into an amendment to the Loan Agreement dated December 19, 2019, under which the Company borrowed $4.5 million from Nikko (the Nikko Loan). Under the terms of the amendment, the Company paid Nikko $0.5 million to reduce the principal balance of the Loan Agreement to $4.0 million, the maturity date of the amended Loan Agreement was extended to March 31, 2020, with an increase in the interest rate to 8.0% per annum, and other terms substantially identical to the December 19, 2019 Nikko Loan.

Selected Quarterly Financial Data

Not applicable for smaller reporting companies.

ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE

None.

ITEM 9A. CONTROLS AND PROCEDURES

(a)Evaluation of Disclosure Controls and Procedures

We maintain disclosure controls and procedures (as that term is defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934 (the Exchange Act) that are designed to provide reasonable assurance that information required to be disclosed in our reports under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the U.S. Securities and Exchange Commission’s rules and forms, and that such information is accumulated and communicated to our management, including our principal executive officer (CEO) and interim chief financial officer (CFO) and, as appropriate, to allow timely decisions regarding required disclosures.

In connection with the preparation of this Annual Report on Form 10-K, we carried out an evaluation under the supervision of and with the participation of management, including our CEO and CFO, as of December 31, 2019, of the effectiveness of the design and operation of our disclosure controls and procedures. Based upon this evaluation, our CEO and CFO concluded that as of December 31, 2019, our disclosure controls and procedures were not effective because of the material weakness in our internal control over financial reporting described below.

To address the material weakness described below, management performed additional analysis and other procedures to ensure that our consolidated financial statements were prepared in accordance with U.S. GAAP. Accordingly, management believes that the consolidated financial statements and disclosures included in this Annual Report on Form 10-K fairly present,

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in all material respects, in accordance with U.S. GAAP, our financial position, results of operations and cash flows for the periods presented.

(b)Management’s Annual Report on Internal Control over Financial Reporting

Our management is responsible for establishing and maintaining adequate internal control over financial reporting and for the assessment of the effectiveness of internal control over financial reporting as defined in Rule 13a-15(f) under the Exchange Act. Our internal control over financial reporting is a process designed by and under the supervision of our CEO and CFO and effected by our board of directors, management, and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of our consolidated financial statements for external purposes in accordance with U.S. GAAP. Our internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that in reasonable detail accurately and fairly reflect the transactions and dispositions of the assets of the Company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of the financial statements in accordance with U.S. GAAP, and that receipts and expenditures of the Company are being made only in accordance with authorizations of management and directors of Company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of the Company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies and procedures may deteriorate.

A “material weakness” is a deficiency, or combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim financial statements will not be prevented or detected on a timely basis.

Management, under the supervision of our CEO and CFO, and oversight of the board of directors, conducted an assessment of the effectiveness of our internal control over financial reporting as of December 31, 2019, based on the criteria set forth in Internal Control–Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO 2013 Framework). Based on this assessment, management has identified the following control deficiency as follows:

•The Company did not have an effective internal and external information and communication process to ensure that relevant and reliable information was communicated timely across the organization, to enable financial personnel to effectively carry out their financial reporting and internal control roles and responsibilities.

As a consequence of the ineffective communication components, the Company did not design, implement, and maintain effective control activities at the transaction level over debt-related liability accounts to mitigate the risk of material misstatement in financial reporting, specifically:

•The Company did not design and operate effective controls over significant non-routine transactions related to certain debt-related contractual obligations.

The control deficiency creates a reasonable possibility that a material misstatement of our annual or interim consolidated financial statements would not be prevented or detected on a timely basis. Therefore, we concluded that this control deficiency is a material weakness and our internal control over financial reporting is not effective as of December 31, 2019.

The Company’s independent registered public accounting firm, Macias, Gini & O’Connell, LLP, who audited the consolidated financial statements included in this annual report, has issued an adverse audit report on the effectiveness of the Company’s internal control over financial reporting as of December 31, 2019, as shown below. Macias, Gini & O’Connell, LLP's report on the consolidated financial statements appears under Part II, Item 8 of this Annual Report on Form 10-K.

(c)Changes in Internal Control over Financial Reporting

Except for the material weakness discussed above in this Item 9A that were identified in the fourth quarter (and that arose in an earlier period), there were no changes in our internal control over financial reporting during the fourth quarter of 2019 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

(d)Remediation Plan

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Management has begun implementing a plan to assess risks of material misstatement over financial reporting, including the enhancement of internal control activities. The plan will be accomplished by the execution of the following:

•Management will enhance internal communication processes through the formalization of internal control documentation.

We believe these activities will remediate the control deficiency identified above and strengthen our internal control over financial reporting. Management, with the oversight of the Audit Committee, has dedicated incremental resources to successfully implement and test effectiveness of the enhanced controls throughout 2020.

As we continue to evaluate and work to improve our internal control over financial reporting, management may determine to take additional measures to address control deficiencies or determine to modify the remediation plan described above. We cannot be certain, however, that we will effectively remediate such material weakness or when we will do so, nor can we be certain of whether additional actions will be required or the costs of any such actions. In designing and evaluating disclosure controls and procedures and internal control over financial reporting, management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives. In addition, the design of disclosure controls and procedures and internal control over financial reporting must reflect the fact that there are resource constraints and that management is required to apply judgement in evaluating the benefits of possible controls and procedures relative to their cost.

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Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of Amyris, Inc.

Opinion on Internal Control over Financial Reporting

We have audited the internal control over financial reporting of Amyris, Inc. and Subsidiaries (the “Company”) as of December 31, 2019, based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (the “COSO criteria”). In our opinion, the Company did not maintain, in all material respects, effective internal control over financial reporting as of December 31, 2019, based on the COSO criteria.

We do not express an opinion or any other form of assurance on management’s statements referring to any corrective actions taken by the company after the date of management’s assessment.

We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (“PCAOB”), the consolidated balance sheets as of December 31, 2019 and 2018 and the related consolidated statement of operations, comprehensive loss, stockholders’ deficit and mezzanine equity and cash flow for each of the two years in the period ended December 31, 2019, and the related notes (collectively referred to as the “consolidated financial statements”) and our report dated March 13, 2020 expressed an unqualified opinion thereon.

Basis for Opinion

The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Item 9A, management’s annual report on internal control over financial reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit of internal control over financial reporting in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on assessed risk. Our audit also included performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion.

A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of the company’s annual or interim financial statements will not be prevented or detected on a timely basis. A material weakness has been identified and an identification of the material weakness described in management’s assessment in Item 9A. The material weakness related to information and communication, as to the lack of processes to ensure that relevant and reliable information was communicated timely across the organization, to enable financial personnel to effectively carry out their financial reporting and internal control roles and responsibilities.

This material weakness contributed to the Company not retaining the required documentation to demonstrate the consistent and timely operation of the controls at a sufficient level of precision to prevent and detect potential misstatements and did not design and operate effective controls over complex, significant, non-routine transactions related to certain debt-related contractual obligations. This material weakness was considered in determining the nature, timing, and extent of audit tests applied in our audit of the 2019 consolidated financial statements, and this report does not affect our report dated March 13, 2020 on those financial statements.

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Definition and Limitations of Internal Control over Financial Reporting

A company's internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with both generally accepted accounting principles and regulatory reporting instructions. A company's internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with both generally accepted accounting principles and regulatory reporting instructions, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company's assets that could have a material effect on the consolidated financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

/s/ Macias Gini & O’Connell LLP

San Francisco, California

March 13, 2020

ITEM 9B. OTHER INFORMATION

None.

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PART III

Certain information required by Part III is omitted from this Form 10-K because the registrant will file with the U.S. Securities and Exchange Commission a definitive proxy statement pursuant to Regulation 14A of the Exchange Act in connection with the solicitation of proxies for the Company’s 2020 Annual Meeting of Stockholders (the 2020 Proxy Statement) within 120 days after the end of the fiscal year covered by this Form 10-K, and certain information included therein is incorporated herein by reference.

ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

The information required under this Item 10 is incorporated by reference to the 2020 Proxy Statement.

ITEM 11. EXECUTIVE COMPENSATION

The information required under this Item 11 is incorporated by reference to the 2020 Proxy Statement.

ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

The information required under this Item 12 is incorporated by reference to the 2020 Proxy Statement.

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

The information required under this Item 13 is incorporated by reference to the 2020 Proxy Statement.

ITEM 14. PRINCIPAL ACCOUNTING FEES AND SERVICES

The information required under this Item 14 is incorporated by reference to the 2020 Proxy Statement.

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PART IV

ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULE

We have filed the following documents as part of this Annual Report on Form 10-K:

1.Financial Statements: See "Index to Consolidated Financial Statements" in Part II, Item 8 of this Annual Report on Form 10-K.

2.Financial Statement Schedule:

a.Allowance for doubtful accounts: see Note 2, "Balance Sheet Details" in Part II, Item 8 of this Annual Report on Form 10-K.

b.Deferred tax assets valuation allowance: see Note 13, "Income Taxes" in Part II, Item 8 of this Annual Report on Form 10-K.

3.Exhibits: See "Index to Exhibits" below.

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INDEX TO EXHIBITS

Exhibit
No.	Description
2.01 a	Quota Purchase Agreement, dated November 17, 2017, among registrant, AB Technologies LLC and DSM Produtos Nutricionais Brasil S.A.
2.02	Amendment No. 1, dated December 28, 2017, to the Quota Purchase Agreement, dated November 17, 2017, among registrant, AB Technologies LLC and DSM Produtos Nutricionais Brasil S.A.
2.03	Amendment No. 2, dated April 16, 2019, to the Quota Purchase Agreement, dated November 17, 2017, among registrant, AB Technologies LLC and DSM Produtos Nutricionais Brasil S.A.
2.04 b	Equity Purchase Agreement, dated October 31, 2019, between registrant and Cosan US, Inc.
3.01	Restated Certificate of Incorporation
3.02	Certificate of Amendment, dated May 9, 2013, to Restated Certificate of Incorporation
3.03	Certificate of Amendment, dated May 12, 2014, to Restated Certificate of Incorporation
3.04	Certificate of Amendment, dated September 18, 2015, to Restated Certificate of Incorporation
3.05	Certificate of Amendment, dated May 18, 2016, to Restated Certificate of Incorporation
3.06	Certificate of Amendment, dated June 5, 2017, to Restated Certificate of Incorporation
3.07	Form of Certificate of Designation of Preferences, Rights and Limitations of Series A 17.38% Convertible Preferred Stock (found at Exhibit A-1, herein)
3.08	Form of Certificate of Designation of Preferences, Rights and Limitations of Series B 17.38% Convertible Preferred Stock (found at Exhibit A-2, herein)
3.09	Certificate of Amendment of the Certificate of Designation of Preferences, Rights and Limitations of Series B 17.38% Convertible Preferred Stock of Amyris, Inc.
3.10	Form of Certificate of Designation of Preferences, Rights and Limitations of Series C Convertible Preferred Stock (found at Exhibit A-3, herein)
3.11	Form of Certificate of Designation of Preferences, Rights and Limitations of Series D Convertible Preferred Stock (found at Exhibit E, herein)
3.12	Restated Bylaws
4.01	Specimen of Common Stock Certificate
4.02	Form of certificate representing the Series A 17.38% Convertible Preferred Stock (found at Exhibit D, herein)
4.03	Form of certificate representing the Series B 17.38% Convertible Preferred Stock (found at Exhibit D, herein)
4.04	Form of certificate representing the Series C Convertible Preferred Stock (found at Exhibit D, herein)
4.05	Form of certificate representing the Series D Convertible Preferred Stock
4.06 a	Amended and Restated Letter Agreement re: Certain Registration Rights dated May 8, 2014 between registrant and the purchasers listed therein
4.07	Warrant to Purchase Stock, dated December 23, 2011, issued to ATEL Ventures, Inc.
4.08 a	Side Letter, dated June 21, 2010, between registrant and Total Gas & Power USA, SAS
4.09	Agreement, dated February 23, 2012, among registrant, Maxwell (Mauritius) Pte Ltd, Naxyris SA, Biolding Investment S.A., and Sualk Capital Ltd.
4.10	Securities Purchase Agreement, dated July 24, 2015, between registrant and the Purchasers listed therein
4.11 c	Warrant to Purchase Stock issued July 29, 2015 by registrant to Total Energies Nouvelles Activités USA
4.12	Exchange Agreement, dated July 26, 2015, between registrant and the investors listed therein

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4.13	Letter Agreement dated as of July 29, 2015 among registrant and registrant’s security holders listed therein
4.14	Warrant to Purchase Stock issued July 29, 2015 by registrant to Total Energies Nouvelles Activités USA
4.15	Warrant to Purchase Stock issued July 29, 2015 by registrant to Maxwell (Mauritius) Pte Ltd
4.16	Warrant to Purchase Stock issued July 29, 2015 by registrant to Maxwell (Mauritius) Pte Ltd
4.17	Registration Rights Agreement, dated October 20, 2015, between registrant and registrant’s security holders listed therein
4.18	Note and Warrant Purchase Agreement, dated February 12, 2016, between registrant and the purchasers listed therein
4.19 d	Warrant to Purchase Stock issued February 12, 2016 by registrant to Foris Ventures, LLC
4.20	Securities Purchase Agreement, dated April 8, 2016, between registrant and Bill & Melinda Gates Foundation
4.21	Letter Agreement re Charitable Purposes and Use of Funds, dated April 8, 2016, between registrant and the Bill & Melinda Gates Foundation
4.22	Warrant to Purchase Stock issued November 16, 2016 by registrant to Nenter & Co., Inc.
4.23	Purchase Money Promissory Note issued December 19, 2016 by registrant to Nikko Chemicals Co. Ltd.
4.24	Form of Securities Purchase Agreement, dated May 8, 2017, between registrant and the other parties thereto
4.25	Amendment No. 1, dated May 30, 2017 to Securities Purchase Agreement, dated May 8, 2017, between registrant and the other parties thereto
4.26	Form of Common Stock Purchase Warrant (Cash Warrant) issued May 11, 2017 by registrant to the purchasers thereof (found at Exhibit C-1, herein)
4.27	Form of Common Stock Purchase Warrant (Dilution Warrant) issued May 11, 2017 by registrant to the purchasers thereof (found at Exhibit C-2, herein)
4.28	Securities Purchase Agreement, dated May 31, 2017, between registrant and the investor named therein
4.29	Securities Purchase Agreement, dated August 2, 2017, between registrant and DSM International B.V.
4.30	Securities Purchase Agreement, dated August 2, 2017, between registrant and affiliates of Vivo Capital LLC
4.31	Form of Common Stock Purchase Warrant (Cash Warrant) issued August 7, 2017 by registrant to DSM International B.V. (found at Exhibit B-1, herein)
4.32	Form of Common Stock Purchase Warrant (Dilution Warrant) issued August 7, 2017 by registrant to DSM International B.V. (found at Exhibit B-2, herein)
4.33	Form of Stockholder Agreement, dated August 3, 2017, between registrant and affiliates of Vivo Capital LLC (found at Exhibit C, herein)
4.34	Common Stock Purchase Warrant (Cash Warrant), issued May 31, 2017, by registrant to the investor named therein
4.35	Common Stock Purchase Warrant (Dilution Warrant), issued May 31, 2017, by registrant to the investor named therein
4.36 a	Stockholder Agreement, dated May 11, 2017, between registrant and DSM International B.V.
4.37 a	Amended and Restated Stockholder Agreement, dated August 7, 2017, between registrant and DSM International B.V.
4.38	Promissory Note issued October 20, 2017 by registrant to Ginkgo Bioworks, Inc.
4.39	Note issued December 28, 2017 by registrant to DSM Finance BV
4.40	Warrant Exercise Agreement, dated August 17, 2018, between registrant and Foris Ventures, LLC
4.41	Warrant Exercise Agreement, dated August 17, 2018, between registrant and Vivo Capital Fund VIII, L.P.
4.42	Warrant Exercise Agreement, dated August 17, 2018, between registrant and Vivo Capital Surplus Fund VIII, L.P.
4.43	Common Stock Purchase Warrant issued August 17, 2018 by registrant to Foris Ventures, LLC

4.44	Common Stock Purchase Warrant issued August 17, 2018 by registrant to Vivo Capital Fund VIII, L.P.
4.45	Common Stock Purchase Warrant issued August 17, 2018 by registrant to Vivo Capital Surplus Fund VIII, L.P.
4.46	Common Stock Purchase Warrant issued August 20, 2018 by registrant to Vivo Capital Fund VIII, L.P.
4.47	Common Stock Purchase Warrant issued August 20, 2018 by registrant to Vivo Capital Surplus Fund VIII, L.P.
4.48	Securities Purchase Agreement, dated November 19, 2018, between registrant and DSM International B.V.
4.49	Securities Purchase Agreement, dated December 6, 2018, among registrant and the investors named therein
4.50	Form of Registration Rights Agreement, dated December 10, 2018, among registrant and the investors party thereto (found at Exhibit B, herein)
4.51	Promissory Note issued April 8, 2019 by registrant to Foris Ventures, LLC
4.52	Securities Purchase Agreement, dated April 15, 2019, between registrant and Foris Ventures, LLC
4.53	Common Stock Purchase Warrant issued April 16, 2019 by registrant to Foris Ventures, LLC
4.54	Warrant Amendment Agreement, dated April 26, 2019, between registrant and Foris Ventures, LLC
4.55	Form of Security Purchase Agreement, dated April 24, April 26 or April 29, 2019, between registrant and certain accredited investors
4.56	Form of Common Stock Purchase Warrant issued April 26, April 29 or May 3, 2019 by registrant to certain accredited investors (found at Exhibit A, herein)
4.57	Common Stock Purchase Warrant issued May 10, 2019 by registrant to LMAP KAPPA Limited
4.58	Common Stock Purchase Warrant issued May 10, 2019 by registrant to Silverback Opportunistic Credit Master Fund Limited
4.59	Warrant to Purchase Common Stock issued May 14, 2019 by registrant to Foris Ventures, LLC
4.60	Form of Senior Convertible Note issued May 15, 2019 by registrant to CVI Investments, Inc. (found at Exhibit A, herein)
4.61	Form of Common Stock Purchase Warrant issued May 15, 2019 by registrant to CVI Investments, Inc. (found at Exhibit B, herein)
4.62	Senior Convertible Note issued May 15, 2019 by registrant to Total Raffinage Chimie
4.63	Senior Convertible Note Maturity Extension, dated June 20, 2019, between registrant and Total Raffinage Chimie
4.64	Promissory Note issued June 11, 2019 by registrant to Foris Ventures, LLC
4.65	Form of Senior Convertible Note issued June 24, 2019 by registrant to B. Riley FBR, Inc. (found at Exhibit A, herein)
4.66	Form of Common Stock Purchase Warrant issued June 24, 2019 by registrant to B. Riley FBR, Inc. (found at Exhibit B, herein)
4.67	Form of Common Stock Purchase Warrant issued July 8, 2019 by registrant to Wolverine Flagship Fund Trading Limited (found at Exhibit A, herein)
4.68	Promissory Note issued July 10, 2019 by registrant to Foris Ventures, LLC
4.69	Warrant Amendment Agreement, dated July 10, 2019, between registrant and Foris Ventures, LLC
4.70	Senior Convertible Note Maturity Extension, dated July 24, 2019, between registrant and Total Raffinage Chimie
4.71	Form of Senior Convertible Note issued July 24, 2019 by registrant to CVI Investments, Inc. (found at Exhibit A, herein)
4.72	Form of Common Stock Purchase Warrant issued July 24, 2019 by registrant to CVI Investments, Inc. (found at Exhibit B, herein)
4.73	Promissory Note issued July 26, 2019 by registrant to Foris Ventures, LLC
4.74	Common Stock Purchase Warrant issued August 14, 2019 by registrant to Naxyris S.A.
4.75	Common Stock Purchase Warrant issued August 14, 2019 by registrant to Foris Ventures, LLC

4.76	Promissory Note issued August 28, 2019 by registrant to Foris Ventures, LLC
4.77	Common Stock Purchase Warrant issued August 28, 2019 by registrant to Foris Ventures, LLC
4.78	Warrant Amendment Agreement, dated August 28, 2019, between registrant and Foris Ventures, LLC
4.79	Warrant Amendment Agreement, dated August 28, 2019, between registrant and Foris Ventures, LLC
4.80	Senior Convertible Note Maturity Extension, dated September 4, 2019, between registrant and Total Raffinage Chimie
4.81	Form of Promissory Note issued September 10, 2019 by registrant to certain accredited investors (found at Exhibit A, herein)
4.82	Form of Common Stock Purchase Warrant issued September 10, 2019 by registrant to certain accredited investors
4.83	Form of Promissory Note issued September 17, 2019, September 19, 2019 and September 23, 2019 by registrant to DSM Finance B.V.
4.84	Form of Senior Convertible Note issued November 14, 2019 by registrant to certain accredited investors (found at Exhibit A, herein)
4.85	Common Stock Purchase Warrant November 14, 2019 by registrant to certain accredited investors
4.86	Form of Common Stock Purchase Agreement issued November 15, 2-10 by registrant to certain accredited investors
4.87	Promissory Note issued November 27, 2019 by registrant to Foris Ventures, LLC
4.88	Common Stock Purchase Warrant issued November 27, 2019 by registrant to Foris Ventures, LLC
4.89	Form of Senior Convertible Note due 2022 issued by Registrant to certain accredited investors
4.90	Description of Registrant’s Securities Registered Under Section 12 of the Exchange Act
10.01	Lease, dated August 22, 2007, between registrant and ES East Associates, LLC
10.02	First Amendment, dated March 10, 2008, to Lease, dated August 22, 2007, between registrant and ES East Associates, LLC
10.03	Second Amendment, dated April 25, 2008, to Lease, dated August 22, 2007, between registrant and ES East Associates, LLC
10.04	Third Amendment, dated July 31, 2008, to Lease, dated August 22, 2007, between registrant and ES East Associates, LLC
10.05	Fourth Amendment, dated November 14, 2009, to Lease, dated August 22, 2007, between registrant and ES East Associates, LLC
10.06	Fifth Amendment, dated October 15, 2010, to Lease, dated August 22, 2007, between registrant and ES East, LLC
10.07	Sixth Amendment, dated April 30, 2013, to Lease, dated August 22, 2007, between registrant and ES East, LLC
10.08	Lease dated April 25, 2008 between registrant and EmeryStation Triangle, LLC
10.09	Letter, dated April 25, 2008, amending Lease between registrant and EmeryStation Triangle, LLC
10.10	Second Amendment, dated February 5, 2010, to Lease, dated April 25, 2008, between registrant and EmeryStation Triangle, LLC
10.11	Third Amendment, dated May 1, 2013, to Lease, dated April 25, 2008, between registrant and EmeryStation Triangle, LLC
10.12	Pilot Plant Expansion Right Letter dated December 22, 2008 between registrant and EmeryStation Triangle, LLC
10.13	Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. And Techno Park Empreendimentos e Administração Imobiliária Ltda.
10.14	First Amendment, dated July 31, 2013, to Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. And Techno Park Empreendimentos e Administração Imobiliária Ltda.
10.15	Second Amendment, dated October 31, 2015, to Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. And Techno Park Empreendimentos e Administração Imobiliária Ltda.
10.16	Third Amendment, dated March 30, 2016, to Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. And Techno Park Empreendimentos e Administração Imobiliária Ltda.

10.17	Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, between Lucio Tomasiello and Amyris Brasil S.A. (including Amendment No. 1, dated July 5, 2008, and Amendment No. 2, dated October 30, 2008)
10.18 ae	Third Amendment, dated October 1, 2012, to the Private Instrument of Non Residential Real Estate Lease Agreement, dated March 31, 2008, between Lucio Tomasiello and Amyris Brasil Ltda.
10.19 ae	Fourth Amendment, dated March 3, 2015, to the Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, among Amyris Brasil Ltda., Lucius Tomasiello and Mauricio Tomasiello
10.20 e	Fifth Amendment, dated September 22, 2015, to the Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, among Amyris Brasil Ltda., Lucius Tomasiello and Mauricio Tomasiello
10.21 e	Sixth Amendment, dated October 17, 2016, to the Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, among Amyris Brasil Ltda., Lucius Tomasiello and Mauricio Tomasiello
10.22 e	Seventh Amendment, dated September 25, 2017, to the Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, among Amyris Brasil Ltda., Lucius Tomasiello and Mauricio Tomasiello
10.23 e	Eight Amendment, dated December 9, 2019, to the Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, among Amyris Brasil Ltda., Lucius Tomasiello and Mauricio Tomasiello
10.24 e	Lease Agreement, dated May 1, 2010, between São Martinho S.A. and SMA Indústria Química S.A.
10.25 e	Amendment No. 2, dated August 31, 2015, to the Lease Agreement, dated May 1, 2010, between São Martinho S.A. and SMA Indústria Química S.A.
10.26 e	Amendment No. 3, dated September 1, 2016, to the Lease Agreement, dated May 1, 2010, between São Martinho S.A. and SMA Indústria Química Ltda. (f.k.a. SMA Indústria Química S.A.)
10.27 e	Amendment No. 4, dated December 26, 2017, to the Lease Agreement, dated May 1, 2010, between São Martinho S.A. and SMA Indústria Química Ltda. (f.k.a. SMA Indústria Química S.A.)
10.28 a	Partnership Agreement, dated October 20, 2017, between registrant and Ginkgo Bioworks, Inc.
10.29	Credit Agreement, dated December 28, 2017, between registrant and DSM Finance BV
10.30 a	Joint Venture Agreement, dated December 6, 2016, among registrant, Nikko Chemicals Co. Ltd., and Nippon Surfactant Industries Co., Ltd.
10.31 a	First Amended and Restated LLC Operating Agreement of Aprinnova, LLC (f/k/a Neossance, LLC) dated December 6, 2016
10.32	Loan and Security Agreement, dated June 29, 2018, among the registrant, certain subsidiaries of the registrant and GACP Finance Co., LLC
10.33	Amendment No. 1, dated August 24, 2018, to Loan and Security Agreement, dated June 29, 2018, among registrant, certain of registrant’s subsidiaries and GACP Finance Co., LLC, as administrative agent and lender
10.34	Amendment No. 2, dated November 14, 2018, to Loan and Security Agreement, dated June 29, 2018, among registrant, certain of registrant’s subsidiaries and GACP Finance Co., LLC, as administrative agent and lender
10.35	Amendment No. 3, dated December 14, 2018, to Loan and Security Agreement, dated June 29, 2018, among registrant, certain of registrant’s subsidiaries and GACP Finance Co., LLC, as administrative agent and lender
10.36	Amendment No. 4, dated April 4, 2019, to Loan and Security Agreement, dated June 29, 2018, among registrant, certain of registrant’s subsidiaries and GACP Finance Co., LLC, as administrative agent and lender
10.37	Amendment No 5 to Loan Agreement and Waiver, dated August 14, 2019, among registrant, certain of registrant’s subsidiaries and Foris Ventures, LLC
10.38 b	Supply Agreement, dated December 28, 2017, between registrant and DSM Produtos Nutricionais Brasil S.A.
10.39 b	Amendment No. 1, dated November 19, 2018, to Supply Agreement, dated December 28, 2017, between registrant and DSM Nutritional Products AG, as assignee of DSM Produtos Nutricionais Brasil S.A.

10.40	Amendment No. 2, dated April 16, 2019, to Supply Agreement, dated December 28, 2017 between registrant and DSM Nutritional Products AG, as assignee of DSM Produtos Nutricionais Brasil S.A.
10.41	Amendment No. 3, dated October 3, 2019, to Supply Agreement, dated December 28, 2017, between registrant and DSM Nutritional Products AG, as assignee of DSM Produtos Nutricionais Brasil S.A.
10.42	Assignment Agreement, dated December 31, 2018, between registrant and Hangzhou Xinfu Science & Tech Co. Ltd
10.43	Lease Agreement, dated May 10, 2019, between Amyris Brotas Fermemtação de Performance Ltda. and Raízen Energia S.A.
10.44	Credit Agreement, dated April 8, 2019, between registrant and Foris Ventures, LLC
10.45	Loan Purchase Agreement, dated April 15, 2019, among registrant, GACP Finance Co., LLC and Foris Ventures, LLC
10.46	Assignment and Assumption Agreement, dated April 16, 2019, among registrant, DSM Nutritional Products AG and DSM Nutritional Products Europe Ltd.
10.47	Joint Venture Agreement dated May 10, 2019, among registrant, Amyris Brotas Fermentacao de Performance Ltda. and Raizen Energia S.A.
10.48	Exchange Agreement, dated May 10, 2019, between registrant and Foris Ventures, LLC
10.49	Exchange Agreement, dated May 10, 2019, among registrant and Silverback Asset Management, LLC
10.50	Exchange Agreement, dated May 13, 2019, between registrant and Maxwell (Mauritius) Pte Ltd.
10.51	Exchange Agreement, dated May 15, 2019, between registrant and Total Raffinage Chimie
10.52	Exchange Agreement, dated May 15, 2019, between registrant and CVI Investments, Inc.
10.53	Credit Agreement, dated June 11, 2019, between registrant and Foris Ventures, LLC
10.54	Exchange Agreement, dated June 24, 2019, between registrant and B. Riley FBR, Inc.
10.55	Consulting Agreement, dated May 28, 2019, between registrant and FLG Partners, LLC
10.56	Exchange Agreement, dated July 2, 2019, between registrant and Wolverine Flagship Fund Trading Limited
10.57	Credit Agreement, dated July 10, 2019, between registrant and Foris Ventures, LLC
10.58	Second Exchange Agreement, dated July 24, 2019, between registrant and CVI Investments, Inc.
10.59	Loan Agreement, dated July 29, 2019, between registrant and Nikko Chemicals Co., Ltd.
10.60	Loan and Security Agreement, dated August 14, 2019, among registrant, certain of registrant’s subsidiaries and Naxyris S.A.
10.61	Credit Agreement, dated August 28, 2019, between registrant and Foris Ventures, LLC
10.62	Form of Credit Agreement, dated September 10, 2019, between registrant and certain accredited investors
10.63	Standstill Agreement, dated September 10, 2019, among registrant and certain accredited investors
10.64	Credit Agreement, dated September 17, 2019, between registrant and DSM Finance B.V.
10.65	Credit and Security Agreement, dated November 14, 2019, by and among the Company, the Subsidiary Guarantors, Schottenfeld Opportunities Fund II, L.P. and Phase Five Partners, LP
10.66	Loan Agreement, dated December 19, 2019, between registrant and Nikko Chemicals Co., Ltd.
10.67	Form of Exchange Agreement, dated December 30, 2019, by and between the Company and each of the Investors
10.68 f	Offer Letter dated September 27, 2006 between registrant and John Melo
10.69 f	Amendment, dated December 18, 2008, to Offer Letter, dated September 27, 2006, between registrant and John Melo
10.70 f	Performance Stock Option Award Agreement, dated May 29, 2018, between the registrant and John Melo
10.71 f	Amendment #1, dated May 30, 2018, to Executive Severance Plan Participation Agreement, dated December 18, 2013, between the registrant and John Melo
10.72 f	Offer Letter, dated November 23, 2016, between registrant and Kathleen Valiasek
10.73 f	Amendment, dated March 6, 2017, to Offer Letter, dated November 23, 2016, between registrant and Kathleen Valiasek
10.74 f	Offer Letter, dated June 5, 2017, between registrant and Nicole Kelsey

10.75 f	Amendment, dated September 18, 2017, to Offer Letter, dated June 5, 2017, between registrant and Nicole Kelsey
10.76 f	Offer Letter, dated October 5, 2017, between registrant and Eduardo Alvarez
10.77 f	2005 Stock Option/Stock Issuance Plan, as amended on July 19, 2011
10.78 f	Form of Notice of Grant of Stock Option under registrant’s 2005 Stock Option/Stock Issuance Plan
10.79 f	Form of Notice of Grant of Stock Option (non-Exempt) under registrant’s 2005 Stock Option/Stock Issuance Plan
10.80 f	Form of Notice of Grant of Stock Option (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan
10.81 f	Form of Stock Option Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan
10.82 f	Form of Stock Option Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan
10.83 f	Form of Stock Purchase Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan
10.84 f	Form of Stock Purchase Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan
10.85 f	2010 Equity Incentive Plan, as amended on May 22, 2018, and forms of award agreements thereunder
10.86 f	2010 Employee Stock Purchase Plan, as amended on May 22, 2018, and form of subscription agreement thereunder
10.87 f	Executive Severance Plan, effective November 6, 2013
10.88 f	Compensation arrangements between registrant and its non-employee directors
10.89 f	Compensation arrangements between registrant and its executive officers
10.90 f	Form of Indemnity Agreement between registrant and its directors and executive officers
21.01	List of subsidiaries
23.01	Consent of Macias Gini & O’Connell LLP, independent registered public accounting firm
24.01	Power of Attorney (included on signature page to this Form 10-K)
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.01 g	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.02 g	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
101.INS	XBRL Instance Document
101.SCH	XBRL Taxonomy Extension Schema Document
101.CAL	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF	XBRL Taxonomy Extension Definition Linkbase Document
101.LAB	XBRL Taxonomy Extension Label Linkbase Document
101.PRE	XBRL Taxonomy Extension Presentation Linkbase Document

a	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
b	Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K promulgated under the Exchange Act.
c	Registrant issued substantially identical warrants to the purchasers under that certain Securities Purchase Agreement entered into on July 24, 2015. Registrant has filed the warrant issued to Total Energies Nouvelles Activites USA and has included with such exhibit a schedule (Schedule A to Exhibit 4.11) identifying each of the warrants and setting forth the material details in which the other warrants differ from the filed warrant (i.e., the names of the purchasers, the certificate numbers and the respective numbers of shares underlying the warrants).
d	Substantially identical warrants were issued to three separate investors. Registrant has filed the warrant issued to Foris Ventures, LLC, which is substantially identical in all material respects to all of such warrants except as to the parties thereto, the issue date and the number of underlying shares.
e	Translation to English from Portuguese in accordance with Rule 12b-12(d) of the regulations promulgated by the Securities and Exchange Commission under the Exchange Act.
f	Indicates management contract or compensatory plan or arrangement.
g	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

	AMYRIS, INC.
By:	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer
	March 13, 2020

POWER OF ATTORNEY

KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints John G. Melo and Jonathan Wolter, and each of them, as his or her true and lawful attorneys-in-fact and agents, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign any and all amendments to this Annual Report on Form 10-K, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the U.S. Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming that all said attorneys-in-fact and agents, or any of them or their or his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual Report on Form 10-K has been signed by the following persons on behalf of the registrant, in the capacities and on the dates indicated.

Signature	Title	Date
/s/ John G. Melo John G. Melo	Director, President and Chief Executive Officer (Principal Executive Officer)	March 13, 2020
/s/ Jonathan Wolter Jonathan Wolter	Interim Chief Financial Officer (Principal Financial Officer)	March 13, 2020
/s/ Anthony Hughes Anthony Hughes	Chief Accounting Officer (Principal Accounting Officer)	March 13, 2020
/s/ John Doerr John Doerr	Director	March 13, 2020
/s/ Geoffrey Duyk Geoffrey Duyk	Director	March 13, 2020
/s/ Philip Eykerman Philip Eykerman	Director	March 13, 2020
/s/ Christoph Goppelsroeder Christoph Goppelsroeder	Director	March 13, 2020
/s/ Frank Kung Frank Kung	Director	March 13, 2020
/s/ James McCann James McCann	Director	March 13, 2020
/s/ Steve Mills Steve Mills	Director	March 13, 2020
/s/ Carole Piwnica Carole Piwnica	Director	March 13, 2020
/s/ Lisa Qi Lisa Qi	Director	March 13, 2020
/s/ R. Neil Williams R. Neil Williams	Director	March 13, 2020
/s/ Patrick Yang Patrick Yang	Director	March 13, 2020

EX-4.87

Exhibit 4.87

SECURED TERM PROMISSORY NOTE

$10,000,000.00 Advance Date: November 27, 2019

Maturity Date: March 31, 2023

FOR VALUE RECEIVED, Amyris, Inc., a Delaware corporation (the “Parent”), for itself and each of its Subsidiaries that has delivered a Joinder Agreement (collectively with Parent, the "Borrowers") hereby promises to pay to the order of Foris Ventures, LLC, a Delaware limited liability company or the holder of this Note ("Foris") at 751 Laurel Street #717, San Carlos, CA or such other place of payment as the holder of this Secured Term Promissory Note (this "Promissory Note") may specify from time to time in writing, in lawful money of the United States of America, the principal amount of Ten Million Dollars ($10,000,000.00) or such other principal amount as Lender has advanced to the Borrowers, together with interest at a fixed rate equal to (i) the greater of (A) 12% or (B) the rate of interest payable by the Borrowers with respect to any Indebtedness (as defined in the Loan Agreement), including, but not limited to, the rate of interest charged pursuant to the Naxos LSA, provided, that for such purpose, the rate of interest charged pursuant to the Naxos LSA shall be the rate of interest payable by the Borrowers pursuant to the Naxos LSA, minus 25 basis points, in each case based upon a year consisting of 360 days, with interest computed daily based on the actual number of days in each month.

This Promissory Note is one of the Term Notes referred to in, and is executed and delivered in connection with, that certain Amended and Restated Loan and Security Agreement, dated as of October 28, 2019 (as the same may from time to time be amended, modified or supplemented in accordance with its terms, the "Loan Agreement"), by and among the Borrowers and Foris, and is entitled to the benefit and security of the Loan Agreement and the other Loan Documents (as defined in the Loan Agreement), to which reference is made for a statement of all of the terms and conditions thereof. All payments shall be made in accordance with the Loan Agreement. All terms defined in the Loan Agreement shall have the same definitions when used herein, unless otherwise defined herein.An Event of Default under the Loan Agreement shall constitute a default under this Promissory Note.

The Borrowers waive presentment and demand for payment, notice of dishonor, protest and notice of protest under the UCC or any applicable law. The Borrowers agree to make all payments under this Promissory Note without setoff, recoupment or deduction and regardless of any counterclaim or defense. This Promissory Note has been negotiated and delivered to Lender and is payable in the State of California. This Promissory Note shall be governed by and construed and enforced in accordance with, the laws of the State of California, excluding any conflicts of law rules or principles that would cause the application of the laws of any other jurisdiction.

[Signature Page Follows]

Exhibit 4.87

THE PARENT FOR ITSELF AND ON BEHALF OF ITS SUBSIDIARIES THAT HAVE DELIVERED A JOINDER AGREEMENT:

AMYRIS, INC.

By: /s/ Kathleen Valiasek

Name: Kathleen Valiasek

Title: Chief Business Officer

[SIGNATURE PAGE TO SECURED TERM PROMISSORY NOTE]

EX-4.88

Exhibit 4.88

NEITHER THIS SECURITY NOR THE SECURITIES INTO WHICH THIS SECURITY IS EXERCISABLE HAS BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO AN AVAILABLE EXEMPTION FROM, OR IN A TRANSACTION NOT SUBJECT TO, THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT AND IN ACCORDANCE WITH APPLICABLE STATE SECURITIES LAWS. THIS SECURITY AND THE SECURITIES ISSUABLE UPON EXERCISE OF THIS SECURITY MAY BE PLEDGED IN CONNECTION WITH A BONA FIDE MARGIN ACCOUNT WITH A REGISTERED BROKER-DEALER OR OTHER LOAN WITH A FINANCIAL INSTITUTION THAT IS AN “ACCREDITED INVESTOR” AS DEFINED IN RULE 501(a) UNDER THE SECURITIES ACT OR OTHER LOAN SECURED BY SUCH SECURITIES.

COMMON STOCK PURCHASE WARRANT

AMYRIS, INC.

Warrant Shares: 1,000,000     Issue Date: November 27, 2019

THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, FORIS VENTURES, LLC or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or after the date hereof (the “Initial Exercise Date”) and on or prior to the close of business on the two (2) year anniversary of the Initial Exercise Date (the “Termination Date”) but not thereafter, to subscribe for and purchase from Amyris, Inc., a Delaware corporation (the “Company”), up to ONE MILLION (1,000,000) shares (as subject to adjustment hereunder, the “Warrant Shares”) of the Company’s common stock, par value $0.0001 per share (the “Common Stock”). The purchase price of one share of Common Stock under this Warrant shall be equal to the Exercise Price, as defined in Section 2(b).

Section 1. Definitions. Capitalized terms used and not otherwise defined herein shall have the meanings set forth in that certain Amended and Restated Loan and Security Agreement, dated October 28, 2019 (as amended or otherwise modified, the “Loan Agreement”), by and among the Company, certain of the Company’s Subsidiaries party thereto, and the Holder.

Section 2. Exercise.

a)Exercise of Warrant. Exercise of the purchase rights represented by this Warrant may be made, in whole or in part, at any time or times on or after the Initial Exercise Date and on or before the Termination Date by delivery to the Company of a duly executed facsimile copy or PDF copy submitted by electronic (or e-mail attachment)

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of the Notice of Exercise in the form annexed hereto (“Notice of Exercise”). Within two (2) Trading Days following the date of exercise as aforesaid, the Holder shall deliver the aggregate Exercise Price for the shares specified in the applicable Notice of Exercise by wire transfer or cashier’s check drawn on a United States bank unless the cashless exercise procedure specified in Section 2(c) below is specified in the applicable Notice of Exercise.No ink-original Notice of Exercise shall be required, nor shall any medallion guarantee (or other type of guarantee or notarization) of any Notice of Exercise form be required. Notwithstanding anything herein to the contrary, the Holder shall not be required to physically surrender this Warrant to the Company until the Holder has purchased all of the Warrant Shares available hereunder and the Warrant has been exercised in full, in which case, the Holder shall surrender this Warrant to the Company for cancellation within three (3) Trading Days of the date the final Notice of Exercise is delivered to the Company. Partial exercises of this Warrant resulting in purchases of a portion of the total number of Warrant Shares available hereunder shall have the effect of lowering the outstanding number of Warrant Shares purchasable hereunder in an amount equal to the applicable number of Warrant Shares purchased. The Company shall maintain records showing the number of Warrant Shares purchased and the date of such purchases. The Company shall deliver any objection to any Notice of Exercise within one (1) Business Day of receipt of such notice. The Holder and any assignee, by acceptance of this Warrant, acknowledge and agree that, by reason of the provisions of this paragraph, following the purchase of a portion of the Warrant Shares hereunder, the number of Warrant Shares available for purchase hereunder at any given time may be less than the amount stated on the face hereof.

b)Exercise Price. The exercise price per share of the Common Stock under this Warrant shall be $3.87, subject to adjustment hereunder (the “Exercise Price”).

c)Cashless Exercise. Notwithstanding anything contained herein to the contrary, if a registration statement covering the resale of the Warrant Shares subject to the applicable Notice of Exercise is not available for the resale of such Warrant Shares, at any time after the six month anniversary of the Initial Exercise Date, this Warrant may be exercised, in whole or in part, at any time or times on or after the Initial Exercise Date and on or before the Termination Date at the election of the Holder (in such Holder’s sole discretion) by means of a “cashless exercise” in which the Holder shall be entitled to receive a number of Warrant Shares equal to the quotient obtained by dividing ((A-B) * (X)) by (A), where:

(A) = as applicable: (i) the VWAP on the Trading Day immediately preceding the date of the applicable Notice of Exercise if such Notice of Exercise is (1) both executed and delivered pursuant to Section 2(a) hereof on a day that is

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not a Trading Day or (2) both executed and delivered pursuant to Section 2(a) hereof on a Trading Day prior to the opening of “regular trading hours” (as defined in Rule 600(b)(64) of Regulation NMS promulgated under the federal securities laws) on such Trading Day, (ii) at the option of the Holder, either (y) the VWAP on the Trading Day immediately preceding the date of the applicable Notice of Exercise or (z) the Bid Price of the Common Stock on the principal Trading Market as reported by Bloomberg L.P. as of the time of the Holder’s execution of the applicable Notice of Exercise if such Notice of Exercise is executed during “regular trading hours” on a Trading Day and is delivered within two (2) hours thereafter (including until two (2) hours after the close of “regular trading hours” on a Trading Day) pursuant to Section 2(a) hereof or (iii) the VWAP on the date of the applicable Notice of Exercise if the date of such Notice of Exercise is a Trading Day and such Notice of Exercise is both executed and delivered pursuant to Section 2(a) hereof after the close of “regular trading hours” on such Trading Day;

(B) = the Exercise Price of this Warrant, as adjusted hereunder; and

(X) = the number of Warrant Shares that would be issuable upon exercise of this Warrant in accordance with the terms of this Warrant if such exercise were by means of a cash exercise rather than a cashless exercise.

If Warrant Shares are issued in such a cashless exercise, the parties acknowledge and agree that in accordance with Section 3(a)(9) of the Securities Act, the Warrant Shares shall take on the characteristics of the Warrants being exercised, and the holding period of the Warrant Shares being issued may be tacked on to the holding period of this Warrant.  The Company agrees not to take any position contrary to this Section 2(c).

“Bid Price” means, for any date, the price determined by the first of the following clauses that applies: (a) if the Common Stock is then listed or quoted on a Trading Market, the bid price of the Common Stock for the time in question (or the nearest preceding date) on the Trading Market on which the Common Stock is then listed or quoted as reported by Bloomberg L.P. (based on a Trading Day from 9:30 a.m. (New York City time) to 4:02 p.m. (New York City time)), (b)  if OTCQB or OTCQX is not a Trading Market, the volume weighted average price of the Common Stock for such date (or the nearest preceding date) on OTCQB or OTCQX as applicable, (c) if the Common Stock is not then listed or quoted for trading on OTCQB or OTCQX and if prices for the Common Stock are then reported in the “Pink Sheets” published by OTC Markets Group, Inc. (or a similar organization or agency succeeding to its functions of reporting prices), the most recent bid price per share of the Common Stock so reported, or (d) in all other cases, the fair market value of a share of Common Stock as determined by an independent appraiser selected in good faith by the Holder and reasonably acceptable to the Company, the fees and expenses of which shall be paid by the Company.

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“Trading Day” means, as applicable, (x) with respect to all price or trading volume determinations relating to the Common Stock, any day on which the Common Stock is traded on the Nasdaq Global Select Market, or, if the Nasdaq Global Select Market is not the principal trading market for the Common Stock, then on the principal securities exchange or securities market on which the Common Stock is then traded, provided that “Trading Day” shall not include any day on which the Common Stock is scheduled to trade on such exchange or market for less than 4.5 hours or any day that the Common Stock is suspended from trading during the final hour of trading on such exchange or market (or if such exchange or market does not designate in advance the closing time of trading on such exchange or market, then during the hour ending at 4:00:00 p.m., New York time) unless such day is otherwise designated as a Trading Day in writing by the Holder or (y) with respect to all determinations other than price determinations relating to the Common Stock, any day on which The New York Stock Exchange (or any successor thereto) is open for trading of securities.

“VWAP” means, for any date, the price determined by the first of the following clauses that applies: (a) if the Common Stock is then listed or quoted on a Trading Market, the daily volume weighted average price of the Common Stock for such date (or the nearest preceding date) on the Trading Market on which the Common Stock is then listed or quoted as reported by Bloomberg L.P. (based on a Trading Day from 9:30 a.m. (New York City time) to 4:02 p.m. (New York City time)), (b)  if OTCQB or OTCQX is not a Trading Market, the volume weighted average price of the Common Stock for such date (or the nearest preceding date) on OTCQB or OTCQX as applicable, (c) if the Common Stock is not then listed or quoted for trading on OTCQB or OTCQX and if prices for the Common Stock are then reported in the “Pink Sheets” published by OTC Markets Group, Inc. (or a similar organization or agency succeeding to its functions of reporting prices), the most recent bid price per share of the Common Stock so reported, or (d) in all other cases, the fair market value of a share of Common Stock as determined by an independent appraiser selected in good faith by the Holder and reasonably acceptable to the Company, the fees and expenses of which shall be paid by the Company.

Notwithstanding anything herein to the contrary, on the Termination Date, if a registration statement covering the resale of the Warrant Shares is not available for the resale of the Warrant Shares, this Warrant shall be automatically exercised via cashless exercise pursuant to this Section 2(c).

d)Mechanics of Exercise.

i.Delivery of Warrant Shares Upon Exercise. Warrant Shares purchased hereunder shall be transmitted by the Company’s stock transfer agent (the “Transfer Agent”) to the Holder by crediting the account of the Holder’s or its designee’s balance account with The Depository Trust Company through its Deposit or Withdrawal at Custodian system (“DWAC”) if the Company is then a participant in such system and either (A) there is an effective

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registration statement permitting the issuance of the Warrant Shares to or resale of the Warrant Shares by the Holder or (B) the Warrant Shares are eligible for resale by the Holder without volume or manner-of-sale limitations pursuant to Rule 144 under the Securities Act (“Rule 144”), and otherwise by physical delivery of a certificate, registered in the Company’s share register in the name of the Holder or its designee, for the number of Warrant Shares to which the Holder is entitled pursuant to such exercise to the address specified by the Holder in the Notice of Exercise by the date that is the earlier of (i) two (2) Trading Days after the delivery to the Company of the Notice of Exercise and (ii) one (1) Trading Day after delivery of the aggregate Exercise Price to the Company (such date, the “Warrant Share Delivery Date”). Upon delivery of the Notice of Exercise, the Holder shall be deemed for all corporate purposes to have become the holder of record of the Warrant Shares with respect to which this Warrant has been exercised, irrespective of the date of delivery of the Warrant Shares, provided that payment of the aggregate Exercise Price (other than in the case of a cashless exercise) is received within two (2) Trading following delivery of the Notice of Exercise. The Company agrees to maintain a transfer agent that is a participant in the FAST program so long as this Warrant remains outstanding and exercisable.

ii.Delivery of New Warrants Upon Exercise. If this Warrant shall have been exercised in part, the Company shall, at the request of the Holder and upon surrender of this Warrant certificate, at the time of delivery of the Warrant Shares, deliver to the Holder a new Warrant evidencing the rights of the Holder to purchase the unpurchased Warrant Shares called for by this Warrant, which new Warrant shall in all other respects be identical with this Warrant.

iii.Rescission Rights. If the Company fails to cause the Transfer Agent to transmit to the Holder the Warrant Shares pursuant to Section 2(d)(i) by the Warrant Share Delivery Date, then the Holder will have the right to rescind such exercise.

iv.Compensation for Buy-In on Failure to Timely Deliver Warrant Shares Upon Exercise. In addition to any other rights available to the Holder, if the Company fails to cause the Transfer Agent to transmit to the Holder the Warrant Shares in accordance with the provisions of Section 2(d)(i) above pursuant to an exercise on or before the Warrant Share Delivery Date, and if after such date the Holder is

5

required by its broker to purchase (in an open market transaction or otherwise) or the Holder’s brokerage firm otherwise purchases, shares of Common Stock to deliver in satisfaction of a sale by the Holder of the Warrant Shares which the Holder anticipated receiving upon such exercise (a “Buy-In”), then the Company shall (A) pay in cash to the Holder the amount, if any, by which (x) the Holder’s total purchase price (including brokerage commissions, if any) for the shares of Common Stock so purchased exceeds (y) the amount obtained by multiplying (1) the number of Warrant Shares that the Company was required to deliver to the Holder in connection with the exercise at issue times (2) the price at which the sell order giving rise to such purchase obligation was executed, and (B) at the option of the Holder, either reinstate the portion of the Warrant and equivalent number of Warrant Shares for which such exercise was not honored (in which case such exercise shall be deemed rescinded) or deliver to the Holder the number of shares of Common Stock that would have been issued had the Company timely complied with its exercise and delivery obligations hereunder. For example, if the Holder purchases Common Stock having a total purchase price of $11,000 to cover a Buy-In with respect to an attempted exercise of shares of Common Stock with an aggregate sale price giving rise to such purchase obligation of $10,000, under clause (A) of the immediately preceding sentence the Company shall be required to pay the Holder $1,000. The Holder shall provide the Company written notice indicating the amounts payable to the Holder in respect of the Buy-In and, upon request of the Company, evidence of the amount of such loss. Nothing herein shall limit the Holder’s right to pursue any other remedies available to it hereunder, at law or in equity including, without limitation, a decree of specific performance and/or injunctive relief with respect to the Company’s failure to timely deliver shares of Common Stock upon exercise of the Warrant as required pursuant to the terms hereof.

v.No Fractional Shares or Scrip. No fractional shares or scrip representing fractional shares shall be issued upon the exercise of this Warrant. As to any fraction of a share which the Holder would otherwise be entitled to purchase upon such exercise, the Company shall, at its election, either pay a cash adjustment in respect of such final fraction in an amount equal to such fraction multiplied by the Exercise Price or round up to the next whole share.

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vi.Charges, Taxes and Expenses. Issuance of Warrant Shares shall be made without charge to the Holder for any issue or transfer tax or other incidental expense in respect of the issuance of such Warrant Shares, all of which taxes and expenses shall be paid by the Company, and such Warrant Shares shall be issued in the name of the Holder or in such name or names as may be directed by the Holder; provided, however, that in the event that Warrant Shares are to be issued in a name other than the name of the Holder, this Warrant when surrendered for exercise shall be accompanied by the Assignment Form attached hereto duly executed by the Holder and the Company may require, as a condition thereto, the payment of a sum sufficient to reimburse it for any transfer tax incidental thereto. The Company shall pay all Transfer Agent fees required for same-day processing of any Notice of Exercise and all fees to the Depository Trust Company (or another established clearing corporation performing similar functions) required for same-day electronic delivery of the Warrant Shares.

vii.Closing of Books. The Company will not close its stockholder books or records in any manner which prevents the timely exercise of this Warrant, pursuant to the terms hereof.

Section 3. Certain Adjustments.

a)Stock Dividends and Splits. If the Company, at any time while this Warrant is outstanding: (i) pays a stock dividend or otherwise makes a distribution or distributions on shares of its Common Stock or any other equity or equity equivalent securities payable in shares of Common Stock (which, for avoidance of doubt, shall not include any shares of Common Stock issued by the Company upon exercise of this Warrant), (ii) subdivides outstanding shares of Common Stock into a larger number of shares, (iii) combines (including by way of reverse stock split) outstanding shares of Common Stock into a smaller number of shares or (iv) issues by reclassification of shares of the Common Stock any shares of capital stock of the Company, then in each case the Exercise Price shall be multiplied by a fraction of which the numerator shall be the number of shares of Common Stock (excluding treasury shares, if any) outstanding immediately before such event and of which the denominator shall be the number of shares of Common Stock outstanding immediately after such event, and the number of shares issuable upon exercise of this Warrant shall be proportionately adjusted such that the aggregate Exercise Price of this Warrant shall remain unchanged.

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Any adjustment made pursuant to this Section 3(a) shall become effective immediately after the record date for the determination of stockholders entitled to receive such dividend or distribution and shall become effective immediately after the effective date in the case of a subdivision, combination or re‑classification.

b)Subsequent Rights Offerings. In addition to any adjustments pursuant to Section 3(a) above, if at any time after the Original Issue Date the Company grants, issues or sells any Common Stock Equivalents or rights to purchase stock, warrants, securities or other property pro rata to the record holders of any class of shares of Common Stock (the “Purchase Rights”), then each Holder will be entitled to acquire, upon the terms applicable to such Purchase Rights, the aggregate Purchase Rights which the Holder could have acquired if the Holder had held the number of shares of Common Stock acquirable upon complete exercise of this Warrant (without regard to any limitations on exercise hereof) immediately before the date on which a record is taken for the grant, issuance or sale of such Purchase Rights, or, if no such record is taken, the date as of which the record holders of shares of Common Stock are to be determined for the grant, issue or sale of such Purchase Rights.

c)Pro Rata Distributions. During such time as this Warrant is outstanding, if the Company shall declare or make any dividend or other distribution of its assets (or rights to acquire its assets) to holders of shares of Common Stock, by way of return of capital or otherwise (including, without limitation, any distribution of cash, stock or other securities, property or options by way of a dividend, spin off, reclassification, corporate rearrangement, scheme of arrangement or other similar transaction, but excluding any dividend that results in adjustment to the Conversion Price pursuant to Section 3(a) above) (a “Distribution”), at any time after the issuance of this Warrant, then, in each such case, the Holder shall be entitled to participate in such Distribution to the same extent that the Holder would have participated therein if the Holder had held the number of shares of Common Stock acquirable upon complete exercise of this Warrant (without regard to any limitations on exercise hereof) immediately before the date of which a record is taken for such Distribution, or, if no such record is taken, the date as of which the record holders of shares of Common Stock are to be determined for the participation in such Distribution.

d)Fundamental Transaction. If, at any time while this Warrant is outstanding, (i) the Company, directly or indirectly, in one or more related

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transactions effects any merger or consolidation of the Company with or into another Person, (ii) the Company, directly or indirectly, effects any sale, lease, license, assignment, transfer, conveyance or other disposition of all or substantially all of its assets in one or a series of related transactions, (iii) any, direct or indirect, purchase offer, tender offer or exchange offer (whether by the Company or another Person) is completed pursuant to which holders of Common Stock are permitted to sell, tender or exchange their shares for other securities, cash or property and has been accepted by the holders of 50% or more of the outstanding Common Stock, (iv) the Company, directly or indirectly, in one or more related transactions effects any reclassification, reorganization or recapitalization of the Common Stock or any compulsory share exchange pursuant to which the Common Stock is effectively converted into or exchanged for other securities, cash or property, or (v) the Company, directly or indirectly, in one or more related transactions consummates a stock or share purchase agreement or other business combination (including, without limitation, a reorganization, recapitalization, spin-off or scheme of arrangement) with another Person or group of Persons whereby such other Person or group acquires more than 50% of the outstanding shares of Common Stock (not including any shares of Common Stock held by the other Person or other Persons making or party to, or associated or affiliated with the other Persons making or party to, such stock or share purchase agreement or other business combination) (each a “Fundamental Transaction”), then, the Holder shall have the right to receive, for each Warrant Share that would have been issuable upon such exercise immediately prior to the occurrence of such Fundamental Transaction (as if the exercise of the Warrant occurred immediately prior to the occurrence of such Fundamental Transaction), at the option of the Holder, the number of shares of common stock of the successor or acquiring corporation or shares of Common Stock of the Company, if it is the surviving corporation, and any additional consideration (the “Alternate Consideration”) receivable as a result of such Fundamental Transaction by a holder of the number of shares of Common Stock for which this Warrant is exercisable immediately prior to such Fundamental Transaction. For purposes of any such exercise, the determination of the Exercise Price shall be appropriately adjusted to apply to such Alternate Consideration based on the amount of Alternate Consideration issuable in respect of one share of Common Stock in such Fundamental Transaction, and the Company shall apportion the Exercise Price among the Alternate Consideration in a reasonable manner reflecting the relative value of any different components of the Alternate Consideration. If holders of Common Stock are given any

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choice as to the securities, cash or property to be received in a Fundamental Transaction, then the Holder shall be given the same choice as to the Alternate Consideration it receives upon any exercise of this Warrant following such Fundamental Transaction.

e)Calculations. All calculations under this Section 3 shall be made to the nearest cent or the nearest 1/100th of a share, as the case may be. For purposes of this Section 3, the number of shares of Common Stock deemed to be issued and outstanding as of a given date shall be the sum of the number of shares of Common Stock (excluding treasury shares, if any) issued and outstanding.

f)Notice to Holder.

i.Adjustment to Exercise Price. Whenever the Exercise Price is adjusted pursuant to any provision of this Section 3, the Company shall within two (2) Trading Days deliver to the Holder by facsimile or email a notice setting forth the Exercise Price after such adjustment and any resulting adjustment to the number of Warrant Shares and setting forth a brief statement of the facts requiring such adjustment.

ii.Notice to Allow Exercise by Holder. If (A) the Company shall declare a dividend (or any other distribution in whatever form) on the Common Stock, (B) the Company shall declare a special nonrecurring cash dividend on or a redemption of the Common Stock, (C) the Company shall authorize the granting to all holders of the Common Stock rights or warrants to subscribe for or purchase any shares of capital stock of any class or of any rights, (D) the approval of any stockholders of the Company shall be required in connection with any reclassification of the Common Stock, any consolidation or merger to which the Company is a party, any sale or transfer of all or substantially all of the assets of the Company, or any compulsory share exchange whereby the Common Stock is converted into other securities, cash or property, or (E) the Company shall authorize the voluntary or involuntary dissolution, liquidation or winding up of the affairs of the Company, then, in each case, the Company shall cause to be delivered by facsimile or email to the Holder at its last facsimile number or email address as it shall appear upon the Warrant Register of the Company, at least 20 calendar days prior to the applicable record or effective date hereinafter specified, a notice stating (x) the date on which a record is to be taken for the purpose of such dividend,

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distribution, redemption, rights or warrants, or if a record is not to be taken, the date as of which the holders of the Common Stock of record to be entitled to such dividend, distributions, redemption, rights or warrants are to be determined or (y) the date on which such reclassification, consolidation, merger, sale, transfer or share exchange is expected to become effective or close, and the date as of which it is expected that holders of the Common Stock of record shall be entitled to exchange their shares of the Common Stock for securities, cash or other property deliverable upon such reclassification, consolidation, merger, sale, transfer or share exchange; provided that the failure to deliver such notice or any defect therein or in the delivery thereof shall not affect the validity of the corporate action required to be specified in such notice. To the extent that any notice provided in this Warrant constitutes, or contains, material, non-public information regarding the Company or any of the Subsidiaries, the Company shall simultaneously file such notice with the Commission pursuant to a Current Report on Form 8-K. The Holder shall remain entitled to exercise this Warrant during the period commencing on the date of such notice to the effective date of the event triggering such notice except as may otherwise be expressly set forth herein.

Section 4. Transfer of Warrant.

a)Transferability. Subject to compliance with any applicable securities laws and the conditions set forth in Section 4(d) hereof, this Warrant and all rights hereunder are transferable, in whole or in part, upon surrender of this Warrant at the principal office of the Company or its designated agent, together with a written assignment of this Warrant substantially in the form attached hereto duly executed by the Holder or its agent or attorney and funds sufficient to pay any transfer taxes payable upon the making of such transfer. Upon such surrender and, if required, such payment, the Company shall execute and deliver a new Warrant or Warrants in the name of the assignee or assignees, as applicable, and in the denomination or denominations specified in such instrument of assignment, and shall issue to the assignor a new Warrant evidencing the portion of this Warrant not so assigned, and this Warrant shall promptly be cancelled. Notwithstanding anything herein to the contrary, the Holder shall not be required to physically surrender this Warrant to the Company unless the Holder has assigned this Warrant in full, in which case, the Holder shall surrender this Warrant to the Company within three (3) Trading Days of the date the Holder delivers an assignment form to the Company assigning this Warrant full.The Warrant, if properly assigned in accordance herewith, may be exercised by a new holder for the purchase of Warrant Shares without having a new Warrant issued.

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b)New Warrants. This Warrant may be divided or combined with other Warrants upon presentation hereof at the aforesaid office of the Company, together with a written notice specifying the names and denominations in which new Warrants are to be issued, signed by the Holder or its agent or attorney. Subject to compliance with Section 4(a), as to any transfer which may be involved in such division or combination, the Company shall execute and deliver a new Warrant or Warrants in exchange for the Warrant or Warrants to be divided or combined in accordance with such notice. All Warrants issued on transfers or exchanges shall be dated the original issue date and shall be identical to this Warrant except as to the holder thereof and the number of Warrant Shares issuable pursuant thereto.

c)Warrant Register. The Company shall register this Warrant, upon records to be maintained by the Company for that purpose (the “Warrant Register”), in the name of the record Holder hereof from time to time. The Company may deem and treat the registered Holder of this Warrant as the absolute owner hereof for the purpose of any exercise hereof or any distribution to the Holder, and for all other purposes, absent actual notice to the contrary.

d)Transfer Restrictions. If, at the time of the surrender of this Warrant in connection with any transfer of this Warrant, the transfer of this Warrant shall not be either (i) registered pursuant to an effective registration statement under the Securities Act and under applicable state securities or blue sky laws or (ii) eligible for resale without volume or manner-of-sale restrictions or current public information requirements pursuant to Rule 144, the Company may require, as a condition of allowing such transfer, that the Holder or transferee of this Warrant, as the case may be, provide to the Company an opinion of counsel selected by the Holder or transferee of this Warrant, as the case may be, and reasonably acceptable to the Company, the form and substance of which opinion shall be reasonably satisfactory to the Company, to the effect that such transfer does not require registration of this Warrant under the Securities Act.

e)Representation by the Holder. The Holder, by the acceptance hereof, represents and warrants that (i) it is an “accredited investor” as defined in Regulation D promulgated under the Securities Act and (ii) it is acquiring this Warrant and, upon any exercise hereof, will acquire the Warrant Shares issuable upon such exercise, for its own account and not with a view to or for distributing or reselling such Warrant Shares or any part thereof in violation of the Securities Act or any applicable state securities law, except pursuant to sales registered or exempted under the Securities Act.

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Section 5. Miscellaneous.

a)No Rights as Stockholder Until Exercise. This Warrant does not entitle the Holder to any voting rights, dividends or other rights as a stockholder of the Company prior to the exercise hereof as set forth in Section 2(d)(i), except as expressly set forth in Section 3.

b)Loss, Theft, Destruction or Mutilation of Warrant. The Company covenants that upon receipt by the Company of evidence reasonably satisfactory to it of the loss, theft, destruction or mutilation of this Warrant or any stock certificate relating to the Warrant Shares, and in case of loss, theft or destruction, of indemnity or security reasonably satisfactory to it (which, in the case of the Warrant, shall not include the posting of any bond), and upon surrender and cancellation of such Warrant or stock certificate, if mutilated, the Company will make and deliver a new Warrant or stock certificate of like tenor and dated as of such cancellation, in lieu of such Warrant or stock certificate.

c)Saturdays, Sundays, Holidays, etc. If the last or appointed day for the taking of any action or the expiration of any right required or granted herein shall not be a Business Day, then, such action may be taken or such right may be exercised on the next succeeding Business Day.

d)Authorized Shares.

1.During the period the Warrant is outstanding from and after the Initial Exercise Date, the Company covenants that it will reserve from its authorized and unissued Common Stock a sufficient number of shares to provide for the issuance of the Warrant Shares upon the exercise of any purchase rights under this Warrant. The Company further covenants that its issuance of this Warrant shall constitute full authority to its officers who are charged with the duty of issuing the necessary Warrant Shares upon the exercise of the purchase rights under this Warrant. The Company will take all such reasonable action as may be necessary to assure that such Warrant Shares may be issued as provided herein without violation of any applicable law or regulation, or of any requirements of the Trading Market upon which the Common Stock may be listed. The Company covenants that all Warrant Shares which may be issued upon the exercise of the purchase rights represented by this Warrant will, upon exercise of the purchase rights represented by this Warrant and payment for such Warrant Shares in accordance herewith, be duly authorized, validly issued, fully paid and nonassessable and free from all taxes, liens and charges created by the Company

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in respect of the issue thereof (other than taxes in respect of any transfer occurring contemporaneously with such issue).

2.Except and to the extent as waived or consented to by the Holder, the Company shall not by any action, including, without limitation, amending its certificate of incorporation or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms of this Warrant, but will at all times in good faith assist in the carrying out of all such terms and in the taking of all such actions as may be necessary or appropriate to protect the rights of Holder as set forth in this Warrant against impairment. Without limiting the generality of the foregoing, the Company will (i) not increase the par value of any Warrant Shares above the amount payable therefor upon such exercise immediately prior to such increase in par value, (ii) take all such action as may be necessary or appropriate in order that the Company may validly and legally issue fully paid and nonassessable Warrant Shares upon the exercise of this Warrant and (iii) use commercially reasonable efforts to obtain all such authorizations, exemptions or consents from any public regulatory body having jurisdiction thereof, as may be, necessary to enable the Company to perform its obligations under this Warrant.

3.Before taking any action which would result in an adjustment in the number of Warrant Shares for which this Warrant is exercisable or in the Exercise Price, the Company shall obtain all such authorizations or exemptions thereof, or consents thereto, as may be necessary from any public regulatory body or bodies having jurisdiction thereof.

e)Jurisdiction. All questions concerning the construction, validity, enforcement and interpretation of this Warrant shall be determined in accordance with the provisions of the Loan Agreement.

f)Restrictions. The Holder acknowledges that the Warrant Shares acquired upon the exercise of this Warrant, if not registered and the Holder does not utilize cashless exercise, will have restrictions upon resale imposed by state and federal securities laws.

g)Nonwaiver and Expenses. No course of dealing or any delay or failure to exercise any right hereunder on the part of Holder shall operate as a waiver of such right or otherwise prejudice the Holder’s rights, powers or remedies, notwithstanding the fact that all rights hereunder terminate on the Termination Date. If the Company willfully and

14

knowingly fails to comply with any provision of this Warrant, which results in any material damages to the Holder, the Company shall pay to the Holder such amounts as shall be sufficient to cover any costs and expenses including, but not limited to, reasonable attorneys’ fees, including those of appellate proceedings, incurred by the Holder in collecting any amounts due pursuant hereto or in otherwise enforcing any of its rights, powers or remedies hereunder.

h)Notices. Any notice, request or other document required or permitted to be given or delivered to the Holder by the Company shall be delivered in accordance with the notice provisions of the Loan Agreement.

i)Limitation of Liability. No provision hereof, in the absence of any affirmative action by the Holder to exercise this Warrant to purchase Warrant Shares, and no enumeration herein of the rights or privileges of the Holder, shall give rise to any liability of the Holder for the purchase price of any Common Stock or as a stockholder of the Company, whether such liability is asserted by the Company or by creditors of the Company.

j)Remedies. The Holder, in addition to being entitled to exercise all rights granted by law, including recovery of damages, will be entitled to specific performance of its rights under this Warrant. The Company agrees that monetary damages would not be adequate compensation for any loss incurred by reason of a breach by it of the provisions of this Warrant and hereby agrees to waive and not to assert the defense in any action for specific performance that a remedy at law would be adequate.

k)Successors and Assigns. Subject to applicable securities laws, this Warrant and the rights and obligations evidenced hereby shall inure to the benefit of and be binding upon the successors and permitted assigns of the Company and the successors and permitted assigns of Holder. The provisions of this Warrant are intended to be for the benefit of any Holder from time to time of this Warrant and shall be enforceable by the Holder or holder of Warrant Shares.

l)Amendment. This Warrant may be modified or amended or the provisions hereof waived with the written consent of the Company and the Holder.

m)Severability. Wherever possible, each provision of this Warrant shall be interpreted in such manner as to be effective and valid under applicable law, but if any provision of this Warrant shall be prohibited by or invalid under applicable law, such provision shall be ineffective to the extent of such prohibition or invalidity, without invalidating the remainder of such provisions or the remaining provisions of this Warrant.

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n)Headings. The headings used in this Warrant are for the convenience of reference only and shall not, for any purpose, be deemed a part of this Warrant.

********************

(Signature Page Follows)

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Exhibit 4.88

IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by its officer thereunto duly authorized as of the date first above indicated.

AMYRIS, INC.

By: /s/ Kathleen Valiasek___________________

     Name: Kathleen Valiasek

     Title: Chief Business Officer

         [Signature page to Warrant]

Exhibit 4.88

NOTICE OF EXERCISE

TO: AMYRIS, INC.

(1)The undersigned hereby elects to purchase ________ Warrant Shares of the Company pursuant to the terms of the attached Warrant (only if exercised in full), and tenders herewith payment of the exercise price in full, together with all applicable transfer taxes, if any.

(2)Applicable Exercise Price: $

(3)Payment shall take the form of (check applicable box):

[ ] in lawful money of the United States; or

[ ] the cancellation of such number of Warrant Shares as is necessary, in accordance with the formula set forth in subsection 2(c), to exercise this Warrant with respect to the maximum number of Warrant Shares purchasable pursuant to the cashless exercise procedure set forth in subsection 2(c).

(4)Please issue said Warrant Shares in the name of the undersigned or in such other name as is specified below:

          _______________________________

The Warrant Shares shall be delivered to the following DWAC Account Number:

          _______________________________

          _______________________________

          _______________________________

         (4) Accredited Investor. The undersigned is an “accredited investor” as defined in Regulation D promulgated under the Securities Act of 1933, as amended.

[SIGNATURE OF HOLDER]

Name of Investing Entity: ______________________________________________________________

Signature of Authorized Signatory of Investing Entity: _______________________________________

Name of Authorized Signatory: __________________________________________________________

Title of Authorized Signatory: ___________________________________________________________

Date: ____________________________________________________________________________

ASSIGNMENT FORM

(To assign the foregoing Warrant, execute this form and supply required information. Do not use this form to purchase shares.)

FOR VALUE RECEIVED, the foregoing Warrant and all rights evidenced thereby are hereby assigned to

Name:
	(Please Print)
Address:
Phone Number: Email Address:	(Please Print) ______________________________________ ______________________________________
Dated: _______________ __, ______
Holder’s Signature:
Holder’s Address:

EX-4.90

Exhibit 4.90

DESCRIPTION OF THE REGISTRANT’S SECURITIES

REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES

EXCHANGE ACT OF 1934

As of December 31, 2019, Amyris, Inc. (the “Company,” or “us”) had one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended: our common stock.

The following is a description of our capital stock, as well as certain provisions of our certificate of incorporation, bylaws and Delaware law. This is only a summary and is qualified in its entirety by reference to the description of our common stock included in our certificate of incorporation and our bylaws, each of which are incorporated by reference as an exhibit to the Annual Report on Form 10-K of which this exhibit is a part, and by the relevant provisions of the Delaware General Corporation Law, or the DGCL. See “Where You Can Find Additional Information”.

Our authorized capital stock consists of 250,000,000 shares of common stock, par value $0.0001 per share, and 5,000,000 shares of preferred stock, par value $0.0001 per share.

Common Stock

Dividend Rights

Subject to preferences that may apply to shares of preferred stock outstanding from time to time, the holders of outstanding shares of our common stock are entitled to receive dividends out of funds legally available if our Board of Directors, in its discretion, determines to issue dividends, and only then at the times and in the amounts that our Board of Directors may determine.

Voting Rights

Each holder of our common stock is entitled to one vote for each share of common stock held on all matters submitted to a vote of stockholders. Our restated certificate of incorporation, as amended, eliminates the right of stockholders to cumulate votes for the election of directors and establishes a classified Board of Directors, divided into three classes with staggered three-year terms. Only one class of directors is elected at each annual meeting of our stockholders, with the other classes continuing in office for the remainder of their respective three-year terms.

No Preemptive or Similar Rights

Our common stock is not entitled to preemptive rights and is not subject to conversion, redemption or sinking fund provisions.

Right to Receive Liquidation Distributions

Upon our dissolution, liquidation or winding-up, the assets legally available for distribution to our stockholders are distributable ratably among the holders of our common stock, subject to prior satisfaction of all outstanding debt and liabilities and the preferential rights and payment of liquidation preferences, if any, on any outstanding shares of preferred stock.

Registration Rights

Certain of our stockholders, including certain entities affiliated with our directors and/or holders of five percent or more of our outstanding common stock, including DSM, Foris, Vivo and Total, hold registration rights pursuant to (i) the Amended and Restated Letter Agreement, dated May 8, 2014, by and among us and certain of our stockholders, (ii) the letter agreement, dated July 29, 2015, by and among us and certain investors, (iii) the Registration Rights Agreement, dated October 20, 2015, by and among us and certain purchasers of our 9.50% Convertible Senior Notes due 2019, (iv) the warrant to purchase common stock issued by us to Nenter & Co., Inc.

on November 16, 2016, (v) the Securities Purchase Agreement, dated May 8, 2017, by and among us and certain investors, (vi) the Securities Purchase Agreement, dated May 31, 2017, by and between us and the investor named therein, (vii) the Securities Purchase Agreement, dated August 2, 2017, by and between us and DSM International B.V., (viii) the Stockholder Agreement, dated August 3, 2017, by and between us and affiliates of Vivo Capital LLC, (ix) the Amended and Restated Stockholder Agreement, dated August 7, 2017, by and between us and DSM International B.V., (x) the Securities Purchase Agreement, dated November 19, 2018, between us and DSM International B.V., (xi) the Registration Rights Agreement, dated December 10, 2018, by and among us and the investors party thereto, (xii) the Security Purchase Agreement, dated April 24, 2019, by and between us and ETP BioHealth (I) Fund LP, (xiii) the common stock purchase warrants issued by us to each of Schottenfeld Opportunities Fund II, L.P., Phase Five Partners, LP and Koyote Trading, LLC on September 10, 2019, (xiv) the common stock purchase warrants issued by us to each of Schottenfeld Opportunities Fund II, L.P and, Phase Five Partners, LP on November 14, 2019, and (xv) the Securities Purchase Agreements, dated January 31, 2020, by and between us and the investor named therein, including Foris Ventures, LLC.

Stock Exchange Listing

Our common stock is listed on The Nasdaq Global Select Market under the symbol “AMRS.”

Anti-Takeover Provisions

The provisions of Delaware law, our restated certificate of incorporation, as amended, and our restated bylaws may have the effect of delaying, deferring or discouraging another person from acquiring control of our company.

Delaware Law

Section 203 of the DGCL (“Section 203”) prevents some Delaware corporations from engaging, under some circumstances, in a business combination, which includes a merger or sale of at least 10% of the corporation’s assets, with any interested stockholder, meaning a stockholder who, together with affiliates and associates, owns or, within three years prior to the determination of interested stockholder status, did own 15% or more of the corporation’s outstanding voting stock, unless:

•the transaction is approved by the Board of Directors prior to the time that the interested stockholder became an interested stockholder;

•upon consummation of the transaction which resulted in the stockholder’s becoming an interested stockholder, the interested stockholder owned at least 85% of the voting stock of the corporation outstanding at the time the transaction commenced; or

•at or subsequent to such time that the stockholder became an interested stockholder, the business combination is approved by the Board of Directors and authorized at an annual or special meeting of stockholders by at least two-thirds of the outstanding voting stock which is not owned by the interested stockholder.

If Section 203 applied to us, these restrictions could prohibit or delay mergers or other takeover or change in control attempts and, accordingly, could discourage attempts to acquire us.

A Delaware corporation may “opt out” of the restrictions on business combinations contained in Section 203 with an express provision in its original certificate of incorporation or an express provision in its certificate of incorporation or bylaws resulting from a stockholders’ amendment approved by at least a majority of its outstanding voting shares. We have agreed to opt out of Section 203 through our restated certificate of incorporation, as amended, but our restated certificate of incorporation as amended, contains substantially similar protections to our company and stockholders as those afforded under Section 203, except that we have agreed with Total that it will not be deemed to be “interested stockholders” for purposes of such protections.

Restated Certificate of Incorporation and Restated Bylaw Provisions

Our restated certificate of incorporation, as amended, and our restated bylaws include a number of provisions that may have the effect of deterring hostile takeovers or delaying or preventing changes in control of our company or management team, including the following:

•Board of Directors Vacancies. Our restated certificate of incorporation, as amended, and restated bylaws authorize only our Board of Directors to fill vacant directorships. In addition, the number of directors constituting our Board of Directors will be set only by resolution adopted by a majority vote of our entire Board of Directors. These provisions prevent stockholders from increasing the size of our Board of Directors and gaining control of our Board of Directors by filling the resulting vacancies with their own nominees.

•Classified Board. Our restated certificate of incorporation, as amended, and restated bylaws provide that our Board of Directors is classified into three classes of directors. The existence of a classified board could delay a successful tender offeror from obtaining majority control of our Board of Directors, and the prospect of that delay might deter a potential offeror. Pursuant to Delaware law, the directors of a corporation having a classified board may be removed by the stockholders only for cause. In addition, stockholders will not be permitted to cumulate their votes for the election of directors.

•Stockholder Action; Special Meeting of Stockholders. Our restated certificate of incorporation, as amended, provides that our stockholders may not take action by written consent, but may only take action at annual or special meetings of our stockholders. Our restated bylaws further provide that special meetings of our stockholders may be called only by a majority of our Board of Directors, the chair of our Board of Directors, our chief executive officer or our president.

•Advance Notice Requirements for Stockholder Proposals and Director Nominations. Our restated bylaws provide for advance notice procedures for stockholders seeking to bring business before our annual meeting of stockholders, or to nominate candidates for election as directors at our annual meeting of stockholders. Our restated bylaws also specify certain requirements regarding the form and content of a stockholder’s notice. These provisions may preclude our stockholders from bringing matters before our annual meeting of stockholders or from making nominations for directors at our annual meeting of stockholders.

•Issuance of Undesignated Preferred Stock. Under our restated certificate of incorporation, as amended, our Board of Directors has the authority, without further action by the stockholders, to issue shares of undesignated preferred stock with rights and preferences, including voting rights, designated from time to time by the Board of Directors. The existence of authorized but unissued shares of preferred stock enables our Board of Directors to render more difficult or to discourage an attempt to obtain control of us by means of a merger, tender offer, proxy contest or otherwise.

EX-10.23

Exhibit 10.23

EIGHTH AMENDMENT TO THE PRIVATE INSTRUMENT NON-RESIDENTIAL REAL ESTATE LEASE AGREEMENT

Entered into by and between:

I - LUCIO TOMASIELLO, Brazilian, single, of age, Entrepreneur, holder of the RG [ID Card] No. SSP/SP, duly enrolled with the Individual Taxpayer’s Registry of the Ministry of Treasury - CPF/MF under the No. , residing and domiciled in and MAURÍCIO TOMASIELLO, Brazilian, single, Entrepreneur, holder of the RG [ID Card] No. , issued by SSP/SP, duly enrolled with the Individual Taxpayer’s Registry of the Ministry of Treasury - CPF/MF under the No. , residing and domiciled in , both of them hereinafter referred to as “LESSORS”; and,

II – AMYRIS BIOTECNOLOGIA DO BRASIL LTDA. (Formerly known as SMA Indústria Química Ltda.), a limited liability company headquartered in the City of Campinas, State of São Paulo, at Rua James Clerk Maxwell, No. 315, Techno Park, CEP [Zip Code]: 13069 - 380, duly enrolled with the Corporate Taxpayer’s Registry of the Ministry of Treasury - CNPJ/MF under the No. 12.065.083/0003-48, represented herein pursuant to its Articles of Organization, hereinafter referred to as “LESSEE”; and,

LESSORS and LESSEE are collectively referred to as the “Parties” and, individually, as a “Party”.

WHEREAS, on March 31, 2008, the Parties entered into the Private Instrument of Non-Residential Real Estate Lease Agreement (“Agreement”), referring to the lease of a commercial warehouse, which has the total built area of 1,368.09 m² (one thousand, three hundred and sixty-eight square meters and nine square centimeters), which is located at Rua James Clerk Maxwell, No. 315, CEP: 13069 - 380, under the enrollment No. 100068 filed with the 2nd Registrar of Deeds of Campinas, State of São Paulo and

Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement  1

registered in the City of Campinas, State of São Paulo, under the cartographic code No. 3162.44.26.0285.00000 (“Real Estate”);

WHEREAS, on July 05, 2008, the Parties entered into the Private Instrument of Amendment to the Non-Residential Real Estate Lease Agreement (“First Amendment”), which modified the lease guarantee conditions set forth in the Agreement;

WHEREAS, on October 30, 2008, the Parties entered into the Second Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Second Amendment”), which expanded and extended the lease term from 36 (thirty-six) months to 60 (sixty) months, namely, May 31, 2013;

WHEREAS, on October 01, 2012, the Parties entered into the Third Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Third Amendment”), which expanded and extended the lease term for 36 (thirty-six) more months, with effective term as of October 01, 2015, and set the increase of the monthly rent price;

WHEREAS,on March 5, 2015, the Parties entered into the Fourth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Fourth Amendment”), which expanded and extended the lease term for 43 (forty-three) more months, with effective term as of October 5, 2018, set once again the increase of the monthly rent Price, and set the accessory clauses to the Agreement;

WHEREAS, on September 22, 2015, the Parties entered into the Fifth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Fifth Amendment”), which provided that the monthly rent price would not undergo any annual adjustment or inflation adjustment at the variation of the General Market Price Index - IGPM, measured by Fundação Getúlio Vargas - FGV, and kept the monthly rent price paid by LESSEE up to October 01, 2016;

Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement  2

WHEREAS, on October 17, 2016, the Parties entered into the Sixth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Sixth Amendment”), which set the increase of the monthly rent price upon adjustment and extended the lease term to October 1, 2019;

WHEREAS, on September 25, 2017, the Parties entered into the Seventh Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Seventh Amendment”), which kept the monthly rent price without the levy of any type of annual adjustment or inflation adjustment of the monthly rent price up to October 1, 2018;

WHEREAS theParties has an interest, under mutual agreement, in (i) extending the effective term of the Agreement; (ii) increasing the monthly rent price; (iii) adjusting the base date for the next adjustments, and (iv) adjusting the provision in clause 12 to the Agreement, as set hereinafter.

Now, therefore, the Parties, under mutual agreement, resolve to enter into the Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement (“Eighth Agreement”), in accordance with the following clauses and conditions.

CLAUSE ONE

EFFECTIVE TERM

1.1 After negotiations of reciprocal agreement between the Parties, both parties agree to extend the effective term of the agreement, in a retroactive manner, from October 01, 2019, for the additional period of 60 (sixty) months, that is, 5 (five) years.

1.2 The term indicated in the foregoing clause may only be extended upon the execution to a new amendment by the Parties.

CLAUSE TWO

PRICE AND ADJUSTMENTS

Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement  3

2.1 The Parties hereby further agree that, upon mutual and express agreement, as of December 01, 2019, the monthly rent price shall be BRL 41,034.31 (forty-one thousand and thirty-four Brazilian Reais and thirty-one cents) to be paid by LESSEE to LESSORS.

2.1.1 Nonetheless, the date of October 01, 2020 is defined as base date for the future annual adjustments at IPCA [Broad Consumer Price Index].

CLAUSE THREE

EARLY REDELIVERY OF THE REAL ESTATE

3.1 The Parties resolve to, under mutual agreement, amend the writing of the paragraph one to Clause 12 to the Agreement, as well as include paragraph three, as follows:

Clause 12 - paragraph one: “In event of early redelivery of the real estate by LESSEE, within a shorter term than the agreed-upon period of 60 (sixty) months and provided that LESSEEhas already performed at least 50% of agreement term, there shall be any enforcement of fine provided that LESSEEearly notifies LESSOR within 120 (one hundred and twenty) days in advance. If such obligation is not fulfilled, the fine shall be due and enforced in the amount equivalent to 3 (three) rents, proportionally reduced with respect to the elapsed time of such lease extension”.

Paragraph three: The fine in concern shall not be due either in case LESSEE redelivers the real estate on an early basis and even before the fulfillment of 50% of the agreement term in virtue of the completion of its activities in the City of Campinas/SP.

CLAUSE FOUR

GENERAL PROVISIONS

Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement  4

4.1 All of the terms, further clauses and conditions in the Agreement and Amendments hereto, which have not been expressly amended by this Eighth Amendment, are hereby ratified.

4.2 The Parties agree that the terms to this Eighth Amendment prevail over the conditions provided for in any other understanding between the Parties from the date of execution to the Agreement and the date of execution to this Eighth Amendment.

4.3  The Agreement may not, as well as this Eighth Amendment, be amended, in any of the provisions hereof, upon the execution in writing of an amendment to the agreement.

4.4. The signatures to this Amendment shall be set in electronic form through the DocuSign platform and expressly represent that they acknowledge the validity of this type of signature.

        4.4.1 Only persons legally vested with representation powers may electronically execute this document; it is hereby assured that, by LESSEE, the e-mail(s) authorized to execute the instrument is(are): and , by LESSORS, the e-mail(s) authorize to execute the instrument is(are): and .

Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement  5

In witness whereof, the Parties execute this instrument in 03 (three) counterparts of equal contents and form, for the same effects, along with 02 (two) legally capable undersigned witnesses.

Campinas, December 9, 2019.

/s/ Lucio Tomasiello /s/ Mauricio Tomasiello

LESSORS: LÚCIO TOMASIELLO / MAURÍCIO TOMASIELLO

/s/ Gianni Valent /s/ Reginaldo Pereira de Souza Scwery

LESSEE: AMYRIS BIOTECNOLOGIA DO BRASIL LTDA.

Witnesses:

1. /s/ Alessi Gabriel Braga    2. /s/ Letícia Bressan Santolim

Name: Alessi Gabriel Braga    Name: Letícia Bressan Santolim

CPF/MF:      CPF/MF:  

Eighth Amendment to the Private Instrument of Non-Residential Real Estate Lease Agreement  6

EX-10.41

Exhibit 10.41

AMENDMENT NO. 3 TO

SUPPLY AGREEMENT

This Amendment No. 3 to the Supply Agreement (this “Amendment”) is entered into as of September 30, 2019, between DSM Nutritional Products AG, Wurmisweg 576, 4303 Kaiseraugst, Switzerland, (hereinafter "DSM”) and Amyris, Inc., 5885 Hollis Street, Emeryville, CA 94608, USA (hereinafter “Amyris”) (each of DSM and Amyris hereinafter referred to as a “Party”, together referred to as the "Parties").

WHEREAS, Amyris entered into a Supply Agreement, dated as of December 28, 2017, with DSM Produtos Nutricionais Brasil S.A. (the “Agreement");

WHEREAS, on January 12, 2018, DSM’s affiliate DSM Produtos Nutricionais Brasil S.A. assigned all of its rights, title and interest in the Agreement to DSM;

WHEREAS, on November 19, 2018 the Parties entered into Amendment No. 1 to the Agreement;

WHEREAS, on April 16, 2019 the Parties entered into Amendment No. 2 to the Agreement; and

WHEREAS, the Parties desire to further amend the Agreement.

NOW, THEREFORE, in consideration of the mutual promises contained herein, and for other good and valuable consideration the receipt and sufficiency of which are hereby acknowledged, the Parties agree as follows;

1. Amendments.

a. Section 6.4 of the Agreement is hereby deleted and amended and restated to read;

“After receipt of a Purchase Order, DSM shall issue an invoice upon Amyris taking title to the ordered Product, with Amyris taking title to and risk for the Product(s) upon the Product(s) being transferred from the Brotas 1 facility to the Amyris chartered transportation (“ex works inco terms"). Unless otherwise agreed in writing, payment of all undisputed amounts of such invoices shall be made by bank transfer within sixty (60) days after receipt of Product by Amyris. Invoices are to be sent via email prior to the paper version in order to avoid delays. Each invoice shall reflect a 1.25% per month finance charge applicable to the later thirty (30) days of the sixty (60) day period for payment, and Amyris shall pay all such finance charges upon payment of each invoice. The currency for invoicing and payment shall be US Dollars. Amyris will notify DSM within ten business (10) days after receipt of an invoice if Amyris disputes the amount or calculation of the fees or other charges set forth therein, describing in reasonable detail the basis for the dispute (and for the avoidance of doubt, will pay when due the undisputed amount of such invoice). In such event, DSM will provide Amyris with additional support for the calculation of the fees and charges in dispute and make available any books and records requested by Amyris related to the elements and calculation of the disputed fees and charges. The Parties will work together in good faith to resolve any such dispute promptly. If the Parties agree on the amount to be paid, Amyris will pay the invoiced amount (or, if applicable, an adjusted amount agreed by the Parties based on such review) within fifteen business (15) days following receipt of the additional materials from DSM. In the event that the Parties are unable to resolve such a dispute, either Party may submit such dispute to the Parties' respective management, for Amyris the Chief Executive Officer and for DSM the President Global Products & Alliances, for resolution, provided the amount in dispute is less than $1,000,000, or to arbitration in accordance with Article 13 in all other events.”

b. The Agreement is hereby modified and amended to add a new Section 6.6 following Section 6.5 as set forth below:

“(a) Payment Default. Notwithstanding anything in this Agreement to the contrary, in the event that (i) the aggregate undisputed amount of payments outstanding under invoices issued by DSM under this Agreement, when added together with any Excess Raw Material Costs borne by DSM, exceeds ten million dollars ($10,000,000), (ii) any invoiced amount has not been paid in full within 60 days in accordance with Section 6.4 or (iii) any Interest Payment Default shall have occurred (any of the circumstances described in the foregoing clauses (i) through (iii), a “Payment Default”), then DSM’s obligations under this Agreement shall be suspended and DSM shall not be obligated to perform any of the Services or to deliver any Product hereunder until such time as such Payment Default shall have been cured.

(b)For purposes of this Agreement, (x) “Excess Raw Materials Costs” means the cost of any Raw Materials purchased by DSM to manufacture Products in accordance with the notices furnished by Amyris pursuant to Section 2.3 to the extent such Raw Materials costs have not yet been included in any invoice issued by DSM for such Products and (y) “Interest Payment Default” means a default in the payment of (1) any interest payment upon Note B-1 issued in connection with the Credit Agreement, dated December 28, 2017, by and between Amyris and DSM Finance BV (and any other notes payable that may be issued under such agreement from time to time after the date hereof) or (2) any interest payment upon any note payable issued in connection with the Credit Agreement, dated September 17, 2019, by and between Amyris and DSM Finance BV, in each case, when such interest becomes due and payable.

(c)In the event that there shall have occurred more than two Payment Defaults in any twelve (12) month period after the date hereof, DSM shall have the right, upon ninety (90) days prior written notice to Amyris, to modify the payment obligations set forth in Section 6 hereof to require payment of all undisputed amount of such invoices within thirty (30) days after receipt of Product by Amyris.”

2 Effective Date. This Amendment shall become effective as of the date set forth above.

3.No Other Amendments. Except as expressly amended hereby, the terms and conditions of the Agreement shall remain unchanged and in full force and effect, and the execution of this Amendment is not a waiver by either Party of any of the terms or provisions of the Agreement. In the event of any conflict between the terms of this Amendment and the terms of the Agreement, the terms of this Amendment shall govern. Capitalized terms used in this Amendment that are not otherwise defined herein shall have the same meanings as such terms are given in the Agreement. For clarity, any cross-references to Agreement Sections refer to those Agreement Sections as amended by this Amendment.

4.Counterparts. This Amendment may be executed in one or more counterparts, each of which shall be deemed and original, but all of which together shall constitute one and the same document.

[Remainder of Page Intentionally Left Blank.]

IN WITNESS WHEREOF, DSM and Amyris have caused this Amendment to be executed as of the date first written above by their respective officers thereunto duly authorized.

             DSM NUTRITIONAL PRODUCTS AG

             By: _/s/ A. Bos_________________________

             Name: A. Bos

             Function:

             By: _/s/ Bruno Mueller___________________

             Name: Bruno Mueller

             Function: Vice-President

AMYRIS, INC.

             By: /s/ John Melo______________________

             Name: John Melo

             Function: President & CEO

EX-10.66

Exhibit 10.66

LOAN AGREEMENT

THIS LOAN AGREEMENT, is made and entered into, as of December 19, 2019 by and between Nikko Chemicals Co., Ltd., a Japanese corporation (“Lender”), and Amyris, Inc., a Delaware corporation (“Borrower”).

WITNESSETH:

WHEREAS, Borrower, Lender and Lender’s affiliate are the parties to a Joint Venture Agreement dated December 12, 2016 (the “JV Agreement”) with respect to Aprinnova, LLC (formerly, Neossance, LLC);

WHEREAS, Borrower previously borrowed US$3,900,000.00 and provided a purchase money promissory note to Lender, and Borrower granted to Lender a first-priority security interest as to 10.0% of Aprinnova, LLC’s shares;

WHEREAS, Borrower subsequently borrowed additional loans in an aggregate principal amount of US$5,000,000.00 and agreed to grant to Lender of first-priority security interests as to an additional 12.8% of Aprinnova LLC's shares;

WHEREAS, Borrower additionally requested that Lender extend to Borrower a loan the amount of US$4,500,000.00 and agreed to grant to Lender a first-priority security interest as to an additional 27.2% of Aprinnova, LLC’s shares; and

WHEREAS, Lender is willing to make the loan described herein to Borrower on the terms and conditions set forth herein.

NOW, THEREFORE, in consideration of the premises and mutual covenants contained herein, the parties hereby agree as follows:

SECTION 1. LOAN

(1)  Subject to the terms and conditions of this Agreement, Lender shall make a loan to Borrower in the total principal amount of US$4,500,000.00 (Four Million Five Hundred Thousand United States Dollars) (the “Loan”) upon satisfaction of the following:

        (a)  Loan A: A loan of $3,000,000.00 will be made to Borrower by Lender upon satisfaction of all of the following:

(i)Borrower grants to Lender a first-priority security interest as to 27.2% of Aprinnova, LLC’s shares, and Lender completes the UCC financial statement covering such security interest; Borrower executes an Escrow Agreement described in Section 1.5 of the JV Agreement.

(2) Loan described above shall be made to the following bank account:

   Bank:

          Branch: 

          Address:  

          Account Number:

          Account Name: 

          Swift Code:

(3) Notwithstanding anything to the contrary in this Agreement, this Agreement shall become null and void in its entirety and any obligations on the part of Lender under this Agreement shall cease to exist if there exists any security interest as to Aprinnova, LLC’s shares. 

Exhibit 10.66

SECTION 2. INTEREST

(1)  Borrower shall pay to Lender interest on the principal amount of the Loan (the “Principal”) at the rate of 2.75 percent per annum from and including the applicable date of Loan to and including January 31, 2020 (the “Interest”).

(2) Any outstanding principal of, or accrued interest on, the Loan that is not paid when due shall bear interest from and including such due date to and excluding the date of payment (both before and after judgement) in full thereof, at the additional rate of 5 per cent per annum (“Default Interest”). Interest (including Default Interest) shall be calculated for the actual number of days elapsed on the basis of a 360 day year.

SECTION 3. PAYMENT

(1)  Borrower shall repay the Principal in full on January 31, 2020 and shall pay all of the Interest on the date of Loan. Lender may at any time apply any sum payable from Lender to Borrower (including without limitation the Principal) in or towards satisfaction of any sum then payable from Borrower to Lender (including without limitation the Interest).

SECTION 4. SECURITY INTEREST

        To secure prompt payment in full when due (whether at stated maturity, by acceleration or otherwise) and performance of Borrower’ obligation hereunder, Borrower hereby pledges and grants to Lender a first-priority security interest in and to all of Borrower’s right, title and interest in, to and under twenty seven point two (27.2) percent of Aprinnova LLC’s shares (i.e., membership interests of Aprinnova, LLC) (the “Pledged Shares”). Borrower hereby agrees that it will not sell, assign, encumber or otherwise transfer or dispose of such shares, except as expressly permitted by the LLC Operating Agreement. Borrower irrevocably appoints Lender as its true and lawful attorney-in-fact of Borrower to make, execute and file UCC financing statement to secure Lender’s security interest in and to 27.2% of Aprinnova LLC’s shares described above.

        In the event of default by Borrower under this Agreement, the Pledges Shares shall be transferred to Lender so that Lender’ shareholding percentage will increase by twenty seven point two (27.2) percent, regardless of the amount repaid by Borrower under this Agreement on or prior to such default.

SECTION 5. COVENANTS

(1)  Borrower hereby covenants that so long as any indebtedness of Borrower under this Agreement remains outstanding an unpaid, Borrower shall promptly give notice in writing to Lender of (a) the occurrence of any Event of Default under this Agreement or any other material agreement of Borrower and (b) any litigation, preceding, investigation or dispute which may exist at any time between Borrower and any third party which might substantially interfere with the normal business activity of Borrower or the performance of any obligation under this Agreement.

(2)  Borrower hereby covenants that so long as any indebtedness of Borrower under this Agreement remains outstanding an unpaid, Borrower shall not, unless otherwise consented to in writing by Lender, enter into any transaction or merger or consolidation or amalgamation, or liquidate, wind up or dissolve itself (or initiate any liquidation or dissolution), or take any action, legal proceeding or step in relation to the appointment of an examiner or receiver to Borrower or any of its assets, or convey, sell, lease, transfer, mortgage, pledge, lien or otherwise dispose of, in one transaction or a series of transactions, all or substantially all of its business, property or assets.

(3) Borrower hereby covenants that so long as any indebtedness of Borrower under this Agreement remains outstanding an unpaid, Borrower shall permit Lender (a) to inspect any of the properties, corporate books and financial records of Borrower, (b) to examine and make copies of the books of accounts and other financial records of Borrower, and (c) to discuss the affairs, financings and accounts of Borrower with, and to be advised as to the same by, its officers at such reasonable times and intervals as Lender may designate.

Exhibit 10.66

SECTION 6. EVENTS OF DEFAULT

If any of the Event of Default (as hereinafter defined) occurs, then the principle amount of the Loan (as well as any interest accrued thereon) shall be immediately due and payable without presentment, demand, protest or other notice of any kind, all of which are expressly waived, anything contained herein to the contrary notwithstanding. For the purpose of this Agreement, the Event of Defaults shall be deemed to have occurred:

(a)If borrower fails to pay the principle of an interest on the Loan when due;

(b)if any representation, warranty or covenant made by Borrower under this Agreement, or any other agreement(s) made with Lender, shall prove to have been untrue or misleading in any material respect when made; or

(c)if Borrower files a petition in bankruptcy or for liquidation or reorganization or for the appointment of an examiner or receiver to Borrower or any of its assets or other similar petition, makes an assignment for the benefit of creditors, consents to the appointment of a receiver, trustee or other custodian for all or a substantial part of its property, is adjudicated at bankrupt, or fails to cause to be vacated, set aside or stayed within 60 days of any court order appointing a receiver, trustee or other custodian for all or a substantial part of its property or ordering relief against it in any involuntary case of bankruptcy.

SECTION 7. INDEMNIFICATION

Borrower agrees to indemnify lender from and against any and all claims, losses and liabilities arising out of or resulting from the occurrence of any event or default (including, but not limited to, the costs for the enforcement hereof). Borrower further agrees to pay all reasonable expenses of Lender, including, without limitation, the fees and expenses of its counsel, incurred in connection with (a) the enforcement of any part of this Agreement, and any waiver or amendment of any provision hereof (b) the administration of this Agreement after the occurrence of any Event of Default or (c) the failure by Borrower to perform or observe any of the provisions of this Agreement.

SECTION 8. WAIVERS

No single or partial waiver by Lender of any Event of Default, right or remedy which it may have shall operate as a waiver of any other Event of Default, right or remedy or of the same Event of Default, right or remedy on a future occasion. Borrower hereby waives presentment, notice of dishonor and protest and all other notices and demands whatsoever, except as a specifically provided in this Agreement.

SECTION 9. AMENDMENT

No amendment, modification or waiver of any provision of this Agreement, nor consent to any departure by borrower herefrom, shall in any event be effective unless the same shall be in writing and signed by Lender and shall otherwise be made in accordance with the provisions hereof, and then such amendment, waiver or consent shall be effective only in the specific instance and the specific purpose for which given.

SECTION 10. SURVIVAL

All agreements, representations in warranties made herein an in any certificates delivered pursuant hereto shall survive the execution and delivery of this Agreement and shall continue in full force and effect until the indebtedness of Borrower under this Agreement has been paid in full.

SECTION 11. ASSIGNMENT

Exhibit 10.66

This Agreement shall be binding upon and inure to the benefit of Borrower and Lender and their respective permitted successors and assigns; provided, however, that Borrower may not transfer or assign any of its rights or obligations hereunder without the prior written consent of Lender.

SECTION 12. NOTICE

All notices under this Agreement shall be sent by registered mail or nationally recognized overnight courier, in each case, with confirmation of receipt, and shall be deemed to have been sent on the date of receipt or on the date of mailing if preceded by transmission of the text of such notice by facsimile (with confirmation of transmission) to the number or by e-mail to the e-mail address given by each Party in writing.

SECTION 13. GOVERNING LAW AND JURISDICTION

This Agreement shall be governed by and construed in accordance with the laws of the State of Delaware.

[SIGNATURE PAGE FOLLOWS]

Exhibit 10.66

IN WITNESS WHEREOF, the parties hereto have executed and delivered this Agreement as of the date first above written.

NIKKO CHEMICALS CO., LTD.
By: /s/ Shizuo Ukaji___________________
Name: Shizuo Ukaji
Title: President & Chief Executive Officer
AMYRIS, INC.
By:	_/s/ John Melo_________________
Name:	John Melo
Title:	President & Chief Executive Officer

EX-20.42

Exhibit 2.04

IN ACCORDANCE WITH ITEM 601(b)(10)(iv) OF REGULATION S-K, CERTAIN CONFIDENTIAL INFORMATION HAS BEEN EXCLUDED FROM THIS DOCUMENT BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) WOULD LIKELY CAUSE COMPETITIVE HARM IF PUBLICLY DISCLOSED. THE CONFIDENTIAL INFORMATION IS DENOTED HEREIN BY [*].

EQUITY PURCHASE AGREEMENT

This EQUITY PURCHASE AGREEMENT (this “Agreement”) is made as of this 31^st day of October, 2019 (the “Effective Date”), by and between AMYRIS, INC., a Delaware corporation (the “Purchaser”), and COSAN US, INC., a Delaware corporation (the “Seller”). Certain capitalized terms used but not otherwise defined herein shall have the meanings ascribed thereto in Article VIII.

RECITALS

WHEREAS, Amyris and Cosan US formed Novvi LLC, a Delaware limited liability company (the “Company”) pursuant to and in accordance with the Delaware Limited Liability Company Act, 6 Del. C. § 18-101, et seq. (as the same may be amended from time to time) and entered into an agreement of limited liability company of Novvi LLC on September 6, 2011, as the same was amended in October of 2011;

WHEREAS, the Company is in the business of research, development, production and commercialization of high performance, certified renewable synthetic lubricant base oils and additives from synthetic molecules derived from sustainable resources, that can deliver performance characteristics comparable to petroleum based synthetic base oils;

WHEREAS, Amyris and Cosan executed and delivered together with American Refining Group, Inc., a Pennsylvania corporation, Chevron Products Company, a division of Chevron U.S.A. Inc., a Pennsylvania corporation and H&R Group US, Inc., a Colorado corporation, (collectively, the “Members”) a Fourth Amended and Restated Operating Agreement of the Company dated March 12, 2018 (the “Operating Agreement”). All terms used herein and not otherwise defined are assigned the definitions set forth in the Operating Agreement;

WHEREAS, Seller is the owner of the Purchased Units (as defined in Section 1.1) and, subject to the terms and conditions set forth herein, Seller desires to sell to the Purchaser and Purchaser desires to purchase from the Seller, the Purchased Units for the Purchase Price (the “Transfer”); and

WHEREAS, the Members have approved the Transfer under the terms of the Operating Agreement.

AGREEMENT

In consideration of the foregoing and the respective representations, warranties, covenants and agreements set forth herein, and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, intending to be legally bound, the parties hereto agree as follows:

ARTICLE I

PURCHASE AND SALE OF THE PURCHASED UNITS

1.1Agreement to Purchase and Sale the Purchased Units. Upon the terms and subject to the conditions set forth herein, the Seller hereby sells to the Purchaser the totality of its interest in the Company, corresponding to one hundred fifty nine thousand, two hundred and ten (159,210) Units (the “Purchased Units”), free and clear of any and all Encumbrances. The Purchased Units are sold and shall be transferred on the date hereof by the Seller together with all rights inherent to them.

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1.2The aggregate purchase price for the Purchased Units shall be ten million, eight hundred thousand United States dollars (US$10,800,000) (the “Purchase Price”), payable according to Section 1.3 below.

1.3Payment of the Purchase Price.

(a)The Purchase Price will be paid in full by the Purchaser to the Seller within five (5) years of the date of formation of R&A Adoçantes S.A., a Brazilian sociedade por ações (the “Sweet JV”), according to the Joint Venture Agreement (the “JVA”) by and between Raizen Energia S.A., the Purchaser and certain subsidiary of the Purchaser, through the assignment of net preferred dividends (the “Preferred Dividends”) distributed by the Sweet JV and received by the Purchaser.

(b)The Purchaser hereby assigns to Seller the Purchaser’s right to receive any Preferred Dividends distributed by the Sweet JV and that should be received by the Purchaser, until the Dividend Assignment Expiration Date, as defined below (the “Dividend Assignment”). Seller hereby accepts such Dividend Assignment. The Dividend Assignment shall expire and terminate at the earlier of expiration of the five (5) year period referred to in item (a) above or Seller’s receipt of the Purchase Price (the “Dividend Assignment Expiration Date”).

(c)In the event Sweet JV fails to pay the Seller as required by Section 1.3(a) and (b) above, any Preferred Dividend distributed by the Sweet JV and received by Purchaser before the Dividend Assignment Expiration Date shall be transferred to Seller within five (5) Business Days from its receipt, by wire transfer of immediately available funds to an account designated in writing by Seller to Purchaser. The Purchaser shall send to Seller true and complete copies of Sweet JV’s unaudited quarterly balance sheets in order to verify if the Sweet JV approved the distribution of Preferred Dividends to the Purchaser.

(d)If, on the Dividend Assignment Expiration Date, any portion of the Purchase Price remains to be paid by the Purchaser to Seller, Purchaser will pay Seller such unpaid portion of the Purchase Price within sixty (60) days by wire transfer of immediately available funds to an account designated in writing by Seller to Purchaser.

(e)If, within the five (5) years term from the formation of the Sweet JV, there is a Liquidity Event of the Sweet JV, and any portion of the Purchase Price at that time remains to be paid by the Purchaser to Seller, Purchaser shall use cash or cash equivalent received by Purchaser in such Liquidity Event to pay to Seller an amount calculated by multiplying the percentage reflecting the percentage reduction in Purchaser’s ownership of Sweet JV by the amount of such unpaid portion of the Purchase Price within sixty (60) days by wire transfer of immediately available funds to an account designated in writing by Seller to Purchaser; and any portion that remains unpaid thereafter shall be paid to the Seller pursuant to Sections 1.3(b), (c) and (d) above.

(f)If, within the five (5) years term from the formation of the Sweet JV, there is a Liquidity Event of the Company, and any portion of the Purchase Price at that time remains to be paid by the Purchaser to Seller, Purchaser shall pay to Seller such unpaid portion of the Purchase Price as follows:

(f.1) in case the Purchaser receives, in cash or cash equivalent, an amount equal to or higher than twenty one million, six hundred thousand dollars (US$ 21,600,000) as a result of the Liquidity Event, Purchaser shall use all cash or cash equivalent received in such Liquidity Event to pay to

2

Seller such unpaid portion of the Purchase Price within sixty (60) days by wire transfer of immediately available funds to an account designated in writing by Seller to Purchaser;

(f.2) in case the Purchaser receives, in cash or cash equivalent, an amount lower than twenty one million, six hundred thousand dollars (US$ 21,600,000) as a result of the Liquidity Event, Purchaser shall use fifty per cent (50%) of the received amount to pay to Seller such unpaid portion of the Purchase Price within sixty (60) days by wire transfer of immediately available funds to an account designated in writing by Seller to Purchaser; and any portion that remains unpaid thereafter shall be paid to the Seller pursuant to Sections 1.3(b), (c) and (d) above.

(g)If, for any or no reason, the Sweet JV is not formed within one (1) year from the date hereof, the Purchase Price shall be paid in full by the Purchaser to the Seller within three (3) years from the date hereof, by wire transfer of immediately available funds to an account designated in writing by Seller to Purchaser.

ARTICLE II

PURCHASER’S REPRESENTATIONS AND WARRANTIES

The Purchaser hereby represents and warrants to the Seller as of the Closing as follows:

2.1.Organization. The Purchaser is a corporation duly organized, validly existing and in good standing under the laws of Delaware.

2.2.Authority, Due Execution and Binding Effect. The execution and delivery of this Agreement and the performance by the Purchaser of its obligations hereunder, have been duly authorized by all necessary corporate action. This Agreement constitutes the legal, valid and binding obligations of the Purchaser enforceable against the Purchaser in accordance with its terms except as enforcement thereof may be limited by applicable Insolvency Laws.

2.3.Transaction Not a Breach. Neither the execution and delivery of this Agreement, nor its performance by the Purchaser will violate or conflict with or result in a breach of any provision of any Law binding on the Purchaser or conflict with or result in the breach of any of the terms, conditions or provisions of the Organizational Documents of the Purchaser or of any contract, agreement, mortgage or other instrument or obligation of any nature to which the Purchaser is a party or by which the Purchaser is bound.

2.4.Constructive Knowledge. The Purchaser understands that its investment in the Company involves substantial risks. The Purchaser: (a) has such knowledge and experience in financial and business matters as is necessary to enable it to evaluate the merits and risks of an investment in the Company; and (b) has no present need for liquidity in its investment in the Company and is able to bear the risk of that investment for an indefinite period and to afford a complete loss thereof.

2.5.Accredited Investor. The Purchaser is an “accredited investor” within the definition set forth in Rule 501(a) of the Securities Act.

2.6.Investment. The Purchaser is acquiring the Purchased Units for its own account for the purpose of investment and not with a view to or for sale in connection with any distribution thereof that would jeopardize the exemption from the registration requirements of any applicable federal or state

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securities laws or regulations upon which the Seller has relied in making the offer and sale of the Purchased Units to the Purchaser, nor with any present intention of distributing or selling the same, and it has no obligation, indebtedness or commitment providing for the disposition thereof that would jeopardize the exemption from any such registration requirements upon which the Seller has relied in making the offer and sale of the Purchased Units to the Purchaser. The Purchaser understands and acknowledges that: (a) the Purchased Units have not been registered under the Securities Act by reason of their issuance in a transaction exempt from such registration requirements predicated upon the Purchaser’s warranties contained in Section 2.5 and this Section 2.6,

and (b) the Purchased Units cannot be sold unless a subsequent disposition thereof is registered under applicable securities laws or is exempt from such registration. The Purchaser understands that no public market now exists for the Purchased Units and that a public market may never exist for the Purchased Units.

2.7.Brokers. Neither the Purchaser nor any of its Affiliates has incurred any liability to any broker, finder or agent, and there are no claims for any brokerage fees, finder’s fees or commissions in connection with the transactions contemplated by this Agreement.

ARTICLE III

SELLER’S REPRESENTATIONS AND WARRANTIES

The Seller hereby represents and warrants to the Purchase as of the Closing as follows:

3.1.Organization. The Seller is a corporation duly organized, validly existing and in good standing under the laws of Delaware.

3.2.Authority, Due Execution and Binding Effect. The execution and delivery of this Agreement and the performance by the Seller of its obligations hereunder, have been duly authorized by all necessary corporate action. This Agreement constitutes the legal, valid and binding obligations of the Seller enforceable against the Seller in accordance with its terms except as enforcement thereof may be limited by applicable Insolvency Laws.

3.3.Transaction Not a Breach. Neither the execution and delivery of this Agreement, nor its performance by the Seller will violate or conflict with or result in a breach of any provision of any Law binding on the Seller or conflict with or result in the breach of any of the terms, conditions or provisions of the Organizational Documents of the Seller or of any contract, agreement, mortgage or other instrument or obligation of any nature to which the Seller is a party or by which the Seller is bound.

3.4.Title to the Purchased Units; No Encumbrances. Seller is the sole beneficial and record holder of the Purchased Units, and upon consummation of the transactions contemplated by this Agreement, Seller shall have transferred to Purchaser and Purchaser shall have obtained from Seller all right, title and interest in the Purchased Units, free and clear of any and all Encumbrances or claims of any kind (whether recorded or unrecorded).

3.5.Exemption from Registration Requirements. Based in part on the representations and warranties of the Purchaser as set forth in Article II hereof, the sale and transfer of the Purchased Units as contemplated by this Agreement are exempt from the registration requirements of the Securities Act and applicable state securities laws.

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3.6.Brokers. Neither the Seller nor any of its Affiliates has incurred any liability to any broker, finder or agent, and there are no claims for any brokerage fees, finder’s fees or commissions in connection with the transactions contemplated by this Agreement.

ARTICLE IV

REVISED MEMBERSHIP RIGHTS AND INTERESTS

4.1. Membership Interest. Each Member’s ownership interest in the Company, adjusted to reflect the Transfer hereunder, is set forth below:

Member	Units Prior to Transfer	Percentage Interest Prior to Transfer	Units Following Transfer	Percentage Interest Following Transfer
Cosan (Seller)	[*]	[*]	–	--
Amyris (Purchaser)	[*]	[*]	[*]	[*]
ARG	[*]	[*]	[*]	[*]
Chevron	[*]	[*]	[*]	[*]
H&R	[*]	[*]	[*]	[*]
Total Units outstanding	[*]	[*]	[*]	[*]

4.2. Capital Accounts. The Capital Accounts of the Purchaser and the Seller shall be adjusted by the Company to reflect the Transfer.

4.3. Resignation as Member; Resignation of Seller’s Managers; Amendment of Operating Agreement. The parties agree that, effective upon the Closing, Seller will have no further rights as a Member in the Company, and immediately prior to the execution of this Agreement, Seller will cause its designated Manager(s) to resign from the Company. The parties agree that upon the purchase of Purchased Units pursuant to this Agreement, Purchaser, Members and the Company, as applicable, shall be free to amend the Operating Agreement and to take any and all such other actions, and amend any and all such other documents, agreements, instruments, certificates, books and records, as may be necessary or appropriate to effectuate and carry out the purpose and intent of the foregoing and the transactions contemplated by this Agreement.

ARTICLE V

CLOSING

5.1. Closing. The Closing shall take place simultaneously with the execution and delivery of this Agreement, electronically or otherwise as the parties may mutually agree. The date on which the Closing occurs is referred to herein as the “Closing Date.”

5.2. Closing Deliveries. At Closing, the parties will execute and deliver or cause to be executed and delivered to each other each of the following items:

(a) Purchaser Deliveries at Closing:

(i)  a certificate of the secretary of the Purchaser certifying that the Board of Directors of the Purchaser has duly approved the execution and delivery of this Agreement and the performance of the transactions contemplated hereby;

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(ii)  executed copies of any required Consents.

(b) Seller Deliveries at Closing:

(i) a certificate of the secretary of the Seller certifying that the Board of Directors of the Seller has duly approved the execution and delivery of this Agreement and the performance of the transactions contemplated hereby.

        (ii) executed copy of the consent from the Board of Directors of Cosan Lubrificantes e Especialidades S.A., indirect controlling shareholder of Seller, for the Seller to consummate the transaction contemplated in this Agreement;

(iii) letter of resignation of the Seller’s Manager, resigning from the Board of Managers of the Company effective as of the Closing Date.

ARTICLE VI

COVENANTS AFTER CLOSING

6.1.Notice of Assignment of Preferred Dividend Rights. The parties hereby agree, upon the incorporation of the Sweet JV, to execute the Notice and Agreement of Assignment of Preferred Dividend Rights in a form substantially similar to the form attached hereto as Exhibit A. Seller agrees to acknowledge payment of the full Purchase Price in writing delivered to Sweet JV and delivered to Purchaser within five (5) business days of receipt of such payment.

6.2.Post-Closing Cooperation. The parties to this Agreement will use their reasonable efforts, and will cooperate with each other to secure any Consents from third parties as shall be required to enable each of them to effect the transactions contemplated hereby, and will otherwise use their commercially reasonable efforts to cause the consummation of such transactions in accordance with the terms and conditions hereof. Each party will execute all documents, including, but not limited to, any amendment to the Operating Agreement, and take such other actions as the other party may reasonably request in order to consummate the transactions provided for herein and to accomplish the purposes of this Agreement. Purchaser shall provide Seller with proper confirmation of the Transfer on the Company’s books and recordsas soon as practicable, but in no event later than fifteen (15) calendar days from the Closing Date.

6.3.Public Announcements. No party hereto or any of their respective Affiliates will issue or cause the publication of any press release or other public announcement with respect to this Agreement or the transactions contemplated hereby without the prior consent of the other, which consent will not be unreasonably withheld or delayed; provided, however, that nothing herein will prohibit any party from issuing or causing publication of any such announcement to the extent that such party determines such action to be required by Law, in which case the party making such determination will, if practicable in the circumstances, use reasonable efforts to allow the other parties reasonable time to comment on such announcement in advance of its issuance.

ARTICLE VII

INDEMNIFICATION

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7.1.Indemnification by the Purchaser. From and after the Closing, the Purchaser agrees to indemnify, defend and save each Seller Indemnified Party forever harmless from and against, and to promptly pay to a Seller Indemnified Party or reimburse a Seller Indemnified Party for, any and all Losses sustained or incurred by any Seller Indemnified Party relating to, resulting from, arising out of or otherwise by virtue of any of the following:

◦any misrepresentation or breach of a representation or warranty made herein by the Purchaser.

◦non-compliance with or breach by the Purchaser of any of the covenants or agreements contained in this Agreement to be performed by the Purchaser.

(c)  (d) any claim for payment of fees and/or expenses as a broker or finder in connection with the origin, negotiation, execution or consummation of the transactions contemplated by this Agreement based upon an alleged agreement between claimant and any of the Purchaser or any of its Affiliates.

7.2.Indemnification by the Seller. From and after the Closing, the Seller agrees to indemnify, defend and save each Purchaser Indemnified Party forever harmless from and against, and to promptly pay to a Purchaser Indemnified Party or reimburse a Purchaser Indemnified Party for, any and all Losses sustained or incurred by any Purchaser Indemnified Party relating to, resulting from, arising out of or otherwise by virtue of any of the following:

◦any misrepresentation or breach of a representation or warranty made herein by the Seller.

◦non-compliance with or breach by the Seller of any of the covenants or agreements contained in this Agreement to be performed by the Seller.

◦the Seller’s failure to transfer the Purchased Units free and clear of any Encumbrances.

(d) any claim for payment of fees and/or expenses as a broker or finder in connection with the origin, negotiation, execution or consummation of the transactions contemplated by this Agreement based upon an alleged agreement between claimant and any of the Seller or any of its Affiliates.

7.3.Indemnification Procedure for Third Party Claims.

◦In the event that subsequent to the Closing any Person entitled to indemnification under this Agreement (an “Indemnified Party”) asserts a claim for indemnification or receives notice of the assertion of any Third Party Claim against such Indemnified Party, against which a party to this Agreement is required to provide indemnification under this Agreement (an “Indemnifying Party”), the Indemnified Party shall give written notice together with a statement of any available information regarding such claim to the Indemnifying Party promptly after learning of such claim. The Indemnifying Party shall have the right, upon written notice to the Indemnified Party (the “Defense Notice”) within thirty (30) days after receipt from the Indemnified Party of notice of such claim, to conduct at his, her or its expense the defense against such claim in his, her or its own name, or if necessary in the name of the Indemnified Party, with counsel reasonably satisfactory to the Indemnified Party. Notwithstanding the foregoing, the Indemnifying Party shall not be entitled to assume control of a Third Party Claim and shall

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pay the reasonable fees and expenses of counsel retained by the Indemnified Party if (i) the Third Party Claim seeks injunctive or other equitable relief, (ii) the Indemnified Party, in the claim notice to the Indemnifying Party, states that, based on advice of counsel, he, she or it believes that his, her or its interests in the Third Party Claim are, or can reasonably be expected to be, adverse to the interests of the Indemnifying Party, or (iii) such Indemnifying Party is unable to provide the Indemnified Party with reasonable assurance of his, her or its ability to pay the expenses of the defense against such Third Party Claim.

◦In the event that the Indemnifying Party shall fail to give such notice described in Section7.3(a), he, she or it shall be deemed to have elected not to conduct the defense of the subject claim, and in such event the Indemnified Party shall have the right to conduct such defense with counsel of its own choosing at the expense of the Indemnifying Party and to compromise and settle the claim, subject to the prior consent of the Indemnifying Party, which shall not be unreasonably withheld or delayed.

◦In the event that the Indemnifying Party does elect to conduct the defense of the subject claim, the Indemnified Party will cooperate with and make available to the Indemnifying Party such assistance and materials as may be reasonably requested by he, she or it, all at the expense of the Indemnifying Party, and the Indemnified Party shall have the right at his, her or its expense to participate in the defense assisted by counsel of his, her or its own choosing and the Indemnified Party shall have the right to compromise and settle the claim only with the prior written consent of the Indemnifying Party, which consent shall not be unreasonably withheld or delayed. Without the prior written consent of the Indemnified Party, the Indemnifying Party will not enter into any settlement of any Third Party Claim or cease to defend against such claim, if pursuant to or as a result of such settlement or cessation, (i) injunctive or other equitable relief would be imposed against the Indemnified Party, or (ii) such settlement or cessation would lead to liability or create any financial or other obligation on the part of the Indemnified Party for which the Indemnified Party is not entitled to indemnification hereunder. If a firm decision is made to settle a Third Party Claim, which offer the Indemnifying Party is permitted to settle under this Section 7.2(c), and the Indemnifying Party desires to accept and agree to such offer, the Indemnifying Party will give written notice to the Indemnified Party to that effect. If the Indemnified Party fails to consent to such firm offer within thirty (30) days after his, her or its receipt of such notice, the Indemnified Party may continue to contest or defend such Third Party Claim and, in such event, the maximum liability of the Indemnifying Party as to such Third Party Claim will not exceed the amount of such settlement offer, plus costs and expenses paid or incurred by the Indemnified Party through the end of such thirty (30) day period.

◦Any judgment entered or settlement agreed upon in the manner provided herein shall be binding upon the Indemnifying Party, and shall conclusively be deemed to be an obligation with respect to which the Indemnified Party is entitled to prompt indemnification hereunder.

7.4.Direct Claims. It is the intent of the parties hereto that all direct claims by an Indemnified Party against a party hereto not arising out of Third Party Claims shall be subject to and benefit from the terms of this Article VII. Any Direct Claim will be asserted by giving the Indemnifying Party reasonably prompt written notice thereof, and the Indemnifying Party will have a period of thirty (30) days within which to satisfy such Direct Claim. If the Indemnifying Party does not so respond within such thirty (30) day period, the Indemnifying Party will be deemed to have rejected such claim, in which event the indemnitee will be free to pursue such remedies as may be available to the indemnitee under this Article VII or otherwise.

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7.5.Failure to Give Timely Notice. A failure by an Indemnified Party to give timely, complete or accurate notice as provided in Sections 7.2 or 7.3 will not affect the rights or obligations of any party hereunder except and only to the extent that, as a result of such failure, any party entitled to receive such notice was deprived of his, her or its right to recover any payment under his, her or its applicable insurance coverage or was otherwise directly and materially damaged as a result of such failure to give timely notice.

7.6.Right of Set Off. To the extent that any Indemnifying Party fails to satisfy an obligation under this Article VII, the Indemnified Party may, in its sole discretion, set off the amount of such obligation against any amounts the Indemnified Party may owe to the Indemnifying Party under this Agreement or any Transaction Document.

7.7.Survival of Representations and Warranties. All representations, warranties, covenants and agreements shall survive the execution and delivery of this Agreement and the Closing for a period of twelve (12) months after the Closing Date whereupon they shall expire and be of no further force or effect.

ARTICLE VIII

DEFINITIONS

“Affiliate” has the meaning given to that term in Rule 405 under the Securities Act and shall include each past and present Affiliate of a Person.

“Business Day” means any day, except a Saturday, Sunday or other day on which commercial banking institutions in the State of California in the United States of America and in the State of São Paulo in Brazil are authorized or directed by applicable Law or executive order to close.

“Closing” means the consummation of the transactions that are the subject of the Agreement that are closed on the Closing Date.

“Consent” means any approval, consent, ratification, permission, waiver, exemptions, or authorization (including any Governmental Authorization) necessary for the consummation of the transactions contemplated by this Agreement, which, if not obtained, would result in a violation of any Law or any liability of the parties.

“Direct Claim” means any claim under Article VIIof the Agreement by an Indemnified Party for indemnification other than indemnification with respect to a Third Party Claim.

“Environmental Law” means all federal, state and local laws, statutes, codes, regulations, rules, ordinances, orders, standards, permits, licenses, actions, policies, principles of common law and other requirements (including consent decrees, judicial decisions, administrative orders and self-implementing closure requirements) relating to the protection of the environment and/or public or worker health and safety, land use, and comprehensive planning and zoning rules and regulations, all as amended or reauthorized, all as amended or reauthorized, including, without limitation, the applicable provisions of state and federal department of transportation regulations.

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“Encumbrances” means encumbrances on, or in respect of title to, the Purchased Units, including, without limitation, mortgages, liens, adverse claims, interests, security interests, pledges, easements, covenants, restrictions, rights of first refusal or offer, “tag” or “drag” along rights or other encumbrances.

“GAAP” means generally accepted accounting principles.

“Governmental Authority” means the United States or any state or local government, or any subdivision, agency or authority thereof.

“Governmental Authorization” means any approval, consent, license, permit, certificate of need, waiver, or other authorization issued, granted, given, or otherwise made available by or under the authority of any Governmental Authority or pursuant to any Law.

“Insolvency Laws” means any bankruptcy, reorganization, insolvency, fraudulent conveyance, moratorium or similar laws affecting the enforcement of creditor’s rights generally and by general principles of equity (regardless of whether enforcement is considered in a proceeding in law or equity).

“Laws” means any law, Environmental Law, rules, ordinances, statutes, regulations, writs, injunctions, judgments, decrees, standards, guidance, orders or other decisions applicable to the operation of the Business.

“Liabilities” means debts, liabilities or obligations of any nature (whether accrued or unaccrued, absolute or contingent, direct or indirect, known or unknown, choate or inchoate, perfected or unperfected, liquidated or unliquidated, or otherwise, and whether due or to become due).

“Liquidity Event” means any event resulting in a full or partial liquidation by Purchaser of its investment in the Company or in the Sweet JV, in exchange for cash or cash equivalent, including, but without limitation, the initial public offering of the Company or the Sweet JV and a direct acquisition of the Units held by the Purchaser in the Company or the equity held by Purchaser in the Sweet JV.

“Losses” means any liabilities (whether absolute or contingent, direct or indirect, fixed or unfixed, liquidated or unliquidated, or otherwise), obligations, deficiencies, demands, claims, suits, actions, or causes of action, assessments, losses, costs, expenses, interest, fines, penalties, actual or punitive damages or costs or expenses of any and all investigations, proceedings, judgments, environmental analyses, remediation, settlements and compromises (including reasonable fees and expenses of attorneys, accountants and other experts).

“Material Adverse Effect” means a material adverse effect on the business, operations, assets, condition (financial or other), results of operations or prospects of the Company, taken as a whole.

“Order” means any judgment, order or decree of any court or Governmental Authority.

“Organizational Documents” means with respect to any Person, (a) the articles or certificate of incorporation and the by-laws or Code of Regulations of a corporation; (b) any charter or similar document adopted or filed in connection with the creation, formation, or organization of a Person (e.g., a certificate of formation, articles of organization or certificate of limited partnership), and any agreement governing such Person (e.g., a limited liability company agreement, operating agreement or partnership agreement); and (c) any amendment to any of the foregoing.

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“Person” means any individual, sole proprietorship, partnership, joint venture, trust, unincorporated association, corporation, limited liability company, entity or Governmental Authority.

“Proceeding” means any claim, suit, litigation, arbitration, hearing, audit, charge, investigation, or other action (whether civil, criminal, administrative, investigative, or informal) commenced, brought, conducted, or heard by or before, or otherwise involving, any Person, Governmental Authority, judge, arbitrator or mediator.

“Purchaser Indemnified Party” means the Purchaser and its Affiliates, and each of their respective officers, directors, managers, employees, and agents.

“Securities Act” means the Securities Act of 1933, as amended.

“Seller Indemnified Party” means the Seller and its Affiliates, and their respective officers, directors, managers, employees and agents.

“Third Party Claim” means a claim or the commencement of any action or Proceeding by any Person who is not a party to this Agreement or an Affiliate of such a Person (including, but not limited, to any domestic or foreign court, government, or Governmental Authority or instrumentality, federal state or local).

A claim, Proceeding, dispute, action, or other matter will be deemed to have been “Threatened” if any notice, demand or statement has been given or made in writing, or if any other event has occurred or any other circumstances exist, that would lead a prudent Person to conclude that such a claim, Proceeding, dispute, action, or other matter is likely to be asserted, commenced, taken, or otherwise pursued in the future.

“Transaction” means the transactions contemplated by this Agreement.

“Units” means a limited liability company interest in the Company.

ARTICLE IX

MISCELLANEOUS

9.1.Notices, Consents, Etc. Any notices, consents or other communication required to be sent or given hereunder by any of the parties shall in every case be in writing and shall be deemed properly served if (a) delivered personally, (b) sent by registered or certified mail, in all such cases with first class postage prepaid, return receipt requested, or (c) delivered by a recognized overnight courier service, to the parties at the addresses set forth below or at such other addresses as may be furnished in writing:

If to the Seller:

Cosan Lubrificantes e Especialidades S.A.

Avenida Brigadeiro Faria Lima, No. 4100, 8° andar

São Paulo − SP − Brazil

CEP: 04538-132

Attention: Legal Department

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        If to the Purchaser:

Amyris, Inc.

5885 Hollis St., Suite 100

Emeryville, CA – USA

94608

Attention: General Counsel

Date of service of such notice shall be (i) the date such notice is personally delivered, (ii) three (3) days after the date of mailing if sent by certified or registered mail, or (iii) one (1) day after date of delivery to the overnight courier if sent by overnight courier.

9.2.Severability. The unenforceability or invalidity of any provision of this Agreement shall not affect the enforceability or validity of any other provision.

9.3.Successors. Except as specifically provided in Section 9.7 hereof, this Agreement shall be binding upon and inure to the benefit of the parties hereto and their respective successors, permitted assigns, heirs and personal representatives.

9.4.Counterparts. This Agreement may be executed simultaneously in one (1) or more counterparts, each of which shall be deemed an original but all of which together shall constitute one and the same instrument. A signed copy of this Agreement delivered by facsimile, email or other means of electronic transmission shall be deemed to have the same legal effect as delivery of an original signed copy of this Agreement.

9.5.Expenses.

(a)Sellers’ Expenses. The Seller shall pay for all costs and expenses incurred by the Seller in negotiating and preparing this Agreement and in closing and carrying out the transactions contemplated by this Agreement.

(b)Purchasers’ Expenses. The Purchaser shall pay for all costs and expenses incurred by the Purchaser in negotiating and preparing this Agreement and in closing and carrying out the transactions contemplated by this Agreement.

9.6.Governing Law. THIS AGREEMENT AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER SHALL BE GOVERNED IN ALL RESPECTS, INCLUDING VALIDITY, INTERPRETATION AND EFFECT, BY THE LAWS OF THE STATE OF DELAWARE, WITHOUT REGARD TO ITS RULES OF CONFLICTS OF LAW. ANY DISPUTE HEREUNDER SHALL BE BROUGHT EXCLUSIVELY IN THE U.S. DISTRICT COURT FOR THE DISTRICT OF DELAWARE, AND THE PARTIES EXPRESSLY SUBMIT THEIR PERSONAL JURISDICTION TO SUCH COURTS, AND WAIVE (AND AGREE NOT TO ASSERT) ANY OBJECTION TO THE LAYING OF VENUE THEREIN.

9.7.Assignment. This Agreement will be binding upon and inure to the benefit of the parties hereto and their respective successors and permitted assigns, but will not be assignable or delegable by any party without the prior written consent of the other party.

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9.8.Entire Agreement. This Agreement and all of the Schedules and Exhibits attached to the Agreement (which shall be deemed incorporated in the Agreement and made a part hereof) set forth the entire understanding of the parties with respect to the subject matter hereof and may be modified only by instruments signed by all of the parties hereto.

9.9.Third Parties. Nothing herein expressed or implied is intended or shall be construed to confer upon or give to any Person, other than the parties to this Agreement, any rights or remedies under or by reason of this Agreement.

9.10.Headings; Interpretative Matters. The subject headings of Articles and Sections of this Agreement are included for purposes of convenience only and shall not affect the construction or interpretation of any of its provisions. Unless the context otherwise requires, (a) all references to Articles, Sections, Schedules or Exhibits are to Articles, Sections, Schedules or Exhibits in this Agreement, (b) each accounting term not otherwise defined in this Agreement has the meaning assigned to it in accordance with GAAP, and (c) words in the singular or plural include the singular and plural and pronouns stated in either the masculine, feminine or neuter gender shall include the masculine, feminine and neuter.

[Signature Page Follows]

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IN WITNESS WHEREOF, the parties have executed this Equity Purchase Agreement as of the date first above written.

THE PURCHASER:

Amyris, Inc.

By: /s/ John Melo    

Name: John Melo    

Title: President and CEO   

THE SELLER:

Cosan US, Inc.

By: /s/ Lineu Paulo Moran Filho  

Name: Lineu Paulo Moran Filho  

Title: Officer     

EX-21.01

Exhibit 21.01

SUBSIDIARIES OF THE REGISTRANT

Subsidiaries	State or Other Jurisdiction of Incorporation or Organization
Amyris Fuels, LLC	Delaware
AB Technologies LLC	Delaware
Amyris Biotecnologia do Brasil Ltda.	Brazil
Amyris Bio Products Portugal, Unipessoal, Lda.	Portugal
Amyris Clean Beauty, Inc.	Delaware
Amyris Biossance do Brasil Comércio de Cosméticos Ltda.	Brazil
Amyris Brotas Fermentacao de Performance Ltda.	Brazil
Aprinnova, LLC	Delaware
DIPA Co., LLC	Delaware

EX-23.01

EXHIBIT 23.01

Consent of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of Amyris, Inc.

We consent to the incorporation by reference in the Registration Statements (Nos. 333‑169715, 333‑172514, 333‑180006, 333‑187598, 333‑188711, 333‑195259, 333‑203213, 333‑210569, 333‑217345, 333‑224316, 333‑225848 and 333‑234135) on Form S-8 of Amyris, Inc. and Subsidiaries (the Company) of our report dated March 13, 2020, relating to the Company’s consolidated financial statements as of and for the years ended December 31, 2019 and 2018, and the effectiveness of internal control over financial reporting as of December 31,2019, which reports appear in this December 31, 2019 Annual Report on Form 10-K of the Company.

Our report on the effectiveness of internal control over financial reporting expresses an adverse opinion on the effectiveness of the Company’s internal control over financial reporting as of December 31, 2019.

Our report on the consolidated financial statements refers to changes in accounting method of accounting for leases on January 1, 2019, due to the adoption of Financial Accounting Standard Board’s Accounting Standards Codification 842, Leases, and amending the classification of certain equity-linked financial instruments with down round features and the respective disclosure requirements in fiscal year 2019 due to adoption of Accounting Standards Update No. 2017‑11. Our report also contains an emphasis paragraph that states that the Company has suffered recurring losses from operations, has an accumulated deficit of $1.8 billion and current debt service requirements that raise substantial doubt about its ability to continue as a going concern. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.

/s/ Macias Gini & O'Connell LLP

San Francisco, California

March 13, 2020

EX-31.01

EXHIBIT 31.01

CERTIFICATION OF PERIODIC REPORT UNDER SECTION 302 OF

THE SARBANES-OXLEY ACT OF 2002

I, John G. Melo, certify that:

1.I have reviewed this annual report on Form 10-K of Amyris, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

/s/ John G. Melo

John G. Melo

President and Chief Executive Officer

March 13, 2020

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EX-31.02

EXHIBIT 31.02

CERTIFICATION OF PERIODIC REPORT UNDER SECTION 302 OF

THE SARBANES-OXLEY ACT OF 2002

I, Jonathan Wolter, certify that:

1.I have reviewed this annual report on Form 10-K of Amyris, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

/s/ Jonathan Wolter

Jonathan Wolter

Interim Chief Financial Officer

March 13, 2020

EX-32.01

EXHIBIT 32.01

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350

AS ADOPTED PURSUANT TO SECTION 906

OF THE SARBANES-OXLEY ACT OF 2002

I, John G. Melo, President and Chief Executive Officer of Amyris, Inc. (Company), do hereby certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that to the best of my knowledge:

•the Annual Report on Form 10-K of the Company for the year ended December 31, 2019 (Report) fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

•the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company for the periods presented therein.

/s/ John G. Melo

John G. Melo

President and Chief Executive Officer

March 13, 2020

EX-32.02

EXHIBIT 32.02

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350

AS ADOPTED PURSUANT TO SECTION 906

OF THE SARBANES-OXLEY ACT OF 2002

I, Jonathan Wolter, Interim Chief Financial Officer of Amyris, Inc. (Company), do hereby certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that to the best of my knowledge:

•the Annual Report on Form 10-K of the Company for the year ended December 31, 2019 (Report) fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

•the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company for the periods presented therein.

/s/ Jonathan Wolter

Jonathan Wolter

Interim Chief Financial Officer

March 13, 2020

1

XML

Related Party Transactions - Aprinnova JV's Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Liabilities	$ 5,249	$ 0
Aprinnova JV | Nikko
Related Party Transaction [Line Items]
Assets	17,390	12,904
Liabilities	$ 3,690	$ 2,364

XML

Related Party Transactions - Related Party Accounts Receivable (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Accounts receivable, net	$ 3,868	$ 1,349
DSM International B.V.
Related Party Transaction [Line Items]
Accounts receivable, net	3,868	1,071
Novvi LLC
Related Party Transaction [Line Items]
Accounts receivable, net	0	188
Total
Related Party Transaction [Line Items]
Accounts receivable, net	$ 0	$ 90

XML

Geographical Information (Tables)

12 Months Ended

Dec. 31, 2019

Segment Reporting [Abstract]

Schedule of Disclosure on Geographic Areas, Long-Lived Assets in Individual Foreign Countries by Country

December 31, (In thousands)	2019		2018
United States	$	13,799	$	10,404
Brazil	14,277		6,447
Europe	854		198
	$	28,930	$	17,049

XML

Revenue Recognition (Tables)

12 Months Ended

Dec. 31, 2019

Revenue from Contract with Customer [Abstract]

Disaggregation of Revenue

The following tables present revenue by primary geographical market, based on the location of the customer, as well as by major product and service:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Europe	$	10,092	$	54,043	$	6,674	$	70,809	$	7,576	$	7,658	$	14,172	$	29,406
United States	34,295		—		24,376		58,671		16,292		—		9,948		26,240
Asia	11,503		—		7,477		18,980		8,664		—		(2,333)		6,331
Brazil	3,612		—		115		3,727		381		—		561		942
Other	370		—		—		370		685		—		—		685
	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Revenue in Connection with Significant Revenue Agreement

For the years ended December 31, 2019 and 2018, the Company recognized revenue in connection with significant revenue agreements and from all other customers as follows:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Revenue from significant revenue agreements with:
DSM (related party)	$	10	$	49,051	$	4,120	$	53,181	$	18	$	5,958	$	4,735	$	10,711
Firmenich	8,591		4,992		1,413		14,996		3,727		1,700		5,717		11,144
Lavvan	—		—		18,342		18,342		—		—		—		—
Givaudan	7,477		—		1,500		8,977		4,078		—		4,358		8,436
DARPA	—		—		5,504		5,504		—		—		8,436		8,436
Subtotal revenue from significant revenue agreements	16,078		54,043		30,879		101,000		7,823		7,658		23,246		38,727
Revenue from all other customers	43,794		—		7,763		51,557		25,775		—		(898)		24,877
Total revenue from all customers	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Contract with Customer, Asset and Liability

The following table provides information about accounts receivable and contract liabilities from contracts with customers:

December 31, (In thousands)	2019		2018
Accounts receivable, net	$	16,322	$	16,003
Accounts receivable - related party, net	$	3,868	$	1,349
Accounts receivable, unbilled - related party	$	—	$	8,021
Contract assets	$	8,485	$	—
Contract assets, noncurrent - related party	$	1,203	$	1,203
Contract liabilities	$	1,353	$	8,236
Contract liabilities, noncurrent(1)	$	1,449	$	1,587

______________

⁽¹⁾The balances in contract liabilities, noncurrent are included in other noncurrent liabilities on the consolidated balance sheets.

Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of December 31, 2019.

(In thousands)	As of December 31, 2019
2020	$	56,719
2021	52,313
2022	30,483
2023 and thereafter	—
Total from all customers	$	139,515

XML

Income Taxes - Activity in the Deferred Tax Assets Valuation Allowance (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Deferred Tax Assets [Roll Forward]
Balance at Beginning of Year	$ 124,025	$ 81,086
Additions	29,610	42,939
Reductions / Charges	0	0
Balance at End of Year	$ 153,635	$ 124,025

XML

Related Party Transactions

12 Months Ended

Dec. 31, 2019

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

Related Party Equity

See Note 6, "Stockholders' Deficit" for details of these related party equity transactions:

•November 2018 DSM Securities Purchase Agreement

•August 2017 DSM Offering

Related Party Debt

See Note 4, "Debt" for details of these related party debt transactions:

•DSM Note (also see Note 12, "Divestiture")

•2014 Rule 144A Convertible Notes

•August 2013 Financing Convertible Notes

•Foris LSA

•Foris $19 million Note

•Naxyris LSA

Related party debt was as follows:

	2019						2018
December 31, (in thousands)	Principal		Unaccreted Debt Discount		Net		Principal		Unaccreted Debt Discount		Net
DSM notes	$	33,000	$	(4,621)	$	28,379	$	25,000	$	(6,311)	$	18,689
Foris
Foris notes	115,351		(9,516)		105,835		—		—		—
2014 Rule 144A convertible notes	—		—		—		5,000		(181)		4,819
	115,351		(9,516)		105,835		5,000		(181)		4,819
Naxyris note	24,437		(822)		23,615		—		—		—
Temasek 2014 Rule 144A convertible note	—		—		—		10,000		(435)		9,565
Total 2014 Rule 144A convertible note	10,178		—		10,178		9,705		(422)		9,283
	$	182,966	$	(14,959)	$	168,007	$	49,705	$	(7,349)	$	42,356

The fair value of the derivative liabilities related to the related party Foris $19 million note, Foris LSA and Naxyris note as of December 31, 2019 and 2018 was $2.6 million and $0.0 million, respectively. The Company recognized losses from change in the fair value of these and previous debt-related derivative liabilities of $0.1 million and $8.5 million for the years ended December 31, 2019 and 2018, respectively; see Note 3, "Fair Value Measurement".

At December 31, 2018, Temasek was no longer a related party. However, the Company and Temasek were related parties when they entered into the 2014 Rule 144A convertible notes transaction, for which terms remained unchanged since the borrowing date.

Related Party Revenue

The Company recognized revenue from related parties and from all other customers as follows:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Revenue from related parties:
DSM	$	10	$	49,051	$	4,120	$	53,181	$	18	$	5,958	$	4,735	$	10,711
Total	46		—		—		46		342		—		—		342
Novvi	—		—		—		—		—		—		—		—
Subtotal revenue from related parties	56		49,051		4,120		53,227		360		5,958		4,735		11,053
Revenue from all other customers	59,816		4,992		34,522		99,330		33,238		1,700		17,613		52,551
Total revenue from all customers	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

See Note 9, "Revenue Recognition" for details of the Company's revenue agreements with DSM.

Related Party Accounts Receivable

Related party accounts receivable was as follows:

December 31, (In thousands)	2019		2018
DSM	$	3,868	$	1,071
Novvi	—		188
Total	—		90
Related party accounts receivable, net	$	3,868	$	1,349

In addition to the amounts shown above, there were the following amounts on the consolidated balance sheet at December 31, 2019 and December 31, 2018, respectively:

•$0 and $8.0 million of unbilled receivables from DSM, in Accounts receivable, unbilled - related party;

•$1.2 million of unbilled receivables from DSM in Contract assets, noncurrent - related party; and

•$3.3 million and $4.3 million of contingent consideration receivable from DSM in Other assets.

Related Party Accounts Payable and Accrued Liabilities

Amounts due to DSM were as follows:

•Accounts payable and accrued and other current liabilities of $14.0 million and $2.1 million at December 31, 2019 and 2018, respectively; and

•Other noncurrent liabilities of $3.8 million and $3.6 million at December 31, 2019 and 2018, respectively.

Related Party DSM Transactions

The Company is party to the following significant agreements (and related amendments) with related party DSM:

Related to	Agreement	For Additional Information, See the Note Indicated
Debt	DSM Credit Agreement	4. Debt
Debt	2019 DSM Credit Agreement	4. Debt
Divestiture	November 2017 Quota Purchase Agreement	12. Divestiture
Divestiture	December 2017 DSM Transition Services Agreement	12. Divestiture
Equity	August 2017 DSM Offering	6. Stockholders' Deficit
Equity	November 2018 DSM Securities Purchase Agreement	6. Stockholders' Deficit
Revenue	July and September 2017 Collaboration and Licensing Agreements	9. Revenue Recognition
Revenue	December 2017 DSM Supply Agreement	9. Revenue Recognition
Revenue	December 2017 DSM Value Sharing Agreement, as amended	9. Revenue Recognition
Revenue	December 2017 DSM Performance Agreement	9. Revenue Recognition
Revenue	November 2017 Intellectual Property License Agreement	9. Revenue Recognition
Revenue	November 2018 Supply Agreement Amendment	9. Revenue Recognition

Concurrent with the sale of Amyris Brasil in December 2017, the Company and DSM entered into a series of commercial agreements including (i) a license agreement to DSM of its farnesene product for DSM to use in the Vitamin E and lubricant markets; (ii) a royalty agreement that DSM will pay the Company specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene under the Nenter Supply Agreement assigned to DSM; (iii) a performance agreement, which provides an option for DSM to elect a technology transfer upon the achievement of certain development milestones associated with the optimization of farnesene strains; and (iv) a transition services agreement for the Company to provide finance, legal, logistics, and human resource services to support the Brotas facility under DSM ownership for a six-month period with a DSM option to extend for six additional months. See Note 12, “Divestiture” for further information regarding the sale of Amyris Brasil and the related commercial agreements. In addition, the Company entered into a credit agreement with DSM under which the Company borrowed $25 million; see Note 4, "Debt" for additional information.

In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for production of its alternative sweetener product through 2022. See Note 9, “Revenue Recognition” for information regarding the November 2018 Supply Agreement Amendment and the November 2018 DSM Securities Purchase Agreement. The Company also entered into other transactions with DSM in November 2018 which resulted in the Company (i) evaluating this series of November 2018 transactions and considering other certain transactions with DSM in 2018 as a combined arrangement, and (ii) determining and allocating the fair value to each element. The other transactions entered into concurrently with the November 2018 Supply Agreement Amendment and November 2018 DSM Securities Purchase Agreement included an agreement to finalize the working capital adjustments related to the Brotas 1 facility sale in December 2017 and an amendment to reduce the exercise price of the Cash Warrant issued to DSM in the August 2017 DSM Offering and to provide a waiver for any potential claims arising from failure to obtain consent prior to amending the exercise price of the August 2017 Vivo Cash Warrant in the August 2017 Warrant transaction.

The contractual consideration transferred to DSM under the combined arrangement was $34.7 million. The Company performed an analysis to determine the fair value of the elements and allocated the resulting $33.3 million total fair value as follows: (i) $24.4 million to the manufacturing capacity, (ii) $6.8 million to the legal settlement and related consent waiver and (iii) $2.1 million to the working capital adjustment. See Note 3, “Fair Value Measurement” for information related to this fair

value allocation. The $1.4 million excess consideration transferred above the combined arrangement’s fair value was recorded as a reduction of royalty revenues in the year ended December 31, 2018. Of the $24.4 million fair value allocated to the manufacturing capacity, $3.3 million was recorded as deferred cost of products sold during 2018. Also, the Company paid an additional $14.1 million in manufacturing capacity fees during 2019, which were recorded as additional deferred cost of products sold. The remaining $7.0 million manufacturing capacity fees will be recorded as deferred cost of products sold in the period the additional payments are made to DSM. The deferred cost of products sold asset will be expensed on a units of production basis as products are sold over the five-year term of the supply agreement. On a quarterly basis, the Company evaluates its future production volumes for its sweetener product and adjusts the unit cost to be expensed over the remaining estimated production volume. The $6.8 million of fair value allocated to the legal settlement and related consent waiver was recorded as legal settlement expense for the year ended December 31, 2018. The $2.1 million of fair value allocated to the working capital adjustment was recorded as a loss on divestiture for the year ended December 31, 2018. The contractual consideration transferred to DSM exceeded the fair value of the elements received by $1.4 million and this excess was recorded as a reduction of licenses and royalties revenues in the three months ended December 31, 2018.

Related Party Joint Venture

In December 2016, the Company, Nikko Chemicals Co., Ltd. an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko (collectively, Nikko) entered into a joint venture (the Aprinnova JV Agreement) pursuant to which the Company contributed certain assets, including certain intellectual property and other commercial assets relating to its business-to-business cosmetic ingredients business (the Aprinnova JV Business), as well as its Leland production facility. The Company also agreed to provide the Aprinnova JV with exclusive (to the extent not already granted to a third party), royalty-free licenses to certain of the Company's intellectual property necessary to make and sell products associated with the Aprinnova JV Business (the Aprinnova JV Products). Nikko purchased their 50% interest in the Aprinnova JV in exchange for the following payments to the Company: (i) an initial payment of $10.0 million and (ii) the profits, if any, distributed to Nikko in cash as members of the Aprinnova JV during the three-year period from 2017 to 2019, up to a maximum of $10.0 million.

The Aprinnova JV operates in accordance with the Aprinnova Operating Agreement under which the Aprinnova JV is managed by a Board of Directors consisting of four directors: two appointed by the Company and two appointed by Nikko. In addition, Nikko has the right to designate the Chief Executive Officer of the Aprinnova JV from among the directors and the Company has the right to designate the Chief Financial Officer. The Company determined that it has the power to direct the activities of the Aprinnova JV that most significantly impact its economic performance because of its (i) significant control and ongoing involvement in operational decision making, (ii) guarantee of production costs for certain Aprinnova JV products, as discussed below, and (iii) control over key supply agreements, operational and administrative personnel and other production inputs. The Company has concluded that the Aprinnova JV is a variable-interest entity (VIE) under the provisions of ASC 810, Consolidation, and that the Company has a controlling financial interest and is the VIE's primary beneficiary. As a result, the Company accounts for its investment in the Aprinnova JV on a consolidation basis in accordance with ASC 810.

Under the Aprinnova Operating Agreement, profits from the operations of the Aprinnova JV, if any, are distributed as follows: (i) first, to the Company and Nikko (the Members) in proportion to their respective unreturned capital contribution balances, until each Member’s unreturned capital contribution balance equals zero and (ii) second, to the Members in proportion to their respective interests. In addition, any future capital contributions will be made by the Company and Nikko on an equal (50%/50%) basis each time, unless otherwise mutually agreed. For the year ended December 31, 2019, a $0.3 million distribution was made to Nikko and was recorded as a decrease in noncontrolling interest.

Pursuant to the Aprinnova JV Agreement, the Company and Nikko agreed to make initial working capital loans to the Aprinnova JV in the amounts of $0.5 million and $1.5 million, respectively, and again in 2019 with additional loans of $0.2 million each. Also in 2019, Nikko provided the Aprinnova JV with $1.2 million of short-term loans to purchase certain manufacturing supplies. These loans are described in more detail in Note 4, “Debt”. In addition, the Company agreed to guarantee a maximum production cost for squalane and hemisqualane to be produced by the Aprinnova JV and to bear any cost of production above such guaranteed costs.

In connection with the contribution of the Leland Facility by the Company to the Aprinnova JV, at the closing of the formation of the Aprinnova JV, Nikko made a loan to the Company in the principal amount of $3.9 million, and the Company in consideration therefore issued a promissory note to Nikko in an equal principal amount, as described in more detail in Note 4, “Debt” under “Nikko Note.”

The following presents the carrying amounts of the Aprinnova JV’s assets and liabilities included in the accompanying consolidated balance sheets. Assets presented below are restricted for settlement of the Aprinnova JV's obligations and all liabilities presented below can only be settled using the Aprinnova JV resources.

December 31, (In thousands)	2019		2018
Assets	$	17,390	$	12,904
Liabilities	$	3,690	$	2,364

The Aprinnova JV's assets and liabilities are primarily comprised of inventory, property, plant and equipment, accounts payable and debt, which are classified in the same categories in the Company's consolidated balance sheets.

Office Sublease

The Company subleases certain office space to Novvi, for which the Company charged Novvi $0.6 million and $0.6 million for the years ended December 31, 2019 and 2018, respectively.

See Note 15, “Subsequent Events” for information regarding related party transactions subsequent to December 31, 2019.

XML

Subsequent Events (Details) - USD ($)												1 Months Ended		12 Months Ended
	May 01, 2020	Mar. 15, 2020	Mar. 12, 2020	Mar. 11, 2020	Mar. 01, 2020	Feb. 28, 2020	Feb. 24, 2020	Feb. 18, 2020	Jan. 31, 2020	Jan. 14, 2020	Jan. 13, 2020	Feb. 29, 2020	May 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Mar. 10, 2020	Aug. 28, 2019	May 14, 2019	Apr. 26, 2019	Sep. 28, 2010
Subsequent Event [Line Items]
Proceeds from exercise of warrants, net of issuance costs														$ 1,000	$ 57,767,000
Issuance of common stock upon exercise of warrants (in shares)														2,649,982
Long-term debt														$ 261,772,000	209,697,000
Equity Incentive Plan, 2010
Subsequent Event [Line Items]
Number of shares authorized (in shares)																				2,000,000
Number of additional shares authorized (in shares)													9,000,000.0
Employee Stock Purchase Plan, 2010
Subsequent Event [Line Items]
Number of shares authorized (in shares)													1,666,666
Number of additional shares authorized (in shares)													1,000,000
August Foris Credit Agreement
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)																	4,900,000	400,000	3,900,000
Exercise price of warrants or rights (in dollars per share)																	$ 3.90
August Foris Credit Agreement | Foris Ventures, LLC
Subsequent Event [Line Items]
Maximum borrowing capacity																	$ 19,000,000.0
Senior Convertible Notes Due 2022
Subsequent Event [Line Items]
Aggregate principal amount redeemed														10,000,000
Proceeds from debt, net of issuance costs														30,000,000
Convertible Debt
Subsequent Event [Line Items]
Long-term debt														50,624,000	$ 120,874,000
Convertible Debt | Senior Convertible Notes Due 2022
Subsequent Event [Line Items]
Aggregate principal amount redeemed														$ 10,000,000
Convertible Debt | Senior Convertible Notes Due 2022 | Forecast
Subsequent Event [Line Items]
Amortization payment, aggregate amount	$ 8,900,000
Subsequent Event
Subsequent Event [Line Items]
Percentage ownership in the Company (greater than)											5.00%
Number of warrants or rights issued (in shares)									1,200,000		4,877,386
Exercise price of warrants or rights (in dollars per share)									$ 2.87	$ 2.87
Proceeds from exercise of warrants, net of issuance costs										$ 14,000,000.0
Issuance of common stock upon exercise of warrants (in shares)									25,326,095	4,877,386
Number of shares issued (in shares)				5,226,481
Price per share issued (in dollars per share)				$ 2.87
Proceeds received on issuance of equity				$ 15,000,000.0					$ 28,300,000
Long-term debt									60,000,000.0
Accrued interest									$ 10,000,000.0
Forbearance agreement, forbearance period						60 days
Forbearance agreement, triggering event, minimum conversion or exchange amount						$ 60,000,000
Forbearance agreement, triggering event, minimum conversion or exchange amount, percentage of certain junior outstanding indebtedness						100.00%
Forbearance agreement, late fee percentage						5.00%
Forbearance agreement, forbearance fee						$ 150,000
Forbearance agreement, partial payment of interest						$ 150,000
Forbearance agreement, exercise price of warrants (in dollars per share)						$ 2.87
Waiver agreement, past due interest waived																$ 6,700,000
Waiver agreement, past due partnership payments plus interest waived																500,000
Waiver agreement, monthly payment amended																$ 500,000
Senior notes				10,200,000
Repayments of notes, interest				1,500,000
Repayments of senior notes				1,100,000
Senior notes, principal balance				$ 9,100,000
Accrued interest rate (as a percent)			8.00%	12.00%
Proceeds from debt, net of issuance costs			$ 4,500,000
Loan, principal amount			$ 4,000,000.0
Subsequent Event | Equity Incentive Plan, 2010
Subsequent Event [Line Items]
Number of additional shares authorized (in shares)												5,887,133
Number of additional shares authorized, percentage of total shares outstanding												5.00%
Subsequent Event | Employee Stock Purchase Plan, 2010
Subsequent Event [Line Items]
Number of additional shares authorized (in shares)												588,713
Number of additional shares authorized, percentage of total shares outstanding												0.50%
Subsequent Event | Foris Ventures, LLC
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)									10,200,000
Subsequent Event | Private Placement
Subsequent Event [Line Items]
Number of shares issued (in shares)									13,989,973
Subsequent Event | January 2020 Private Placement to Foris
Subsequent Event [Line Items]
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Number of shares issued (in shares)									5,279,171
Aggregate purchase price received									$ 15,200,000
Subsequent Event | January 2020 Private Placement
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)									8,710,802
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Number of shares issued (in shares)									8,710,802
Class of warrant or right, term									12 months
Aggregate purchase price received									$ 25,000,000
Subsequent Event | January 2020 Rights Issued
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)									18,649,961
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Class of warrant or right, term									12 months
Subsequent Event | Rights Issued in January 2020 Warrant Amendments
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)									1,160,929
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Proceeds from exercise of warrants, net of issuance costs									$ 3,300,000
Issuance of common stock upon exercise of warrants (in shares)									1,160,929
Class of warrant or right, term									12 months
Subsequent Event | January 2020 Warrant Exercises
Subsequent Event [Line Items]
Exercise price of warrants or rights (in dollars per share)									$ 2.84
Proceeds from exercise of warrants, net of issuance costs									$ 54,800,000
Issuance of common stock upon exercise of warrants (in shares)									19,287,780
Subsequent Event | January 2020 Rights Issued to Foris
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)									8,778,230
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Class of warrant or right, term									12 months
Subsequent Event | August Foris Credit Agreement | Foris Ventures, LLC
Subsequent Event [Line Items]
Cancellation of debt									$ 70,000,000
Subsequent Event | Senior Convertible Notes Due 2022
Subsequent Event [Line Items]
Proceeds from debt, net of issuance costs		$ 75,000,000
Subsequent Event | Convertible Debt | Senior Convertible Notes Due 2022
Subsequent Event [Line Items]
Debt instrument, face amount										$ 51,000,000
Shares issued in convertible debt exchange (in shares)										2,742,160
Cash fees										$ 1,000,000.0
Aggregate principal amount redeemed										10,000,000
Aggregate net cash proceeds (at least)								$ 50,000,000		$ 80,000,000
Redemption percentage										107.00%
Required aggregate net cash proceeds										$ 50,000,000
Amortization payment, aggregate amount					$ 10,000,000.0
Amortization stock payment price (in dollars per share)					$ 3.00
Subsequent Event | Convertible Debt | Senior Convertible Notes Due 2022 | Rights Issued in Exchange for Convertible Senior Notes Due 2020
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)										2,484,321
Issuance of common stock upon exercise of rights (in shares)							2,484,321
Subsequent Event | Convertible Debt | Senior Convertible Notes Due 2022 | Warrants Issued in Exchange for Convertible Senior Notes Due 2020
Subsequent Event [Line Items]
Number of warrants or rights issued (in shares)										3,000,000
Exercise price of warrants or rights (in dollars per share)										$ 3.25
Class of warrant or right, term										2 years

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Balance Sheet Details

12 Months Ended

Dec. 31, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Balance Sheet Details

Balance Sheet Details

Allowance for Doubtful Accounts

Allowance for doubtful accounts activity and balances were as follows:

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Year
Allowance for doubtful accounts:
Year Ended December 31, 2019	$	642	$	110	$	(707)	$	45
Year Ended December 31, 2018	$	642	$	—	$	—	$	642

Inventories

December 31, (In thousands)	2019		2018
Raw materials	$	3,255	$	3,901
Work in process	7,204		539
Finished goods	17,311		5,253
Total inventories	$	27,770	$	9,693

Deferred cost of products sold — related party

December 31, (In thousands)	2019		2018
Deferred cost of products sold - related party	$	3,677	$	489
Deferred cost of products sold, noncurrent - related party	12,815		2,828
Total	$	16,492	$	3,317

In November 2018, the Company amended the supply agreement with DSM to secure manufacturing capacity at the Brotas facility for sweetener production through 2022. See Note 9, “Revenue Recognition” for information regarding the November 2018 Supply Agreement Amendment. The supply agreement was included as an element of a combined transaction with DSM, which resulted in a fair value allocation of $24.4 million to the manufacturing capacity fees. See Note 3, “Fair Value Measurement” for information related to this fair value allocation. Of the $24.4 million fair value allocated to the manufacturing capacity fee, $3.3 million was recorded as deferred cost of products sold during 2018. Also, the Company paid an additional $14.1 million in manufacturing capacity fees during 2019, which were recorded as additional deferred cost of products sold. The remaining $7.0 million manufacturing capacity fees will be recorded as deferred cost of products sold in the period the additional payments are made to DSM. The manufacturing capacity deferred cost of products sold asset is expensed to cost of products sold on a units of production basis as the Company's sweetener product is sold over the five-year term of the

supply agreement. During the years ended December 31, 2019 and 2018, the Company expensed $0.9 million and $0, respectively, of the deferred cost of products sold asset.

Prepaid expenses and other current assets

December 31, (In thousands)	2019		2018
Non-inventory production supplies	$	5,376	$	2,391
Prepayments, advances and deposits	4,726		5,644
Recoverable taxes from Brazilian government entities	79		631
Other	2,569		1,900
Total prepaid expenses and other current assets	$	12,750	$	10,566

Property, plant and equipment, net

December 31, (In thousands)	2019		2018
Machinery and equipment	$	48,041	$	43,713
Leasehold improvements	41,478		39,922
Computers and software	9,822		9,987
Furniture and office equipment, vehicles and land	3,510		3,016
Construction in progress	9,752		1,749
Total property, plant and equipment, gross	112,603		98,387
Less: accumulated depreciation and amortization	(83,673)		(78,631)
Total property, plant and equipment, net	$	28,930	$	19,756

Property, plant and equipment, net at December 31, 2018 includes $5.0 million of machinery and equipment under capital lease. Accumulated amortization of assets under capital lease totaled $2.3 million as of December 31, 2018. For the year ended December 31, 2018, amortization expense in connection with capital lease assets was $0.7 million. Beginning January 1, 2019, capital lease assets are classified as right-of-use assets under financing leases, net; see "Leases" below.

Losses on disposal of property, plant and equipment were $0.2 million and $0.9 million for the years ended December 31, 2019 and 2018, respectively. Such losses or gains were included in the lines captioned "Research and development expense" and "Sales, general and administrative expense" in the consolidated statements of operations.

Leases

Prior to the modified prospective adoption of ASU 2016-02 on January 1, 2019, the Company leased certain facilities and certain laboratory equipment under operating and financing leases, respectively. The Company recognized rent expense for operating leases on a straight-line basis over the noncancelable lease term and recorded the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Where leases contained escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applied them as straight-line rent expense over the lease term. The Company had noncancelable operating lease agreements for office, research and development, and manufacturing space that expired at various dates, with the latest expiration in May 2023. Rent expense under operating leases was $5.8 million for the year ended December 31, 2018. See below for the Company’s account treatment of leases upon adoption of new leasing standard.

Operating Leases

The Company has entered into operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 year to 5 years, and often include one or more options to renew. These renewal terms can extend the lease term from 1 to 5 years and are included in the lease term when it is reasonably certain that the Company will exercise the option. The operating leases are classified as Right-of-use assets under operating leases, net (ROU assets) on the Company's December 31, 2019 consolidated balance sheet, and represent the Company’s right to use the underlying asset for the lease term. The Company’s obligation to make operating lease payments is included in

"Operating lease liabilities" and "Operating lease liabilities, net of current portion" on the Company's December 31, 2019 consolidated balance sheet. Based on the present value of the lease payments for the remaining lease term of the Company's existing leases, the Company recognized ROU assets of $29.7 million and operating lease liabilities of $33.6 million on January 1, 2019. Operating lease ROU assets and liabilities commencing after January 1, 2019 are recognized at commencement date based on the present value of lease payments over the lease term. As of December 31, 2019, total ROU assets and operating lease liabilities were $13.2 million and $19.7 million, respectively. All operating lease expense is recognized on a straight-line basis over the lease term. In the year ended December 31, 2019, the Company recorded $16.4 million of operating lease amortization that was charged to expense, of which $7.0 million was recorded to cost of products sold.

Because the rate implicit in each lease is not readily determinable, the Company uses its incremental borrowing rate to determine the present value of the lease payments. The Company has certain contracts for real estate and marketing which may contain lease and non-lease components which it has elected to treat as a single lease component.

Information related to the Company's right-of-use assets and related lease liabilities were as follows:

	Year Ended December 31, 2019
Cash paid for operating lease liabilities, in thousands	$	17,809
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$	33,264
Weighted-average remaining lease term	3.35
Weighted-average discount rate	18.1		%

⁽¹⁾ Includes $29.7 million for operating leases existing on January 1, 2019 and $3.6 million for operating leases that commenced during the year ended December 31, 2019. Also, the Company renegotiated one of its operating leases during 2019, which resulted in a new financing lease. Approximately $7.7 million of Right-of-use assets under operating leases, net were reclassified to Right-of-use assets under financing leases, net related to this operating lease modification.

Financing Leases

The Company has entered into financing leases primarily for laboratory and computer equipment. Assets purchased under financing leases are included in Right-of-use assets under financing leases, net on the consolidated balance sheets. For financing leases, the associated assets are depreciated or amortized over the shorter of the relevant useful life of each asset or the lease term. At December 31, 2019, accumulated amortization of assets under financing lease was $1.7 million.

Maturities of Financing and Operating Leases

Maturities of lease liabilities as of December 31, 2019 were as follows:

Years Ending December 31 (In thousands)	Financing Leases		Operating Leases		Total Lease Obligations
2020	$	4,490	$	7,798	$	12,288
2021	4,565		7,541		12,106
2022	—		7,719		7,719
2023	—		3,363		3,363
2024	—		192		192
Thereafter	—		—		—
Total future minimum payments	9,055		26,613		35,668
Less: amount representing interest	(1,424)		(6,951)		(8,375)
Present value of minimum lease payments	7,631		19,662		27,293
Less: current portion	(3,465)		(4,625)		(8,090)
Long-term portion	$	4,166	$	15,037	$	19,203

Other assets

December 31, (In thousands)	2019		2018
Equity-method investment	$	4,734	$	—
Contingent consideration	3,303		4,286
Deposits	295		2,465
Other	1,373		1,207
Total other assets	$	9,705	$	7,958

In September 2019, the Company was notified by DSM that certain contingent consideration payable to the Company upon the realization of certain NOL tax benefits transferred to DSM with the sale of the Brotas facility in December 2017 would not be realized due to changes in DSM’s Brazilian legal entity structure. The Company considered this information in conjunction with the probability and timing of DSM’s realization of the underlying NOL tax benefits and determined that a portion of the contingent consideration receivable was not recoverable as of December 31, 2018 and recorded a $3.9 million impairment in the statement of operations as Impairment of other assets. The Company reassessed the recoverability of this receivable at December 31, 2019 based on projected utilization of the underlying tax credits by DSM and recorded an additional impairment of $0.2 million for the year ended December 31, 2019.

In October 2019, the Company agreed to purchase the ownership interest previously held by Cosan in Novvi LLC, a joint venture among the Company, Cosan and certain other members, for $10.8 million (Purchase Price). The Company is obligated to pay the Purchase Price through the assignment of certain preferred dividends to be distributed by the proposed joint venture between the Company and Raizen Energia S.A., provided that, if the joint venture is not formed by October 2021, the Purchase Price shall be paid in full by October 31, 2022. The Company measured and recorded the fair value of the investment based on the present value of the unsecured $10.8 million obligation, which was deemed to be more readily determinable than the fair value of the Novvi partnership interest. In accordance with equity-method accounting, the Company records its share of Novvi's earnings or losses for each accounting period and adjusts the investment balance accordingly. However, the Company is not obligated to fund Novvi's potential future losses, so the Company will not record equity-method losses that would result in the investment in Novvi falling to below zero and becoming a liability. For additional information regarding the Company's accounting for equity-method investments, see Note 1, "Basis of Presentation and Summary of Significant Accounting Policies".

Accrued and other current liabilities

December 31, (In thousands)	2019		2018
Accrued interest	$	8,209	$	3,853
Payroll and related expenses	7,296		9,220
Contract termination fees	5,347		4,092
Ginkgo partnership payments obligation	4,319		2,155
Asset retirement obligation(1)	3,184		3,063
Professional services	2,968		1,173
Tax-related liabilities	1,685		2,139
Other	3,647		3,284
Total accrued and other current liabilities	$	36,655	$	28,979

______________

(1) The asset retirement obligation represents liabilities incurred but not yet discharged in connection with our 2013 abandonment of a partially constructed facility in Pradópolis, Brazil.

Other noncurrent liabilities

December 31, (In thousands)	2019		2018
Liability for unrecognized tax benefit	$	7,204	$	6,582
Liability in connection with acquisition of equity-method investment	5,249		—
Ginkgo partnership payments, net of current portion (See Note 4)	4,492		6,185
Refund liability	3,750		—
Contract liabilities, net of current portion(1)	1,449		1,587
Deferred rent, net of current portion	—		6,440
Contract termination fees, net of current portion	—		1,530
Capital leases, net of current portion	—		195
Other	880		673
Total other noncurrent liabilities	$	23,024	$	23,192

______________

(1) Contract liabilities, net of current portion at December 31, 2019 and 2018 includes $1,204 at each date in connection with DSM, which is a related party.

In relation to the refund liability item above, in April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in variable consideration of $12.5 million in the form of a stand-ready obligation to refund some or all of the $12.5 million consideration if certain criteria are not met by December 2021. The Company periodically updates its estimate of amounts to be retained and reduces the refund liability and records additional license and royalty revenue as the criteria are met. The Company recorded an additional $8.8 million of license and royalty revenue during the year ended December 31, 2019 related to a change in the estimated refund liability, which reduced the balance to $3.8 million.

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Stockholders' Deficit

12 Months Ended

Dec. 31, 2019

Stockholders' Equity Note [Abstract]

Stockholders' Deficit

Stockholders’ Deficit

Shares Issuable under Convertible Notes and Convertible Preferred Stock

In connection with various debt transactions (see Note 4, "Debt"), the Company issued certain convertible notes and preferred shares that are convertible into shares of common stock as follows as of December 31, 2019, at any time at the election of each debtholder:

	Number of Shares Instrument Is Convertible into as of December 31, 2019
Senior convertible notes due 2022	13,200,000
2014 Rule 144A convertible notes	181,238
Series D preferred stock (8,280 shares outstanding at December 31, 2019)	1,943,661
	15,324,899

2014 Rule 144A Convertible Notes Exchanges

On May 10, 2019, the Company exchanged $13.5 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by certain non-affiliated investors, including accrued and unpaid interest thereon, for an aggregate of 3.5 million shares of common stock and warrants to purchase an aggregate of 1.4 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, in a private exchange.

On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Foris, including accrued and unpaid interest thereon, for 1.1 million shares of common stock and a warrant to purchase up to 0.4 million shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from issuance, in a private exchange. On August 28, 2019, the Company and Foris agreed to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share. See “August 2019 Foris Warrant Issuance” below for additional information and Note 15, “Subsequent Events” for information regarding the amendment and exercise of the warrants on January 31, 2020.

On May 15, 2019, the Company exchanged $10.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Maxwell (Mauritius) Pte Ltd for 2.5 million shares of common stock in a private exchange.

The Company issued 7.1 million shares of common stock with a fair value totaling $30.8 million based on the Company's closing stock price at the date of each exchange upon exchange of the 2014 Rule 144A Convertible Notes described above. The Company also issued warrants (collectively, the May 2019 6.50% Note Exchange warrant) to purchase a total of 1.7 million

shares of common stock with a fair value of $3.8 million. The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the convertible notes and will be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrants were measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $4.27 - $4.54, strike price $4.56 - $5.02, volatility 96%, risk-free interest rate 2.20% - 2.26%, and expected dividend yield 0%. The warrant had a fair value of $5.9 million that was recorded as a loss of debt extinguishment. See Note 4, "Debt" for information about the accounting treatment for this debt exchange and related fair value of the warrant.

The exercise price of the warrants issued in the foregoing exchanges is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of the exercisability of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, (i) the exercisability of the warrant issued to Foris is subject to stockholder approval in accordance with Nasdaq rules and regulations, which the Company is seeking at its 2019 annual meeting of stockholders, and (ii) each other warrant provides that the Company may not affect any exercise of such warrant to the extent that, after giving effect to such exercise, the applicable holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding after giving effect to such exercise.

August 2013 Financing Convertible Note Conversion into Equity

On July 8, 2019, Wolverine exchanged $5.1 million principal and accrued and unpaid interest related to its August 2013 Financing Convertible Note for 1.8 million shares of common stock and a warrant (the July 2019 Wolverine Warrant) to purchase 1.1 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The common stock had a fair value of $5.9 million or $3.30 per share and the warrant had a fair value of $1.9 million. The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the convertible note and will be classified in equity, as the warrant is both indexed to the Company’s own stock and meets the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrant to be reclassified to an asset or liability. The fair value of the warrant was measured using the Black-Scholes-Merton option pricing model, with the following parameters: stock price $3.33, strike price $2.87, volatility 94%, risk-free interest rate 1.88%, and expected dividend yield 0%. The resulting $1.9 million fair value was recorded as a loss of debt extinguishment. See Note 4, “Debt” for additional information regarding the loss on debt extinguishment.

Pre-Delivery Shares Issued with Senior Convertible Notes Due 2022

In connection with the issuance of the Senior Convertible Notes Due 2022 on November 15, 2019, the Company issued 7.5 million shares of common stock (the Pre-Delivery Shares) to the note holders which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the note holders to sell, trade or hold, subject to certain limitations, for as long as the Senior Convertible Notes Due 2022 are outstanding. The issuance of these shares resulted in no cash proceeds to the Company. However, the Company may elect or be required to apply some or all of the value of the pre-delivered shares to satisfy periodic principal and interest payments or other repayment events. If the Pre-Delivery Shares are used in satisfaction of a payment(s) due under the Senior Convertible Notes Due 2022, the Company must provide additional shares of common stock to the note holders in order to maintain a 7.5 million share balance on deposit with the holder. The Holder will not (A) loan any Pre-Delivery shares to any third party, (B) prior to February 1, 2020 sell or otherwise transfer or dispose of any Pre-Delivery Shares to any unaffiliated third party and (C) on or after February 1, 2020 sell or otherwise transfer or dispose of any Pre-Delivery Shares to any unaffiliated third party if the amount of such sales, transfers or dispositions on any day would exceed 10% of the composite trading volume (as reported on Bloomberg) of the Common Stock on such day. Within ten business days following redemption or repayment of in full the Senior Convertible Notes Due 2022 and the satisfaction or discharge by the Company of all outstanding Company obligations hereunder, the Holder shall deliver 7.5 million shares of the Company’s common stock to the Company.

The Company concluded the Pre-Delivery Shares provision is a freestanding instrument that is legally detachable and separately exercisable from the Senior Convertible Notes Due 2022 and will be classified in equity as the common shares issued is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the Pre-Delivery Shares within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the shares to be reclassified to an asset or liability. The Company measured the issue date fair value of the Pre-Delivery Shares under an expected borrowing cost approach using a 9.75% annual

borrowing rate over an 18-month estimated repayment term for the Senior Convertible Notes Due 2022. The resulting $4.2 million fair value was recorded in equity as additional paid in capital with an offset to the fair value of the Senior Convertible Notes Due 2022. See Note 3, “Fair Value Measurements” for further information regarding the fair value measurement and accounting for this freestanding instrument.

Series B Preferred Stock Beneficial Ownership Limitation

On October 24, 2019, the Company filed a certificate of amendment (the Certificate of Amendment) to the Certificate of Designation (the Certificate of Designation) relating to the Company’s Series B 17.38% Convertible Preferred Stock, par value $0.0001 per share (the Series B Preferred Stock), with the Secretary of State of Delaware. The Company had originally filed the Certificate of Designation on May 8, 2017, pursuant to which the conversion of the Series B Preferred Stock was subject to a beneficial ownership limitation of 4.99%, or such other percentage as determined by the holder, not to exceed 9.99% of the number of shares of the Company’s common stock outstanding after giving effect to such conversion (the Beneficial Ownership Limitation). In addition, pursuant to the Certificate of Designation, each share of Series B Preferred Stock automatically converted on October 9, 2017, subject to the Beneficial Ownership Limitation.

Pursuant to the Certificate of Amendment, the Beneficial Ownership Limitation was eliminated, permitting the conversion of any outstanding shares of Series B Preferred Stock, the conversion of which was previously prevented by the Beneficial Ownership Limitation. As such, on October 24, 2019, the remaining 6,376.28 shares of Series B Preferred Stock, which were all held by Foris, automatically converted into 1.0 million shares of the Company’s common stock.

April 2019 Private Placements

On April 16, 2019, the Company sold and issued to Foris 6.7 million shares of common stock at a price of $2.87 per share, for aggregate proceeds to the Company of $20.0 million (the Foris Investment), as well as a warrant (the April 2019 Foris Warrant) to purchase up to 5.4 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance, in a private placement, for aggregate cash proceeds to the Company of $20.0 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

On April 26, 2019, the Company sold and issued (i) 2.8 million shares of common stock at a price of $5.12 per share, as well as a warrant (the April 2019 PIPE Warrants) to purchase up to 4.0 million shares of common stock at an exercise price of $5.12 per share, with an exercise term of two years from issuance, to Foris and (ii) an aggregate of 2.0 million shares of common stock at a price of $4.02 per share, as well as warrants (the April 2019 PIPE Warrants) to purchase up to an aggregate of 1.6 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to certain other non-affiliated investors, in each case in private, for aggregate cash proceeds to the Company of $15.0 million from Foris and $8.2 million from non-affiliated investors, for a total of $23.2 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

On April 29, 2019, the Company sold and issued (i) 0.9 million shares of common stock at a price of $4.76 per share, as well as warrants (the April 2019 PIPE Warrants) to purchase up to an aggregate of 1.2 million shares of common stock at an exercise price of $4.76 per share, with an exercise term of two years from issuance, to affiliates of Vivo Capital LLC (Vivo), an entity affiliated with director Frank Kung and which owns greater than five percent of our outstanding common stock and has the right to designate one member of the Company’s Board of Directors) and (ii) an aggregate of 0.3 million shares of common stock at a price of $4.02 per share, as well as warrants (the April 2019 PIPE Warrants) to purchase up to an aggregate of 0.3 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to certain other non-affiliated investors, in each case in private placements, for aggregate cash proceeds to the Company of $4.5 million from Vivo and $1.3 million from non-affiliated investors, for a total of $5.8 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

On May 3, 2019, the Company sold and issued 1.2 million shares of common stock at a price of $4.02 per share, as well as a warrant (the April 2019 PIPE Warrants) to purchase up to 1.0 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to a non-affiliated investor in a private placement, for aggregate cash proceeds to the Company of $5.0 million. The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity.

The exercise price of the warrants issued in the foregoing private placements is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month

anniversary of issuance of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, in connection with the foregoing private placements, the Company agreed not to effect any exercise or conversion of any Company security, and the investors agreed not to exercise or convert any portion of any Company security, to the extent that after giving effect to such exercise or conversion, the applicable investor, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding immediately after giving effect to such exercise or conversion, and the warrant contained a similar limitation. The Company obtained stockholder approval for Foris to exceed such limitation in accordance with Nasdaq rules and regulations at its annual meeting of stockholders on November 19, 2019.

See Note 15, “Subsequent Events” for information regarding the amendment and exercise of certain April 2019 PIPE Warrants on January 31, 2020.

November 2018 DSM Securities Purchase Agreement – Related Party

On November 20, 2018, the Company issued 1,643,991 shares of common stock (the DSM Shares) at $3.68 per share to DSM in a private placement pursuant to a securities purchase agreement, dated November 19, 2018, between the Company and DSM (the DSM SPA), in consideration of certain agreements of DSM set forth in the Supply Agreement Amendment described in Note 9, "Revenue Recognition". The Company also agreed to pay DSM the difference between the DSM SPA purchase price of $4.41 and the closing share price of the Company's common stock on March 28, 2019, multiplied by 1,643,991 million. At inception, the Company recorded a $1.2 million derivative liability for the difference between $4.41 and the Company’s closing stock price on November 20, 2018. At December 31, 2018 fair value based on the Company’s closing stock price was $1.8 million, resulting in a $0.6 million loss from change in fair value of derivative instruments for the year ended December 31, 2018. At March 28, 2019, the Company's stock price was $2.10, and the Company owed DSM $3.8 million in connection with this agreement. Pursuant to the DSM SPA, the Company agreed to file a registration statement providing for the resale by DSM of the DSM Shares and to use commercially reasonable efforts to (i) cause such registration statement to become effective within 181 days following the date of the DSM SPA and (ii) keep such registration statement effective until DSM does not own any DSM Shares or the DSM Shares are eligible for resale under Rule 144 without regard to volume limitations. See Note 10, "Related Party Transactions" for additional information about the accounting for this transaction and other November 2018 transactions with DSM. In April 2019, in connection with the assignment by the Company of its rights under the Value Sharing Agreement (see Note 9, "Revenue Recognition"), the Company satisfied its obligation under the Supply Agreement Amendment relating to the difference between $4.41 and the price of the Company’s common stock on March 28, 2019.

Warrants

The Company issues warrants in certain debt and equity transactions in order to facilitate raising equity capital or reduce borrowing costs. In connection with various debt and equity transactions (see Note 4, "Debt" and below), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrant activity for the year ended December 31, 2019:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2018	Additional Warrants Issued	Exercises	Expiration	Exercise Price per Share of Warrants Exercised		Number Outstanding as of December 31, 2019	Exercise Price per Share as of December 31, 2019
Foris LSA warrants	2019	August 14, 2021	—	3,438,829	—	—	$	—	3,438,829	$2.87
November 2019 Foris warrant	2019	November 27, 2021	—	1,000,000	—	—	$	—	1,000,000	$3.87
August 2019 Foris warrant	2019	August 28, 2021	—	4,871,795	—	—	$	—	4,871,795	$3.90
April 2019 PIPE warrants	2019	April 6, 2021, April 29, 2021 and May 3, 2021	—	8,084,770	—	—	$	—	8,084,770	$3.90/$4.76/$5.02
April 2019 Foris warrant	2019	April 16, 2021	—	5,424,804	—	—	$	—	5,424,804	$2.87
September and November 2019 Investor Credit Agreement warrants	2019	September 10, 2021 and November 14, 2021	—	5,233,551	—	—	$	—	5,233,551	$3.87/$3.90
Naxyris LSA warrants	2019	October 28, 2021	—	2,000,000	—	—	$	—	2,000,000	$2.87
October 2019 Naxyris warrant	2019	October 28, 2021	—	2,000,000	—	—	$	—	2,000,000	$3.87
May-June 2019 6% Note Exchange warrants	2019	May 15, 2021 and June 24, 2021	—	2,181,818	—	—	$	—	2,181,818	$2.87/$5.12
May 2019 6.50% Note Exchange warrants	2019	May 10, 2021 and May 14, 2021	—	1,744,241	—	—	$	—	1,744,241	$3.90/$5.02
July 2019 Wolverine warrant	2019	July 8, 2021	—	1,080,000	—	—	$	—	1,080,000	$2.87
August 2018 warrant exercise agreements	2018	May 17, 2020 and May 20, 2020	12,097,164	—	—	—	$	—	12,097,164	$2.87/$7.52
April 2018 warrant exercise agreements	2018	July 12, 2019	3,616,174	—	—	(3,616,174)	$	—	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,244,820	—	(166,664)	—	$	2.87000	6,078,156	$2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	0.00015	3,968,116	$2.87
May 2017 dilution warrants	2017	July 10, 2022	47,978	4,795,924	(1,758,009)	—	$	0.00015	3,085,893	$0.0015
August 2017 dilution warrants	2017	May 23, 2023	—	3,028,983	—	—	$	—	3,028,983	$0.0001
February 2016 related party private placement	2016	February 12, 2021	171,429	—	—	—	$	—	171,429	$0.15
July 2015 related party debt exchange	2015	July 29, 2020 and July 29, 2025	133,334	—	—	—	$	—	133,334	$0.15
July 2015 private placement	2015	July 29, 2020	81,197	—	(8,547)	—	$	0.15000	72,650	$0.15
July 2015 related party debt exchange	2015	July 29, 2020	58,690	—	—	—	$	—	58,690	$0.15
July 2015 related party debt exchange	2015	July 29, 2020	471,204	245,558	(716,762)	—	$	0.15000	—	$	—
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$160.05
			26,891,512	45,130,273	(2,649,982)	(3,616,174)	$	0.22166	65,755,629

For information regarding warrants issued or exercised subsequent to December 31, 2019, see Note 15, “Subsequent Events”.

Due to certain down-round adjustments to other equity-related instruments during the year ended December 31, 2019, approximately 8.1 million shares became available under the May 2017 and August 2017 dilution warrants and the Temasek Funding Warrant (July 2015 related party debt exchange warrant in the table above). Approximately 2.6 million shares were exercised under the May 2017 cash and dilution warrants and the Temasek Funding Warrant during the year ended December 31, 2019 and resulted in zero proceeds to the Company. Also, a portion of the warrant exercises occurring during 2019 was net share settled, and as a result only 2.5 million shares were legally issued upon exercise of warrants during the year ended December 31, 2019.

Warrant Issuances, Exercises and Modifications in the Year Ended December 31, 2019

July 2019 Foris Credit Agreement Warrant Modification

In connection with the entry into the July Foris Credit Agreement on July 10, 2019 (see Note 4, “Debt”), the Company and Foris amended a warrant to purchase up to 4.9 million shares of common stock issued to Foris on August 17, 2018 to reduce the exercise price of such warrant from $7.52 per share to $2.87 per share. The warrant modification was measured on a before and after modification basis using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.21, strike price $2.87, volatility 124%, risk-free interest rate 1.82%, term 0.9 years, and expected dividend yield 0%. The warrant had an incremental fair value of $4.0 million, which was accounted for as an increase to additional paid in capital and a debt discount to the $16 million July Foris Notes. See Note 4, “Debt” for additional information regarding the debt discount recorded in connection with the modification of the warrant.

6% Convertible Note Exchange Warrants and Modification

In connection with the May 15, 2019 and June 24, 2019 6% Convertible Note Exchanges (see Note 4, “Debt”), the Company issued warrants (the May-June 2019 6% Note Exchange Warrants) to purchase up to 2.0 million and 0.2 million shares of common stock, respectively, at an exercise price of $5.12 per share, with an exercise term of two years from issuance.

The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. The holders may not exercise the warrants, and the Company may not affect any exercise of the warrants, to the extent that, after giving effect to such exercise, the applicable holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding after giving effect to such exercise.

The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the convertible notes and should be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The fair value of the warrants totaled $4.4 million and were measured using the Black-Scholes-Merton option pricing model with the following parameters: 94% - 96% volatility, 1.72% - 2.16% risk-free interest rate, $3.55 - $4.39 issuance-date stock price, term 2.0 years, and 0% expected dividend yield. The Company concluded that the $4.4 million fair value of the equity-classified May 15, 2019 and June 24, 2019 warrants should be recorded as an increase to additional paid in capital and a charge to interest expense in the statement of operations at the date of issuance. See Note 4, “Debt” for additional information regarding the accounting for the fair value of these warrants.

Further, on July 24, 2019, Company exchanged the May 15, 2019 warrant to purchase up to 2.0 million shares of common stock, for a new warrant to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from May 15, 2019. The exchange warrant has substantially identical terms as the original warrant issued on May 15, 2019, except that the exercise price was reduced from $5.12 to $2.87 per share. The warrant modification was measured on a before and after modification basis using the Black-Scholes-Merton option pricing model with the following parameters: strike price $2.87, volatility 93%, risk-free interest rate 1.86%, term 1.8 years, and expected dividend yield 0%; and resulted in $0.9 million of incremental fair value. The Company concluded that the increase in the fair value of the exchange warrant should be recorded as an increase to additional paid in capital and a charge to interest expense in the statement of operations at the date of modification. See Note 4, “Debt” for additional information regarding the charge to interest expense in connection with the fair value of this warrant.

Foris LSA Warrant Issuances

In connection with the entry into the LSA Amendment and Waiver (see Note 4, “Debt”), on August 14, 2019 the Company issued to Foris a warrant (the Foris LSA Warrant) to purchase up to 1.4 million shares of Common Stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. Pursuant to the terms of the warrant, Foris may not exercise the LSA Warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company obtained at its 2019 annual meeting of stockholders on November 19, 2019.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the LSA Amendment and Waiver and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.59, strike price $2.87, volatility 94%, risk-free interest rate 1.58%, term 2.0 years, and expected dividend yield 0%. The warrant had a fair value of $2.9 million which was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the fair value of this warrant.

In connection with October 2019 LSA Amendment (see Note 4, “Debt”), on October 10, 2019, the Company issued a warrant (the October 2019 Foris LSA Warrant) to purchase 2.0 million shares of common stock, at an exercise price of $2.87 per share, with an exercise term of two years from issuance. Also, in connection with additional borrowings under the October 28, 2019 A&R LSA, on November 27, 2019, the Company issued a warrant (the November 2019 Foris Warrant) to purchase 1.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance. The exercise price of the warrants are subject to standard adjustments but do not contain any anti-dilution protection, and the

warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrants. In addition, Foris may not exercise the warrants to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company obtained at its 2019 annual meeting of stockholders on November 19, 2019.

The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the October 2019 LSA Amendment and A&R LSA and will be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrants were measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.65 and $4.00, strike price $2.87 and $3.87, volatility 94%, risk-free interest rate 1.63% and expected dividend yield 0%. The October 2019 Foris LSA Warrant had a fair value of $4.1 million and was recorded as an increase to additional paid in capital and as a loss on debt extinguishment as a non-cash fee paid to the lender. The November 2019 Foris Warrant had a fair value of $2.1 million and was recorded as an increase to additional paid in capital and additional debt discount to be amortized over the remaining term of the A&R LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the fair value of each warrant. See Note 15, “Subsequent Events” for information regarding the amendment and exercise of the October 2019 Foris LSA Warrant on January 31, 2020.

Naxyris LSA Warrant Issuances

In connection with the entry into the Naxyris Loan Agreement (see Note 4, “Debt”), on August 14, 2019 the Company issued to Naxyris a warrant (the Naxyris LSA Warrant) to purchase up to 2.0 million shares of the Company’s common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments and permits “cashless” or “net” exercise any time after issuance.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Naxyris Loan Facility and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.59, strike price $2.87, volatility 94%, risk-free interest rate 1.58%, term 2.0 years, and expected dividend yield 0%. The warrant had a $4.0 million fair value and a $3.0 million relative fair value after allocating the Naxyris Loan Facility proceeds to the fair value of an embedded mandatory redemption feature contained in the Naxyris Loan Facility. The $3.0 million relative fair value of the Naxyris LSA Warrant was recorded as an increase to additional paid in capital and a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the relative fair value of this warrant.

Also, in connection with the entry into the A&R Naxyris LSA, on October 28, 2019 the Company issued to Naxyris a warrant (the October 2019 Naxyris Warrant) to purchase up to 2.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments and permits “cashless” or “net” exercise any time after issuance.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Naxyris Loan Facility and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.69, strike price $3.87, volatility 94%, risk-free interest rate 1.64%, term 2.0 years, and expected dividend yield 0%. The warrant had a $3.6 million fair value and a $2.8 million relative fair value after allocating the October 2019 Naxyris Loan proceeds to the fair value of the embedded mandatory redemption feature contained in the October 2019 Naxyris Loan. The $2.8 million relative fair value of the October 2019 Naxyris Warrant was recorded as an increase to additional paid in capital and as a loss on debt extinguishment as a non-cash fee paid to the lender. See Note 4, “Debt” for further information regarding the accounting treatment for the relative fair value of this warrant.

August 2019 Foris Warrant Issuance

In connection with the entry into the August 2019 Foris Credit Agreement (see Note 4, “Debt”), on August 28, 2019 the Company issued to Foris a warrant (the August 2019 Foris Warrant) to purchase up to 4.9 million shares of Common Stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permits “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. In addition, Foris may not exercise the warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company obtained at its 2019 annual meeting of stockholders on November 19, 2019.

The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Foris $19 Million Note and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.67, strike price $3.90, volatility 94%, risk-free interest rate 1.50%, term 2.0 years, and expected dividend yield 0%. The warrant had a $8.7 million fair value and a $5.2 million relative fair value after allocating the Foris $19 Million Note proceeds to the fair value of an embedded mandatory redemption feature contained in the Foris $19 Million Note. See Note 4, “Debt” for further information regarding the accounting treatment for the relative fair value of this warrant.

Also, on August 28, 2019 in connection with the entry into the August 2019 Foris Credit Agreement, the Company and Foris amended the warrant to purchase up to 3.9 million shares of common stock issued to Foris on April 26, 2019 to reduce the exercise price of such warrant from $5.12 per share to $3.90 per share, and amended the warrant to purchase up to 0.4 million shares of common stock issued to Foris on May 14, 2019 to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share (see above under “Private Placements” for more information regarding these warrants). The warrant modifications were measured on a before and after modification basis using the Black-Scholes-Merton option pricing model with the following parameters: stock price $3.67, strike price $3.90, volatility 98% - 100%, risk-free interest rate 1.50%, term 1.7 years, and expected dividend yield 0%, resulting in $1.1 million of incremental fair value, which was accounted for as an increase to additional paid in capital and a debt discount to the Foris $19 Million Note. See Note 4, “Debt” for additional information regarding the debt discount recorded in connection with the modification of these warrants. See Note 15, “Subsequent Events” for information regarding the amendment and exercise of the August 2019 Foris Warrant on January 31, 2020.

September and November 2019 Investor Credit Agreements Warrants Issuances

In connection with the entry into the Investor Credit Agreements (see Note 4, “Debt”), on September 10, 2019, the Company issued to the Investors warrants (the Investor Warrants) to purchase up to an aggregate of 3.2 million shares of common stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. The exercise price of the warrants is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, no Investor may exercise its warrant to the extent that, after giving effect to such exercise, such Investor, together with its affiliates, would beneficially own in excess of 9.99% of the number of shares of common stock outstanding after giving effect to such exercise. In addition, the Company agreed to file a registration statement providing for the resale by the Investors of the shares of common stock underlying the warrants with the SEC within 60 days following the date of the issuance of the warrants and to use commercially reasonable efforts to (i) cause such registration statement to become effective within 120 days following the date of the issuance of the warrants and (ii) keep such registration statement effective until the Investors no longer beneficially own any such shares of common stock or such shares of common stock are eligible for resale under Rule 144 under the Securities Act without regard to volume limitations. If the Company fails to file the registration statement by the filing deadline or the registration statement is not declared effective by the effectiveness deadline, or the Company fails to maintain the effectiveness of the registration statement as required by the warrants, then the exercise price of the warrants will be reduced by 10%, and by an additional 5% if such failure continues for longer than 90 days, subject to an exercise price floor of $3.31 per share, provided that upon the cure by the Company of such failure, the exercise price of the warrants will revert to $3.90 per share.

In connection with the November 2019 Schottenfeld CSA, on November 14, 2019, the Company warrants (the November 2019 Schottenfeld CSA Warrants) to purchase an aggregate of 2.0 million shares of common stock at an exercise price of $3.87 per share, with an exercise term of 2 years from issuance. In connection with the warrant issuance, the Company will be

required to pay the November 2019 Schottenfeld CSA Warrants holders and the Investor Warrants holders a fee if the Company issues equity securities in connection with the $50 million or greater financing provision that have an issue, conversion or exercise price of less than $3.90 or $3.87 per share, respectively. In such case, the fee will be the difference between the exercise price of such warrants (i.e., $3.90 or $3.87) and the issue, conversion or exercise price of the equity securities issued in the $50 million or greater financing, times the total number of warrants issued to such investors in November 2019 and September 2019. See Note 15, “Subsequent Events” for information regarding the amendment of the Investor Warrants and the November 2019 Schottenfeld CSA Warrants on February 28, 2020.

The Company concluded the Investor Warrants and the November 2019 Schottenfeld CSA Warrants are freestanding instruments that are legally detachable and separately exercisable from the underlying debt host instruments and should be classified and accounted for as a liability as the warrants contain certain price and share count adjustment protection, and other modification protection provisions that cause the warrants to fail the fixed-for-fixed criterion, and thus, are not considered indexed to the Company’s stock. Accordingly, the Company has accounted for the Investor Warrants and November 2019 Schottenfeld CSA Warrants as a liability and will subsequently remeasure to fair value at each reporting period with changes in fair value recorded in the statement of operations. The warrants were measured using the Black-Scholes-Merton option pricing model with the following parameters as of the September 10, 2019 and November 14, 2019 issuance dates: stock price $4.56 and $3.89, strike price $3.90 and $3.87, volatility 94% and 95%, risk-free interest rate 1.67% and 1.58%, term 2 years, and expected dividend yield 0%. The warrants had an initial fair value of $7.9 million and $4.0 million, respectively and were recorded as derivative liabilities with an offset to either debt discount or loss on debt extinguishment (as a non-cash fee paid to the lender). See Note 3, “Fair Value Measurements” for information regarding the subsequent fair value measurement for this liability classified warrant and see Note 4, “Debt” for further information regarding the initial accounting treatment of the offsetting debt discount or loss on debt extinguishment.

Standstill Agreement

In connection with the September 10, 2019 entry into the Investor Credit Agreements discussed in Note 4, “Debt” and the issuance of the Investor Warrants discussed in the "September and November 2019 Investor Credit Agreements Warrants Issuances " section above, the Company and the Investors entered into a Standstill Agreement (the Investor Standstill Agreement), pursuant to which the Investors agreed that, until the earliest to occur of (i) the Investors no longer beneficially owning any shares underlying the warrants, (ii) the Company entering into a definitive agreement involving the direct or indirect acquisition of all or a majority of the Company’s equity securities or all or substantially all of the Company’s assets or (iii) a person or group, with the prior approval of the Company’s Board of Directors (the Board), commencing a tender offer for all or a majority of the Company's equity securities, neither the Investors nor any of their respective affiliates (together, the Investor Group) will (without the prior written consent of the Board), among other things, (a) acquire any loans, debt securities, equity securities, or assets of the Company or any of its subsidiaries, or rights or options with respect thereto, except that the Investor Group shall be permitted to (y) purchase the shares underlying the warrants pursuant to the exercise of the warrants and (z) acquire beneficial ownership of up to 6.99% of the Company's common stock, or (b) make any proposal, public announcement, solicitation or offer with respect to, or otherwise solicit, seek or offer to effect, or instigate, encourage, or assist any third party with respect to: (1) any business combination, merger, tender offer, exchange offer, or similar transaction involving the Company or any of its subsidiaries; (2) any restructuring, recapitalization, liquidation, or similar transaction involving the Company or any of its subsidiaries; (3) any acquisition of any of the Company’s loans, debt securities, equity securities or assets, or rights or options with respect thereto; or (4) any proposal to seek representation on the Board or otherwise seek to control or influence the management, Board, or policies of the Company, in each case subject to certain exceptions.

May 2017 Warrants

In May 2017, the Company issued 14,768,380 shares of common stock in the aggregate to certain investors (collectively, the May 2017 Cash Warrants). The exercise price of the May 2017 Cash Warrants is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following the issuance of such warrants at a per share price less than the then-current exercise price of the May 2017 Cash Warrants, subject to certain exceptions. As of December 31, 2019, the exercise prices of the May 2017 Cash Warrants were $2.87 per share, and 6,078,156 of May 2017 Cash Warrants were unexercised.

In addition to the May 2017 Cash Warrants, the Company issued to each investor a warrant, with an exercise price of $0.0015 per share (collectively, the May 2017 Dilution Warrants), to purchase a number of shares of common stock sufficient to provide the investor with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the May 2017 Dilution Period at a per share price less than $2.87. As of December 31, 2019, the May 2017 Dilution Warrants were exercisable for an aggregate of 3,085,893 shares.

The May 2017 Warrants each have a term of five years from the date such warrants initially became exercisable on July 10, 2017. The May 2017 Cash Warrants are freestanding financial instruments and upon adoption of ASU 2017-11 on January 1, 2019 are no longer accounted for as derivative liabilities, but are classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company reclassified the derivative balance at December 31, 2018 to equity at the January 1, 2019 adoption date.

August 2017 DSM Offering – Related Party

On August 7, 2017, the Company issued and sold the following securities to DSM in a private placement (August 2017 DSM Offering):

•25,000 shares of Series B Preferred Stock (August 2017 DSM Series B Preferred Stock) at a price of $1,000 per share;

•a warrant to purchase 3,968,116 shares of common stock at an initial exercise price of $6.30 per share expiring in five years (August 2017 DSM Cash Warrant); and

•the August 2017 DSM Dilution Warrant (as described below).

Net proceeds to the Company were $25.9 million after payment of offering expenses and the allocation of total fair value received to the elements in the arrangement.

The exercise price of the August 2017 DSM Cash Warrant is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following August 7, 2017 (DSM Dilution Period) at a per share price less than the then-current exercise price of the August 2017 DSM Cash Warrant, subject to certain exceptions. As of December 31, 2019, the exercise price of the August 2017 DSM Cash Warrant was $2.87 per share, and 3,968,116 of May 2017 Cash Warrants were unexercised. The August 2017 DSM Dilution Warrants are freestanding financial instruments and upon adoption of ASU 2017-11 on January 1, 2019 are no longer accounted for as derivative liabilities, but are classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company reclassified the derivative balance at December 31, 2018 to equity at the January 1, 2019 adoption date.

The August 2017 DSM Dilution Warrant allows DSM to purchase a number of shares of common stock sufficient to provide DSM with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the DSM Dilution Period at a per share price less than $2.87. The August 2017 DSM Dilution Warrant expires five years from the date it is initially exercisable.

In connection with the August 2017 DSM Offering, the Company and DSM also entered into an amendment to the stockholder agreement dated May 11, 2017 (DSM Stockholder Agreement) between the Company and DSM (Amended and Restated DSM Stockholder Agreement). Under the DSM Stockholder Agreement, DSM was granted the right to designate one director selected by DSM, subject to certain restrictions and a minimum beneficial ownership level of 4.5%, to the Board. Furthermore, DSM has the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. Pursuant to the DSM Stockholder Agreement, DSM agreed not to sell or transfer any of the Series B Preferred Stock or warrants purchased by DSM, or any shares of common stock issuable upon conversion or exercise thereof, other than to its affiliates, without the consent of the Company through May 2018 and to any competitor of the Company thereafter. DSM also agreed that, subject to certain exceptions, until three months after there is no DSM director on the Board, DSM will not, without the prior consent of the Board, acquire common stock or rights to acquire common stock that would result in DSM beneficially owning more than 33% of the Company’s outstanding voting securities at the time of acquisition. The Amended and Restated DSM Stockholder Agreement provides that (i) DSM has the right to designate a second director to the Board, subject to certain restrictions and a minimum beneficial ownership level of 10%, and (ii) the shares of common stock issuable upon conversion or exercise of the securities purchased by DSM in the August 2017 DSM Offering are (a) entitled to the registration rights provided for in the DSM Stockholder Agreement and (b) subject to the transfer restrictions set forth in the DSM Stockholder Agreement.

August 2017 Vivo Offering – Related Party

On August 3, 2017, the Company issued and sold 12,958 shares of Series D Preferred Stock at a price of $1,000 per share along with other securities to Vivo in a private placement (August 2017 Vivo Offering), resulting in net proceeds to the Company of $24.8 million after payment of offering expenses. In the third quarter of 2018 Vivo converted 4,678 shares of August 2017 Offerings Series D Preferred Stock and the Company recognized a $6.8 million deemed dividend for the

unamortized discounts created from the allocation of proceeds, as a reduction to Additional Paid in Capital and increasing net loss attributable to Amyris, Inc. common stockholders. At December 31, 2019 and 2018, 8,280 shares of Series D Preferred Stock were outstanding. The conversion of the Series D Preferred Stock is subject to a beneficial ownership limitation of 9.99% (August 2017 Vivo Offering Beneficial Ownership Limitation), which limitation may be waived by the holders on 61 days’ prior notice.

Each share of Series D Preferred Stock has a stated value of $1,000 and, subject to the August 2017 Vivo Offering Beneficial Ownership Limitation, is convertible at any time, at the option of the holders, into common stock at a conversion price of $4.26 per share. The Series D Conversion Rate is subject to adjustment in the event of any dividends or distributions of the common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

Prior to declaring any dividend or other distribution of its assets to holders of common stock, the Company shall first declare a dividend per share on the Series D Preferred Stock equal to $0.0001 per share. In addition, the Series D Preferred Stock will be entitled to participate with the common stock on an as-converted basis with respect to any dividends or other distributions to holders of common stock. There were no dividends declared as of December 31, 2019 or 2018.

Unless and until converted into common stock in accordance with its terms, the Series D Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Series D Preferred Stock. The Series D Preferred Stock is classified as permanent equity, as the Company controls all actions or events required to settle the optional conversion feature in shares.

In the event of a Fundamental Transaction, the holders of the Series D Preferred Stock will have the right to receive the consideration receivable as a result of such Fundamental Transaction by a holder of the number of shares of common stock for which the Series D Preferred Stock is convertible immediately prior to such Fundamental Transaction (without regard to whether such Series D Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock. A Fundamental Transaction is defined in the Certificate of Designation of Preferences, Rights and Limitations relating to the Series D Preferred Stock as any of the following: (i) merger with or consolidation into another legal entity; (ii) sale, lease, license, assignment, transfer or other disposition of all or substantially all of the Company’s assets in one or a series of related transactions; (iii) purchase offer, tender offer or exchange offer of the Company’s common stock pursuant to which holders of the Company’s common stock are permitted to sell, tender or exchange their shares for other securities, cash or property and has been accepted by the holders of 50% or more of the outstanding common stock; (iv) reclassification, reorganization or recapitalization of the Company’s stock; or (v) stock or share purchase agreement that results in another party acquiring more than 50% of the Company’s outstanding shares of common stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series D Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder of common stock would receive if the Series D Preferred Stock were fully converted to common stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series D Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock.

In connection with the August 2017 Vivo Offering, the Company and Vivo also entered into a Stockholder Agreement (Vivo Stockholder Agreement) setting forth certain rights and obligations of Vivo and the Company. Pursuant to the Vivo Stockholder Agreement, Vivo will have the right, subject to certain restrictions and a minimum beneficial ownership level of 4.5%, to (i) designate one director selected by Vivo to the Board and (ii) appoint a representative to attend all Board meetings in a nonvoting observer capacity and to receive copies of all materials provided to directors, subject to certain exceptions. Furthermore, Vivo will have the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. Vivo agreed not to sell or transfer any of the shares of common stock, Series D Preferred Stock or warrants purchased by Vivo in the August 2017 Vivo Offering, or any shares of common stock issuable upon conversion or exercise thereof, other than to its affiliates, without the consent of the Company through August 2018 and to any competitor of the Company thereafter. Vivo also agreed that, subject to certain exceptions, until the later of (i) three years from the closing of the August 2017 Vivo Offering and (ii) three months after there is no Vivo director on the Board, Vivo will not, without the prior consent of the Board, acquire common stock or rights to acquire common stock that would result in Vivo beneficially owning more than 33% of the Company’s outstanding voting securities at the time of acquisition. Under the Vivo Stockholder Agreement, the Company agreed to use its commercially reasonable efforts to register, via one or more registration statements filed with the SEC under the Securities Act, the shares of common stock purchased in the August 2017 Vivo Offering as well as the shares of common stock issuable upon conversion or exercise of the Series D Preferred Stock and warrants purchased by Vivo in the August 2017 Vivo Offering.

For information regarding issuances of equity securities subsequent to December 31, 2019, see Note 15, “Subsequent Events”.

Right of First Investment to Certain Investors

In connection with investments in the Company has granted certain investors, including Vivo and DSM, a right of first investment if the Company proposes to sell securities in certain financing transactions. With these rights, such investors may subscribe for a portion of any such new financing and require the Company to comply with certain notice periods, which could discourage other investors from participating in, or cause delays in its ability to close, such a financing.

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Debt - Nikko Loan Agreements (Details) - USD ($)	Aug. 08, 2019	Jul. 30, 2019	Jan. 31, 2020	Dec. 31, 2019	Dec. 19, 2019	Jul. 29, 2019	Dec. 31, 2018
Debt Conversion [Line Items]
Long-term debt				$ 261,772,000			$ 209,697,000
Subsequent Event
Debt Conversion [Line Items]
Long-term debt			$ 60,000,000.0
Nikko Loan Agreement
Debt Conversion [Line Items]
Debt instrument, face amount					$ 4,500,000	$ 5,000,000.0
Long-term debt						$ 100,000
Interest rate per annum					2.75%	5.00%
Nikko Loan Agreement | Subsequent Event
Debt Conversion [Line Items]
Debt instrument, face amount			$ 4,500,000
Nikko Loan Agreement | Aprinnova JV
Debt Conversion [Line Items]
First priority lien on interests owned by the company					27.20%	12.80%
Nikko Loan Agreement, First Installment
Debt Conversion [Line Items]
Debt instrument, face amount		$ 3,000,000.0				$ 3,000,000.0
Proceeds from issuance of long-term debt		2,800,000
Nikko Loan Agreement, First Installment | Nikko
Debt Conversion [Line Items]
Proceeds from issuance of long-term debt, withheld as prepayment of interest payable		$ 200,000
Nikko Loan Agreement, Second Installment
Debt Conversion [Line Items]
Debt instrument, face amount	$ 2,000,000.0					$ 2,000,000.0
Proceeds from issuance of long-term debt	$ 1,900,000

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Debt - Naxyris LSA Amendment (Details) - USD ($) $ / shares in Units, shares in Millions			1 Months Ended	12 Months Ended
	Oct. 28, 2019	Aug. 14, 2019	Oct. 31, 2019	Dec. 31, 2019	Dec. 31, 2018	Aug. 28, 2019
Debt Conversion [Line Items]
Warrants and rights outstanding						$ 8,700,000
Debt instrument, fair value				$ 194,800,000	$ 149,300,000
Loss upon extinguishment of debt				$ (44,208,000)	$ (17,424,000)
The Naxyris Loan Agreement
Debt Conversion [Line Items]
Debt instrument, fee		$ 500,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	2.0	2.0
Exercise price of warrants or rights (in dollars per share)	$ 3.87	$ 2.87
Warrants and rights outstanding	$ 3,600,000	$ 4,000,000.0
Debt instrument, unamortized discount		$ 400,000
Class of warrant or right, term	2 years	2 years
The Naxyris Loan Agreement
Debt Conversion [Line Items]
Debt instrument, additional face amount		$ 10,400,000
Basis spread on variable rate		0.25%	5.00%
Unused borrowing capacity fee			$ 2,000,000.0
Debt instrument, fee		$ 400,000
Debt instrument, face amount	$ 24,400,000	10,400,000
Loan and Security Agreement Amendment and Waiver | The Naxyris Loan Agreement
Debt Conversion [Line Items]
Warrants and rights outstanding		3,000,000.0				$ 2,800,000
Debt instrument, fair value	500,000
Loss upon extinguishment of debt	9,700,000
Debt instrument, unamortized discount	4,000,000.0
Fair value of embedded derivative liability		$ 300,000
Debt conversion, original debt	$ 2,900,000

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Debt - Foris LSA Assignment, Amendments and Waivers (Details) - USD ($) $ / shares in Units, shares in Millions	Aug. 14, 2019	Apr. 15, 2019	Apr. 04, 2019	Aug. 28, 2019
Debt Conversion [Line Items]
Warrants and rights outstanding				$ 8,700,000
LSA Amendment Warrants
Debt Conversion [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	1.4
Exercise price of warrants or rights (in dollars per share)	$ 2.87
Loan and Security Agreement Amendment and Waiver | Base Rate | Maximum
Debt Conversion [Line Items]
Basis spread on variable rate	12.00%
Loan and Security Agreement Amendment and Waiver | Unsecured Promissory Note
Debt Conversion [Line Items]
Debt instrument, face amount	$ 32,500,000
Loan and Security Agreement Amendment and Waiver | Great American Capital Partners, LLC
Debt Conversion [Line Items]
Payments for debt agreement amendment			$ 800,000
Debt instrument, periodic payment, principal		$ 36,000,000.0
Purchases from related party		$ 2,500,000
Debt instrument, face amount	$ 71,000,000.0
Class of warrant or right, number of securities called by warrants or rights (in shares)	1.4
Warrants and rights outstanding	$ 2,900,000
Basis spread on variable rate	0.25%
Class of warrant or right, term	2 years

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Debt - 6% Convertible Notes Due 2021 (Details) - USD ($)		1 Months Ended	12 Months Ended
	Jun. 24, 2019	Dec. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Nov. 15, 2019	Nov. 08, 2019	Jul. 24, 2019
Debt Conversion [Line Items]
Interest expense			$ 58,665,000	$ 42,703,000
Convertible Senior Notes, 6 Percent Due in 2021
Debt Conversion [Line Items]
Debt conversion, original debt		$ 60,000,000.0		$ 57,918,000
Proceeds from debt, net of issuance costs		$ 56,200,000
Interest rate per annum		6.00%		6.00%	6.00%	6.00%
Interest expense	$ 4,400,000	$ 5,300,000
Debt instrument, face amount						$ 66,000,000.0
Senior Convertible Notes Due 2022
Debt Conversion [Line Items]
Debt conversion, original debt			10,000,000
Proceeds from debt, net of issuance costs			$ 30,000,000
Interest rate per annum			15.00%		5.00%		5.00%

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Debt - DSM $8 Million Note (Details) - DSM International B.V. - USD ($)		12 Months Ended
	Sep. 23, 2019	Dec. 31, 2019	Sep. 19, 2019	Sep. 17, 2019
The 2019 DSM Credit Agreement, First Installment
Debt Conversion [Line Items]
Line of Credit Facility, Incremental Draw Down Amount				$ 3,000,000.0
Debt instrument, face amount				3,000,000.0
The 2019 DSM Credit Agreement, Second Installment
Debt Conversion [Line Items]
Line of Credit Facility, Incremental Draw Down Amount				3,000,000.0
Debt instrument, face amount			$ 3,000,000.0
The 2019 DSM Credit Agreement, Third Installment
Debt Conversion [Line Items]
Line of Credit Facility, Incremental Draw Down Amount	$ 2,000,000.0			2,000,000.0
Debt instrument, face amount	2,000,000.0
Extinguishment of debt	$ 1,500,000
The 2019 DSM Credit Agreement
Debt Conversion [Line Items]
Maximum borrowing capacity				$ 8,000,000.0
Interest rate per annum				12.50%
Debt instrument, percent of face amount				100.00%
Proceeds from sale of equity securities, gross, trigger repayment of amounts outstanding under line of credit		$ 50,000,000.0
Debt instrument, fee				$ 300,000

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Stockholders' Deficit - Number of Callable Shares (Details)	12 Months Ended
	Dec. 31, 2019 shares	Dec. 31, 2018 shares
Class of Stock [Line Items]
Preferred stock, shares outstanding	8,280	14,656
Convertible Senior Notes, 6.0% Due in 2021
Class of Stock [Line Items]
Debt instrument, convertible, number of equity instruments	13,200,000
The 2014 144A Notes
Class of Stock [Line Items]
Debt instrument, convertible, number of equity instruments	181,238
Series D Preferred Stock
Class of Stock [Line Items]
Debt instrument, convertible, number of equity instruments	1,943,661
Convertible Notes
Class of Stock [Line Items]
Debt instrument, convertible, number of equity instruments	15,324,899

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Fair Value Measurement - 6% Convertible Notes Due 2021 (Details) - Convertible Senior Notes, 6.0% Due in 2021 - USD ($)	Dec. 10, 2018	Dec. 06, 2018
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument, face amount	$ 60,000,000.0
Interest rate per annum	6.00%	6.00%
Change in fair value of derivative liabilities	$ 23,200,000

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Fair Value Measurement - Market-based Assumption and Estimates for Compound Embedded Derivative Liabilities Valuation (Details)	Dec. 31, 2019 $ / shares	Mar. 28, 2019 $ / shares	Dec. 31, 2018 $ / shares
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Stock price (in dollars per share)	$ 3.09	$ 2.10	$ 3.34
Stock price volatility | Minimum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.450		0.450
Stock price volatility | Maximum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control			0.850
Probability of change in control
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.050		0.000
Measurement Input, Risk Free Interest Rate | Minimum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.016		0.025
Measurement Input, Risk Free Interest Rate | Maximum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.017		0.030
Risk-adjusted discount yield | Minimum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.200		0.170
Risk-adjusted discount yield | Maximum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.270		0.273
Credit spread | Minimum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.184		0.146
Credit spread | Maximum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Probability of change in control	0.254		0.249

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Consolidated Statements of Stockholders' Deficit and Mezzanine Equity (Parentheticals) $ in Thousands	12 Months Ended
	Dec. 31, 2018 USD ($)
Issuance costs	$ 0
Additional Paid-in Capital
Issuance costs	$ 0

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Related Party Transactions - Related Party Debt (Details) - USD ($) $ in Millions	Dec. 31, 2019	Jan. 01, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Derivative liabilities	$ 41.0	$ 41.0
Capitalized Contract Cost, Amortization Period	5 years
Foris Ventures, LLC
Related Party Transaction [Line Items]
Derivative liabilities	$ 19.0
Related Party Convertible Notes
Related Party Transaction [Line Items]
Derivative liabilities	2.6		$ 0.0
Derivative Liability, Debt-related
Related Party Transaction [Line Items]
Derivative liabilities	$ (0.1)		$ (8.5)

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Debt - Foris Credit Agreements (Details) - USD ($)			12 Months Ended
	Jul. 10, 2019	Apr. 08, 2019	Dec. 31, 2019	Aug. 17, 2019	Jul. 26, 2019	Jul. 09, 2019	Jun. 11, 2019
Debt Conversion [Line Items]
Fair value adjustments of warrants			$ (4,800,000)
July Foris Credit Agreement
Debt Conversion [Line Items]
Exercise price of warrants or rights (in dollars per share)	$ 2.87			$ 7.52		$ 7.52
Fair value adjustments of warrants	$ 4,000,000.0
July Foris Credit Agreement | Foris Ventures, LLC
Debt Conversion [Line Items]
Debt instrument, face amount	8,000,000.0
Maximum borrowing capacity	$ 8,000,000.0
Interest rate per annum	12.50%
Long-term line of credit	$ 16,000,000				$ 8,000,000.0
April Foris Credit Agreement | Foris Ventures, LLC
Debt Conversion [Line Items]
Debt instrument, face amount		$ 8,000,000.0
Maximum borrowing capacity		8,000,000.0
Debt instrument, fee		$ 1,000,000.0
Debt instrument, term		6 months
April Foris Credit Agreement | Foris Ventures, LLC | Maximum
Debt Conversion [Line Items]
Debt instrument, fee		$ 500,000
June Foris Credit Agreement | Foris Ventures, LLC
Debt Conversion [Line Items]
Debt instrument, face amount							$ 8,500,000
Maximum borrowing capacity							$ 8,500,000
Interest rate per annum							12.50%

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Net Loss Per Share Attributable to Common Stockholders - Calculation of Basic and Diluted Net Loss Per Share of Common Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Earnings Per Share [Abstract]
Net loss attributable to Amyris, Inc.	$ (242,767)	$ (230,235)
Less deemed dividend to preferred shareholder on issuance and modification of common stock warrants	(34,964)	0
Less deemed dividend related to proceeds discount upon conversion of Series D preferred stock	0	(6,852)
Add: losses allocated to participating securities	(7,380)	(13,991)
Net loss attributable to Amyris, Inc. common stockholders	(270,351)	(223,096)
Adjustment to losses allocated to participating securities	(137)	0
Gain from change in fair value of derivative instruments	(4,963)	0
Net loss attributable to Amyris, Inc. common stockholders, diluted	$ (275,177)	$ (223,096)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted (in shares)	101,370,632	60,405,910
Earnings per share, basic (in dollars per share)	$ (2.67)	$ (3.69)
Effect of dilutive common stock warrants	(74,057)	0
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted (in shares)	101,296,575	60,405,910
Earnings per share, diluted (in dollars per share)	$ (2.72)	$ (3.69)

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Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Revenues [Abstract]
Revenue	$ 152,557	$ 63,604
Costs and Expenses [Abstract]
Cost of products sold	76,185	36,698
Research and development	71,460	68,722
Sales, general and administrative	126,586	90,902
Impairment of other assets	216	3,865
Total cost and operating expenses	274,447	200,187
Loss from operations	(121,890)	(136,583)
Other income (expense)
Loss on divestiture	0	(1,778)
Interest expense	(58,665)	(42,703)
Gain (loss) from change in fair value of derivative instruments	2,777	(30,880)
(Loss) gain from change in fair value of debt	(19,369)	2,082
Loss upon extinguishment of debt	(44,208)	(17,424)
Other expense, net	(783)	(2,949)
Total other expense, net	(120,248)	(93,652)
Loss before income taxes	(242,138)	(230,235)
Provision for income taxes	(629)	0
Net loss attributable to Amyris, Inc.	(242,767)	(230,235)
Deemed Dividend related to Preferred Shareholder on Issuance and Modifications of Common Stock Warrants	34,964	0
Less deemed dividend related to proceeds discount upon conversion of Series D preferred stock	0	6,852
Add: losses allocated to participating securities	7,380	13,991
Net loss attributable to Amyris, Inc. common stockholders	$ (270,351)	$ (223,096)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic (in shares)	101,370,632	60,405,910
Earnings per share, basic (in dollars per share)	$ (2.67)	$ (3.69)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted (in shares)	101,296,575	60,405,910
Earnings per share, diluted (in dollars per share)	$ (2.72)	$ (3.69)
Product
Revenues [Abstract]
Revenue	$ 59,872	$ 33,598
Licenses and Royalties
Revenues [Abstract]
Revenue	54,043	7,658
Grants and Collaborations
Revenues [Abstract]
Revenue	$ 38,642	$ 22,348

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Debt - Debt Components (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Debt Instrument [Line Items]
Principal	$ 297,462	$ 228,921
Unaccreted Debt (Discount) Premium	(20,314)	(17,142)
Fair Value Adjustment	15,376	(2,082)
Net	261,772	209,697
Less: current portion	(63,805)	(147,677)
Long-term debt, net of current portion	197,967	62,020
Convertible Debt
Debt Instrument [Line Items]
Principal	66,000	126,306
Unaccreted Debt (Discount) Premium	0	(3,350)
Fair Value Adjustment	15,376	(2,082)
Net	50,624	120,874
Convertible Debt | Convertible Senior Notes 6.0% due in 2022
Debt Instrument [Line Items]
Principal	66,000	0
Unaccreted Debt (Discount) Premium	0	0
Fair Value Adjustment	15,376	0
Net	50,624	0
Convertible Debt | Convertible Senior Notes, 6.0% Due in 2021
Debt Instrument [Line Items]
Principal	0	60,000
Unaccreted Debt (Discount) Premium	0	0
Fair Value Adjustment	0	(2,082)
Net	0	57,918
Convertible Debt | The 2015 144A Notes
Debt Instrument [Line Items]
Principal	0	37,887
Unaccreted Debt (Discount) Premium	0	(2,413)
Fair Value Adjustment	0	0
Net	0	35,474
Convertible Debt | The 2014 144A Notes
Debt Instrument [Line Items]
Principal	0	24,004
Unaccreted Debt (Discount) Premium	0	(867)
Fair Value Adjustment	0	0
Net	0	23,137
Convertible Debt | August 2013 Convertible Notes
Debt Instrument [Line Items]
Principal	0	4,415
Unaccreted Debt (Discount) Premium	0	(70)
Fair Value Adjustment	0	0
Net	0	4,345
Related Party Convertible Notes
Debt Instrument [Line Items]
Principal	10,178	24,705
Unaccreted Debt (Discount) Premium	0	(1,038)
Fair Value Adjustment	0	0
Net	10,178	23,667
Related Party Convertible Notes | The 2014 144A Notes
Debt Instrument [Line Items]
Principal	10,178	24,705
Unaccreted Debt (Discount) Premium	0	(1,038)
Fair Value Adjustment	0	0
Net	10,178	23,667
Loans Payable
Debt Instrument [Line Items]
Principal	48,496	52,910
Unaccreted Debt (Discount) Premium	(5,355)	(6,443)
Fair Value Adjustment	0	0
Net	43,141	46,467
Loans Payable | Schottenfeld Notes
Debt Instrument [Line Items]
Principal	20,350	0
Unaccreted Debt (Discount) Premium	(1,315)	0
Fair Value Adjustment	0	0
Net	19,035	0
Loans Payable | Nikko Notes
Debt Instrument [Line Items]
Principal	14,318	4,598
Unaccreted Debt (Discount) Premium	(901)	(1,047)
Fair Value Adjustment	0	0
Net	13,417	3,551
Loans Payable | Ginkgo Collaboration Note
Debt Instrument [Line Items]
Principal	12,000	12,000
Unaccreted Debt (Discount) Premium	(3,139)	(4,047)
Fair Value Adjustment	0	0
Net	8,861	7,953
Loans Payable | Other Loans Payable
Debt Instrument [Line Items]
Principal	1,828	312
Unaccreted Debt (Discount) Premium	0	0
Fair Value Adjustment	0	0
Net	1,828	312
Nonrelated Party Debt | GACP Term Loan Facility
Debt Instrument [Line Items]
Principal	0	36,000
Unaccreted Debt (Discount) Premium	0	(1,349)
Fair Value Adjustment	0	0
Net	0	34,651
Related Party Loan Payable
Debt Instrument [Line Items]
Principal	172,788	25,000
Unaccreted Debt (Discount) Premium	(14,959)	(6,311)
Fair Value Adjustment	0	0
Net	157,829	18,689
Related Party Loan Payable | Foris Debt
Debt Instrument [Line Items]
Principal	115,351	0
Unaccreted Debt (Discount) Premium	(9,516)	0
Fair Value Adjustment	0	0
Net	105,835	0
Related Party Loan Payable | DSM Note
Debt Instrument [Line Items]
Principal	33,000	25,000
Unaccreted Debt (Discount) Premium	(4,621)	(6,311)
Fair Value Adjustment	0	0
Net	28,379	18,689
Related Party Loan Payable | The Naxyris Loan Agreement
Debt Instrument [Line Items]
Principal	24,437	0
Unaccreted Debt (Discount) Premium	(822)	0
Fair Value Adjustment	0	0
Net	$ 23,615	$ 0

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Debt - 2014 Rule 144A Convertible Notes (Details) - USD ($)	1 Months Ended
	May 31, 2019	Dec. 31, 2019	Aug. 28, 2019
Debt Conversion [Line Items]
Warrants and rights outstanding			$ 8,700,000
Warrants Issued in Connection with Rule 144A Convertible Notes Conversion
Debt Conversion [Line Items]
Warrants and rights outstanding		$ 3,800,000
Convertible Senior Notes, 6.5%
Debt Conversion [Line Items]
Debt instrument, interest rate	6.50%
Debt conversion, original debt	$ 38,200,000
Convertible Senior Notes, 6.5% | Warrants Issued in Connection with Rule 144A Convertible Notes Conversion
Debt Conversion [Line Items]
Warrants and rights outstanding		$ 10,500,000

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Revenue Recognition - Revenue in Connection With Significant Revenue Agreement (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 152,557	$ 63,604
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	59,872	33,598
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	54,043	7,658
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	38,642	22,348
All Other Customers
Disaggregation of Revenue [Line Items]
Revenue	51,557	24,877
All Other Customers | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	43,794	25,775
All Other Customers | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
All Other Customers | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	7,763	(898)
Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	101,000	38,727
Significant Revenue Agreement | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	16,078	7,823
Significant Revenue Agreement | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	54,043	7,658
Significant Revenue Agreement | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	30,879	23,246
Significant Revenue Agreement | DSM International B.V.
Disaggregation of Revenue [Line Items]
Revenue	53,181	10,711
Significant Revenue Agreement | DSM International B.V. | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	10	18
Significant Revenue Agreement | DSM International B.V. | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	49,051	5,958
Significant Revenue Agreement | DSM International B.V. | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	4,120	4,735
Significant Revenue Agreement | Firmenich
Disaggregation of Revenue [Line Items]
Revenue	14,996	11,144
Significant Revenue Agreement | Firmenich | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	8,591	3,727
Significant Revenue Agreement | Firmenich | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	4,992	1,700
Significant Revenue Agreement | Firmenich | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	1,413	5,717
Significant Revenue Agreement | Lavvan
Disaggregation of Revenue [Line Items]
Revenue	18,342	0
Significant Revenue Agreement | Lavvan | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	0	0
Significant Revenue Agreement | Lavvan | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
Significant Revenue Agreement | Lavvan | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	18,342	0
Significant Revenue Agreement | Givaudan International, SA
Disaggregation of Revenue [Line Items]
Revenue	8,977	8,436
Significant Revenue Agreement | Givaudan International, SA | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	7,477	4,078
Significant Revenue Agreement | Givaudan International, SA | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
Significant Revenue Agreement | Givaudan International, SA | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	1,500	4,358
Significant Revenue Agreement | DARPA
Disaggregation of Revenue [Line Items]
Revenue	5,504	8,436
Significant Revenue Agreement | DARPA | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	0	0
Significant Revenue Agreement | DARPA | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
Significant Revenue Agreement | DARPA | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	$ 5,504	$ 8,436

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Balance Sheet Details - Maturities of Financing and Operating Leases (Details) $ in Thousands	Dec. 31, 2019 USD ($)
Finance Lease, Liability, Payment, Due [Abstract]
2020	$ 4,490
2021	4,565
2022	0
2023	0
2024	0
Thereafter	0
Total future minimum payments	9,055
Less: amount representing interest	(1,424)
Present value of minimum lease payments	7,631
Less: current portion	(3,465)
Long-term portion	4,166
Lessee, Operating Lease, Liability, Payment, Due [Abstract]
2020	7,798
2021	7,541
2022	7,719
2023	3,363
2024	192
Thereafter	0
Total future minimum payments	26,613
Less: amount representing interest	(6,951)
Present value of minimum lease payments	19,662
Less: current portion	(4,625)
Long-term portion	15,037
2020	12,288
2021	12,106
2022	7,719
2023	3,363
2024	192
Thereafter	0
Total future minimum payments	35,668
Less: amount representing interest	(8,375)
Present value of minimum lease payments	27,293
Less: current portion	(8,090)
Long-term portion	$ 19,203

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Balance Sheet Details - Deferred Cost of Product Sold (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Deferred cost of products sold - related party	$ 3,677	$ 489
Deferred cost of products sold, noncurrent - related party	12,815	2,828
Total	$ 16,492	$ 3,317

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Geographical Information

12 Months Ended

Dec. 31, 2019

Segment Reporting [Abstract]

Geographical Information

Geographical Information

The chief operating decision maker is the Company's Chief Executive Officer, who makes resource allocation decisions and assesses performance based on financial information presented on a consolidated basis. There are no segment managers who are held accountable by the chief operating decision maker, or anyone else, for operations, operating results, and planning for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

Revenue

Revenue by geography, based on each customer's location, is shown in Note 9, "Revenue Recognition".

Property, Plant and Equipment

December 31, (In thousands)	2019		2018
United States	$	13,799	$	10,404
Brazil	14,277		6,447
Europe	854		198
	$	28,930	$	17,049

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Balance Sheet Details (Tables)

12 Months Ended

Dec. 31, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Allowance for Doubtful Accounts

Allowance for doubtful accounts activity and balances were as follows:

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Year
Allowance for doubtful accounts:
Year Ended December 31, 2019	$	642	$	110	$	(707)	$	45
Year Ended December 31, 2018	$	642	$	—	$	—	$	642

Inventories

Inventories

December 31, (In thousands)	2019		2018
Raw materials	$	3,255	$	3,901
Work in process	7,204		539
Finished goods	17,311		5,253
Total inventories	$	27,770	$	9,693

Deferred Cost of Products Sold

Deferred cost of products sold — related party

December 31, (In thousands)	2019		2018
Deferred cost of products sold - related party	$	3,677	$	489
Deferred cost of products sold, noncurrent - related party	12,815		2,828
Total	$	16,492	$	3,317

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets

December 31, (In thousands)	2019		2018
Non-inventory production supplies	$	5,376	$	2,391
Prepayments, advances and deposits	4,726		5,644
Recoverable taxes from Brazilian government entities	79		631
Other	2,569		1,900
Total prepaid expenses and other current assets	$	12,750	$	10,566

Property, Plant and Equipment, Net

Property, plant and equipment, net

December 31, (In thousands)	2019		2018
Machinery and equipment	$	48,041	$	43,713
Leasehold improvements	41,478		39,922
Computers and software	9,822		9,987
Furniture and office equipment, vehicles and land	3,510		3,016
Construction in progress	9,752		1,749
Total property, plant and equipment, gross	112,603		98,387
Less: accumulated depreciation and amortization	(83,673)		(78,631)
Total property, plant and equipment, net	$	28,930	$	19,756

Lease, Cost

Information related to the Company's right-of-use assets and related lease liabilities were as follows:

	Year Ended December 31, 2019
Cash paid for operating lease liabilities, in thousands	$	17,809
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$	33,264
Weighted-average remaining lease term	3.35
Weighted-average discount rate	18.1		%

⁽¹⁾ Includes $29.7 million for operating leases existing on January 1, 2019 and $3.6 million for operating leases that commenced during the year ended December 31, 2019. Also, the Company renegotiated one of its operating leases during 2019, which resulted in a new financing lease. Approximately $7.7 million of Right-of-use assets under operating leases, net were reclassified to Right-of-use assets under financing leases, net related to this operating lease modification.

Lessee Lease Liability Maturity

Maturities of lease liabilities as of December 31, 2019 were as follows:

Years Ending December 31 (In thousands)	Financing Leases		Operating Leases		Total Lease Obligations
2020	$	4,490	$	7,798	$	12,288
2021	4,565		7,541		12,106
2022	—		7,719		7,719
2023	—		3,363		3,363
2024	—		192		192
Thereafter	—		—		—
Total future minimum payments	9,055		26,613		35,668
Less: amount representing interest	(1,424)		(6,951)		(8,375)
Present value of minimum lease payments	7,631		19,662		27,293
Less: current portion	(3,465)		(4,625)		(8,090)
Long-term portion	$	4,166	$	15,037	$	19,203

Other Assets

Other assets

December 31, (In thousands)	2019		2018
Equity-method investment	$	4,734	$	—
Contingent consideration	3,303		4,286
Deposits	295		2,465
Other	1,373		1,207
Total other assets	$	9,705	$	7,958

Accrued and Other Current Liabilities

Accrued and other current liabilities

December 31, (In thousands)	2019		2018
Accrued interest	$	8,209	$	3,853
Payroll and related expenses	7,296		9,220
Contract termination fees	5,347		4,092
Ginkgo partnership payments obligation	4,319		2,155
Asset retirement obligation(1)	3,184		3,063
Professional services	2,968		1,173
Tax-related liabilities	1,685		2,139
Other	3,647		3,284
Total accrued and other current liabilities	$	36,655	$	28,979

______________

(1) The asset retirement obligation represents liabilities incurred but not yet discharged in connection with our 2013 abandonment of a partially constructed facility in Pradópolis, Brazil.

Other Noncurrent Liabilities

Other noncurrent liabilities

December 31, (In thousands)	2019		2018
Liability for unrecognized tax benefit	$	7,204	$	6,582
Liability in connection with acquisition of equity-method investment	5,249		—
Ginkgo partnership payments, net of current portion (See Note 4)	4,492		6,185
Refund liability	3,750		—
Contract liabilities, net of current portion(1)	1,449		1,587
Deferred rent, net of current portion	—		6,440
Contract termination fees, net of current portion	—		1,530
Capital leases, net of current portion	—		195
Other	880		673
Total other noncurrent liabilities	$	23,024	$	23,192

______________

(1) Contract liabilities, net of current portion at December 31, 2019 and 2018 includes $1,204 at each date in connection with DSM, which is a related party.

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Stock-based Compensation - Share-based Payment Award, Stock Options, Valuation Assumptions (Details) - $ / shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Compensating Balances [Line Items]
Weighted average exercise price (in dollars per share)	$ 10.27	$ 11.55
Share-based Payment Arrangement, Option
Compensating Balances [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Fair Value Assumptions, Expected Dividend Rate	0.00%	0.00%
Risk-free interest rate	1.80%	2.80%
Expected term (in years) (Year)	6 years 10 months 24 days	6 years 10 months 24 days
Expected volatility	84.00%	80.00%

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Income Taxes - Components of Income Loss (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Income Tax Disclosure [Abstract]
United States	$ (227,614)	$ (218,109)
Foreign	(14,524)	(12,125)
Loss before income taxes	$ (242,138)	$ (230,234)

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Stockholders' Deficit - Warrant Activity (Details) - $ / shares	12 Months Ended
	Dec. 31, 2019	Nov. 30, 2019	Oct. 28, 2019
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	26,891,512
Additional Warrants Issued (in shares)	45,130,273
Exercises (in shares)	(2,649,982)
Expiration (in shares)	(3,616,174)
Exercise price per share of warrants exercised (in dollars per share)	$ 0.22166
Number outstanding, ending balance (in shares)	65,755,629
Foris LSA warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	3,438,829
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	3,438,829
Exercise price of warrants or rights (in dollars per share)	$ 2.87
November 2019 Foris warrant
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	1,000,000
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	1,000,000
Exercise price of warrants or rights (in dollars per share)	$ 3.87	$ 3.87
August 2019 Foris warrant
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	4,871,795
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	4,871,795
Exercise price of warrants or rights (in dollars per share)	$ 3.90
April 2019 PIPE warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	8,084,770
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	8,084,770
April 6th 2019 PIPE Warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	$ 3.9
August 2018 Warrant Exercise Agreements, Due May 20, 2020
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	7.52
August 2018 Warrant Exercise Agreements, Due May 17, 2020
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	2.87
May 2019 6.5% Note Exchange Warrants, Due May 14, 2021
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	5.02
May 2019 6.5% Note Exchange Warrants, Due May 2021
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	3.9
June 2019 Note Exchange Warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	5.12
May 2019 Note Exchange Warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	2.87
November 2019 Investor Credit Agreement Warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	3.9
September 2019 Investor Credit Agreement Warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	3.87
APril 2019 PIPE Warrants Due May 3 2021
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	5.02
April 29 2021 PIPE Warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Exercise price of warrants or rights (in dollars per share)	$ 4.76
April 2019 Foris warrant
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	5,424,804
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	5,424,804
Exercise price of warrants or rights (in dollars per share)	$ 2.87
September and November 2019 Investor Credit Agreement warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	5,233,551
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	5,233,551
Naxyris LSA warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	2,000,000
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	2,000,000
Exercise price of warrants or rights (in dollars per share)	$ 2.87
October 2019 Naxyris warrant
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	2,000,000
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	2,000,000
Exercise price of warrants or rights (in dollars per share)	$ 3.87		$ 3.87
May-June 2019 6% Note Exchange warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	2,181,818
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	2,181,818
May 2019 6.50% Note Exchange warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	1,744,241
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	1,744,241
July 2019 Wolverine warrant
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	1,080,000
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	1,080,000
Exercise price of warrants or rights (in dollars per share)	$ 2.87
August 2018 warrant exercise agreements
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	12,097,164
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	12,097,164
April 2018 warrant exercise agreements
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	3,616,174
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	(3,616,174)
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	0
Exercise price of warrants or rights (in dollars per share)	$ 0
May 2017 cash warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	6,244,820
Additional Warrants Issued (in shares)	0
Exercises (in shares)	(166,664)
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 2.87000
Number outstanding, ending balance (in shares)	6,078,156
Exercise price of warrants or rights (in dollars per share)	$ 2.87
August 2017 cash warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	3,968,116
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0.00015
Number outstanding, ending balance (in shares)	3,968,116
Exercise price of warrants or rights (in dollars per share)	$ 2.87
May 2017 dilution warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	47,978
Additional Warrants Issued (in shares)	4,795,924
Exercises (in shares)	(1,758,009)
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0.00015
Number outstanding, ending balance (in shares)	3,085,893
Exercise price of warrants or rights (in dollars per share)	$ 0.0015
August 2017 dilution warrants
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	0
Additional Warrants Issued (in shares)	3,028,983
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	3,028,983
Exercise price of warrants or rights (in dollars per share)	$ 0.0001
February 2016 related party private placement
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	171,429
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	171,429
Exercise price of warrants or rights (in dollars per share)	$ 0.15
July 2015 related party debt exchange
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	133,334
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	133,334
Exercise price of warrants or rights (in dollars per share)	$ 0.15
July 2015 private placement
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	81,197
Additional Warrants Issued (in shares)	0
Exercises (in shares)	(8,547)
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0.15000
Number outstanding, ending balance (in shares)	72,650
Exercise price of warrants or rights (in dollars per share)	$ 0.15
July 2015 related party debt exchange
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	58,690
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	58,690
Exercise price of warrants or rights (in dollars per share)	$ 0.15
July 2015 related party debt exchange
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	471,204
Additional Warrants Issued (in shares)	245,558
Exercises (in shares)	(716,762)
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0.15000
Number outstanding, ending balance (in shares)	0
Exercise price of warrants or rights (in dollars per share)	$ 0
Other
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Number of Shares [Roll Forward]
Number outstanding, beginning balance (in shares)	1,406
Additional Warrants Issued (in shares)	0
Exercises (in shares)	0
Expiration (in shares)	0
Exercise price per share of warrants exercised (in dollars per share)	$ 0
Number outstanding, ending balance (in shares)	1,406
Exercise price of warrants or rights (in dollars per share)	$ 160.05

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Fair Value Measurement - Allocation of Consideration Fair Value (Details) $ in Thousands	Nov. 19, 2018 USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Manufacturing capacity reservation fee	$ 24,395
Legal settlement and consent waiver	6,764
Working capital adjustment	2,145
Total fair value of consideration transferred	33,304
DSM Supply Agreement
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of consideration transferred	$ 33,300

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Consolidated Statements of Operations (Parentheticals) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Revenues, related party	$ 56	$ 360
Product
Revenues, related party	49,051	5,958
Licenses and Royalties
Revenues, related party	4,120	4,735
Grants and Collaborations
Revenues, related party	$ 53,227	$ 11,053

XML

Document And Entity Information - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Mar. 06, 2020	Jun. 28, 2019
Cover page.
Entity Registrant Name	AMYRIS, INC.
Entity Central Index Key	0001365916
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Well-known Seasoned Issuer	No
Entity Emerging Growth Company	false
Document Transition Report	false
Entity Small Business	true
Entity Common Stock, Shares Outstanding		163,843,407
Entity Public Float			$ 226.5
Entity Shell Company	false
Document Type	10-K
Document Period End Date	Dec. 31, 2019
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	FY
Amendment Flag	false

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Debt - 2015 Rule 144A Convertible Notes Extinguishment (Details)	Apr. 16, 2019 USD ($)
Rule 144A Convertible Note Offering | Affiliated Entity
Debt Conversion [Line Items]
Debt instrument, repurchased face amount	$ 37,900,000
Convertible Senior Notes, 9.5%
Debt Conversion [Line Items]
Interest rate per annum	9.50%

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Revenue Recognition - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 152,557	$ 63,604
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	59,872	33,598
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	54,043	7,658
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	38,642	22,348
Europe
Disaggregation of Revenue [Line Items]
Revenue	70,809	29,406
Europe | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	10,092	7,576
Europe | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	54,043	7,658
Europe | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	6,674	14,172
United States
Disaggregation of Revenue [Line Items]
Revenue	58,671	26,240
United States | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	34,295	16,292
United States | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
United States | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	24,376	9,948
Asia
Disaggregation of Revenue [Line Items]
Revenue	18,980	6,331
Asia | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	11,503	8,664
Asia | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
Asia | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	7,477	(2,333)
Brazil
Disaggregation of Revenue [Line Items]
Revenue	3,727	942
Brazil | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	3,612	381
Brazil | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
Brazil | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	115	561
Other
Disaggregation of Revenue [Line Items]
Revenue	370	685
Other | Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	370	685
Other | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	0	0
Other | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	$ 0	$ 0

XML

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Operating activities
Net loss attributable to Amyris, Inc.	$ (242,767)	$ (230,235)
Adjustments to Reconcile Net Income (Loss) to Cash Provided by (Used in) Operating Activities [Abstract]
Loss upon conversion or extinguishment of debt	44,208	17,424
Loss (gain) from change in fair value of debt	19,369	(2,082)
Amortization of right-of-use assets under operating leases	12,597
Stock-based compensation	12,554	9,190
Accretion of debt discount	11,665	16,602
Expense for warrants issued for covenant waivers	5,358	0
Depreciation and amortization	4,581	4,921
Impairment of other assets	1,354	0
Loss in equity-method investee	297	0
Loss on disposal of property, plant and equipment	212	941
(Gain) loss from change in fair value of derivative instruments	(2,777)	30,880
Gain on foreign currency exchange rates	(22)	(2,223)
Modification of warrants recorded as legal expense	0	6,764
Issuance costs on warrant exercises for cash	0	4,389
Loss on impairment of other assets	216	3,865
Debt issuance costs expensed due to fair value option	0	3,810
Loss on divestiture	0	1,778
Changes in assets and liabilities:
Accounts receivable	(2,818)	7,448
Contract assets	(8,485)	0
Contract assets - related party	8,021	8,056
Inventories	(17,989)	(4,416)
Deferred cost of products sold - related party	(13,175)	(3,317)
Prepaid expenses and other assets	(8,064)	(6,383)
Accounts payable	23,748	11,603
Accrued and other liabilities	18,981	8,461
Lease liabilities	(17,125)
Contract liabilities	(6,872)	3,158
Net cash used in operating activities	(156,933)	(109,366)
Investing activities
Purchases of property, plant and equipment	(13,080)	(12,472)
Net cash used in investing activities	(13,080)	(12,472)
Financing activities
Proceeds from issuance of debt, net of issuance costs	189,175	94,371
Proceeds from issuance of common stock in private placements, net of issuance costs - related party	39,500	0
Proceeds from issuance of common stock in private placements, net of issuance costs	14,221	1,415
Proceeds from ESPP purchases	1,078	777
Proceeds from exercises of common stock options	27	288
Proceeds from exercise of warrants, net of issuance costs	1	57,767
Principal payments on debt	(112,393)	(41,668)
Principal payments on financing leases	(5,268)	(981)
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(1,103)	(260)
Capital distribution to noncontrolling interest	(328)	0
Debt issuance costs incurred in connection with debt instrument accounted at fair value	0	(3,752)
Net cash provided by financing activities	124,910	107,957
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(252)	(77)
Net decrease in cash, cash equivalents and restricted cash	(45,355)	(13,958)
Cash, cash equivalents and restricted cash at beginning of year	47,054	61,012
Cash, cash equivalents and restricted cash at end of year	1,699	47,054
Reconciliation of cash, cash equivalents and restricted cash to the consolidated balance sheets
Cash and cash equivalents	270	45,353
Restricted cash, current	469	741
Restricted cash, noncurrent	960	960
Total cash, cash equivalents and restricted cash	47,054	47,054
Supplemental disclosures of cash flow information:
Cash paid for interest	20,780	18,524
Supplemental disclosures of non-cash investing and financing activities:
Cumulative effect of change in accounting principle for ASU 2017-11	41,043	0
Lease liabilities recorded upon adoption of ASC 842	33,552	0
Right of Use Assets Under Operating Leases Recorded Upon Adoption of ASC842	29,713	0
Cumulative effect adjustment of ASC 606	0	762
Accrued interest added to debt principal	7,292	3,664
Acquisition of additional interest in equity-method investee in exchange for payment obligation	5,031	0
Acquisition of property, plant and equipment under accounts payable, accrued liabilities and notes payable	2,576	0
Acquisition of right-of-use assets under operating leases	3,551	0
Debt fair value adjustment in connection with debt issuance	11,575	0
Derecognition of derivative liabilities upon exercise of warrants	0	108,670
Fair value of embedded features in connection with debt issuances and modifications	237	0
Fair value of embedded features in connection with debt issuances and modifications - related party	1,954	0
Fair value of pre-delivery shares in connection with debt issuance	4,215	0
Fair value of warrants recorded as debt discount in connection with debt issuances	8,965	0
Fair value of warrants recorded as debt discount in connection with debt issuances - related party	16,155	0
Fair value of warrants recorded as debt discount in connection with debt modification	398	0
Fair value of warrants recorded as debt discount in connection with debt modification - related party	2,050	0
Financing of equipment under financing leases	7,436	271
Financing of insurance premium under note payable	253	495
Issuance of common stock - related party	0	6,050
Issuance of common stock for settlement of debt principal and interest payments	0	1,800
Issuance of common stock upon conversion of convertible notes	$ 62,860	$ 24,970

XML

Revenue Recognition - Remaining Performance Obligations (Details) $ in Thousands	Dec. 31, 2019 USD ($)
Revenue from Contract with Customer [Abstract]
Revenue, remaining performance obligation, amount	$ 139,515
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue from Contract with Customer [Abstract]
Revenue, remaining performance obligation, amount	$ 56,719
Disaggregation of Revenue [Line Items]
Revenue, remaining performance obligation, period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue from Contract with Customer [Abstract]
Revenue, remaining performance obligation, amount	$ 52,313
Disaggregation of Revenue [Line Items]
Revenue, remaining performance obligation, period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2022-01-01
Revenue from Contract with Customer [Abstract]
Revenue, remaining performance obligation, amount	$ 30,483
Disaggregation of Revenue [Line Items]
Revenue, remaining performance obligation, period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2023-01-01
Revenue from Contract with Customer [Abstract]
Revenue, remaining performance obligation, amount	$ 0
Disaggregation of Revenue [Line Items]
Revenue, remaining performance obligation, period	1 year

XML

Debt - Foris Related Party Debt (Details) - USD ($) $ in Thousands			12 Months Ended
	Aug. 28, 2019	Apr. 15, 2019	Dec. 31, 2019	Nov. 27, 2019	Dec. 31, 2018
Debt Instrument [Line Items]
Long-term debt, gross			$ 297,462		$ 228,921
Related Party Loan Payable
Debt Instrument [Line Items]
Long-term debt, gross			172,788		25,000
Foris $19 Million Note | Related Party Loan Payable
Debt Instrument [Line Items]
Debt conversion, original debt	$ 19,000
Long-term debt, gross			19,000
Interest rate per annum	1200.00%
Foris LSA | Related Party Loan Payable
Debt Instrument [Line Items]
Debt conversion, original debt		$ 36,000
Long-term debt, gross			96,351
Interest rate per annum		1250.00%
Debt instrument, face amount				$ 81,000
Debt instrument, additional face amount				$ 10,000
Foris Debt | Related Party Loan Payable
Debt Instrument [Line Items]
Debt conversion, original debt			55,000
Long-term debt, gross			$ 115,351		$ 0

XML

Balance Sheet Details - Other Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Equity-method investment	$ 4,734	$ 0
Contingent consideration	3,303	4,286
Deposits	295	2,465
Other	1,373	1,207
Total other assets	$ 9,705	$ 7,958

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Balance Sheet Details - Prepaid Expenses and Other Current Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Non-inventory production supplies	$ 5,376	$ 2,391
Prepayments, advances and deposits	4,726	5,644
Recoverable taxes from Brazilian government entities	79	631
Other	2,569	1,900
Total prepaid expenses and other current assets	$ 12,750	$ 10,566

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Stock-based Compensation - Options Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Compensating Balances [Line Items]
Weighted average exercise price (in dollars per share)	$ 10.27	$ 11.55
Grants in period, (in shares)	530,140	4,337,119
Weighted average grant date fair value, grants in period	$ 3.83	$ 5.18
Share-based payment arrangement, expense	$ 12,554	$ 9,190
Share-based payment arrangement, nonvested award, cost not yet recognized, amount	4,500	8,500
Share-based Payment Arrangement, Option
Compensating Balances [Line Items]
Share-based payment arrangement, expense	$ 2,000	$ 2,600

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Divestiture (Details) - USD ($)		1 Months Ended			12 Months Ended
	Dec. 28, 2017	Mar. 31, 2019	Nov. 30, 2018	Jun. 30, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Loss on divestiture					$ 0	$ (1,778,000)
Revenue					152,557,000	63,604,000
Future Nonrefundable Minimum Annual Royalty Payments					18,100,000
Proceeds From Non-refundable Minimum Royalty Payment		$ 7,400,000		$ 9,300,000
Non-refundable Minimum Royalty Payment Early Payment Discount		$ 700,000		$ 700,000
DSM International B.V.
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Post-closing working capital adjustment payment recorded as loss on divestiture					2,100,000
Contract with customer, liability					$ 34,700,000
DSM Credit Agreement
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Maximum borrowing capacity	$ 25,000,000.0					25,000,000.0
Royalty | DSM International B.V.
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Maximum borrowing capacity						$ 25,000,000
License | DSM International B.V.
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Revenue							$ 54,700,000
Performance Option and Transition Services Agreements | DSM International B.V.
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Contract with customer, liability							$ 2,100,000
DSM
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Disposal group, including discontinued operation, consideration	17,800,000
DSM | License and Service
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Revenue	27,500,000
DSM | Royalty
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Revenue	15,000,000.0
Amyris Brasil
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Divestiture of Business, Consideration Transferred	56,900,000
Loss on divestiture	5,700,000
Proceeds from Divestiture of Businesses	54,800,000
Amyris Brasil | DSM
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Post-closing working capital adjustment payment recorded as loss on divestiture			$ 1,800,000
Amyris Brasil | Disposal Group, Not Discontinued Operations
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Disposal group, including discontinued operation, consideration	33,000,000.0
Repayments of debt	$ 12,600,000

XML

Income Taxes

12 Months Ended

Dec. 31, 2019

Income Tax Disclosure [Abstract]

Income Taxes

Income Taxes

The components of loss before income taxes are as follows:

Years Ended December 31, (In thousands)	2019		2018
United States	$	(227,614)	$	(218,109)
Foreign	(14,524)		(12,125)
Loss before income taxes	$	(242,138)	$	(230,234)

The components of the provision for income taxes are as follows:

Years Ended December 31, (In thousands)	2019		2018
Current:
Federal	$	621	$	—
State	—		—
Foreign	8		—
Total current provision	629		—
Deferred:
Federal	—		—
State	—		—
Foreign	—		—
Total deferred benefit	—		—
Total provision for income taxes	$	629	$	—

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:

Years Ended December 31,	2019		2018
Statutory tax rate	(21.0)	%	(21.0)	%
Federal R&D credit	(0.7)	%	(0.6)	%
Derivative liability	4.7	%	4.3	%
Nondeductible interest	1.0	%	1.0	%
Other	2.4	%	(0.1)	%
Foreign losses	0.9	%	0.9	%
Change in valuation allowance	13.0	%	15.5	%
Effective income tax rate	0.3	%	—	%

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows:

December 31, (In thousands)	2019		2018
Net operating loss carryforwards	$	88,513	$	57,921
Property, plant and equipment	8,239		9,269
Research and development credits	15,002		12,046
Foreign tax credit	—		—
Accruals and reserves	13,934		8,526
Stock-based compensation	6,164		6,496
Disallowed interest carryforward	7,072		2,359
Capitalized research and development costs	21,723		27,888
Intangible and others	2,503		3,114
Equity investments	304		156
Total deferred tax assets	163,454		127,775
Operating leases right-of-use assets	(2,643)		—
Debt discount and derivatives	(7,176)		(3,750)
Total deferred tax liabilities	(9,819)		(3,750)
Net deferred tax assets prior to valuation allowance	153,635		124,025
Less: valuation allowance	(153,635)		(124,025)
Net deferred tax assets	$	—	$	—

Activity in the deferred tax assets valuation allowance is summarized as follows:

(In thousands)	Balance at Beginning of Year		Additions		Reductions / Charges		Balance at End of Year
Deferred tax assets valuation allowance:
Year ended December 31, 2019	$	124,025	$	29,610	$	—	$	153,635
Year ended December 31, 2018	$	81,086	$	42,939	$	—	$	124,025

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. Based on the weight of available evidence, especially the uncertainties surrounding the realization of deferred tax assets through future taxable income, the Company believes that it is more likely than not that the net deferred tax assets will not be fully realizable. Accordingly, the Company has provided a full valuation allowance against its net deferred tax assets as of December 31, 2019 and 2018. The valuation allowance increased by $42.9 million during the year ended December 31, 2018 and increased by $29.6 million during the year ended December 31, 2019.

As of December 31, 2019, the Company had federal net operating loss carryforwards of approximately $411.3 million and state net operating loss carryforwards $158.1 million, available to reduce future taxable income, if any. The Internal Revenue Code of 1986, as amended, imposes restrictions on the utilization of net operating losses in the event of an “ownership change” of a corporation. Accordingly, a company’s ability to use net operating losses may be limited as prescribed under Internal Revenue Code Section 382 (IRC Section 382). Events that may cause limitations in the amount of the net operating losses that the Company may use in any one year include, but are not limited to, a cumulative ownership change of more than 50% over a three-year period. During the year ended December 31, 2019, the Company experienced a cumulative ownership change of greater than 50%. As such, net operating losses generated prior to that change are subject to an annual limitation on their use. Due to the limitations imposed, the Company wrote-off $396.5 million of federal NOL carryover and $90.6 million of state NOL carryover that is expected to expire before it can be utilized. Additionally, the Company wrote-off $14.4 million of its historical federal research and development credit carryovers as a result of the limitations. As of December 31, 2019, the Company had foreign net operating loss carryovers of approximately $22.0 million.

As of December 31, 2019, the Company had federal research and development credit carryforwards of $3.3 million and California research and development credit carryforwards of $15.2 million.

If not utilized, the federal net operating loss carryforward will begin expiring in 2034, and the California net operating loss carryforward will begin expiring in 2031. The federal research and development credit carryforwards will expire starting in 2037 if not utilized. The California research and development credit carryforwards can be carried forward indefinitely.

A reconciliation of the beginning and ending amounts of unrecognized tax benefits is as follows:

(In thousands)
Balance at December 31, 2017	$	28,833
Increases in tax positions for prior period	55
Increases in tax positions during current period	1,239
Balance at December 31, 2018	30,127
Increases in tax positions for prior period	—
Increases in tax positions during current period	1,411
Balance at December 31, 2019	$	31,538

The Company’s policy is to include interest and penalties related to unrecognized tax benefits within the provision for taxes. The Company accrued $0.6 million and $0 for interest as of December 31, 2019 and 2018, respectively.

None of the unrecognized tax benefits, if recognized, would affect the effective income tax rate for any of the above years due to the valuation allowance that currently offsets deferred tax assets. The Company does not anticipate that the total amount of unrecognized income tax benefits will significantly increase or decrease in the next 12 months.

The Company’s primary tax jurisdiction is the United States. For United States federal and state tax purposes, returns for tax years 2006 and forward remain open and subject to tax examination by the appropriate federal or state taxing authorities. Brazil tax years 2011 and forward remain open and subject to examination.

As of December 31, 2019, the U.S. Internal Revenue Service (the IRS) has completed its audit of the Company for tax year 2008 and concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the U.S. federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

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Basis of Presentation and Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedules of Concentration of Risk, by Risk Factor

Customers representing 10% or greater of accounts receivable were as follows:

As of December 31,	2019	2018
Customer A (related party)	19%	**
Customer B	21%	24%
Customer C	**	19%
Customer E	**	11%
Customer F	10%	**

______________

** Less than 10%

Customers representing 10% or greater of revenue were as follows:

Years Ended December 31,	Year First Customer	2019	2018
Customer A (related party)	2017	35%	17%
Customer B	2014	10%	18%
Customer C	2014	**	13%
Customer D	2014	**	13%
Customer G	2019	12%	*

______________

* Not a customer

** Less than 10%

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Basis of Presentation and Summary of Significant Accounting Policies - Additional Information (Details) R$ in Millions			1 Months Ended	12 Months Ended
	May 10, 2019 BRL (R$)	Jan. 01, 2019 USD ($)	Jan. 31, 2020 USD ($)	Dec. 31, 2019 USD ($)	Dec. 31, 2018 USD ($)	Dec. 15, 2019 USD ($)	Oct. 28, 2019 USD ($)	Aug. 14, 2019 USD ($)	May 10, 2019 USD ($)	Dec. 10, 2018 USD ($)	Dec. 06, 2018
Debt Instrument [Line Items]
Working capital				$ (86,700,000)
Accumulated deficit				1,755,653,000	$ 1,521,417,000
Deferred discount and issuance costs				20,314,000	17,142,000
Loss (gain) from change in fair value of debt				(15,376,000)	2,082,000
Long-term debt				261,772,000	209,697,000
Long-term debt, current maturities, including due to related parties				(63,805,000)	(147,677,000)
Debt, current portion				45,313,000	124,010,000
Long term debt, excluding current maturities				48,452,000	43,331,000
Debt Instrument, Amount, Failed To Pay						$ 5,200,000
Cash, cash equivalents, and short-term investments				270,000
Loss on divestiture				0	(1,778,000)
Accumulated other comprehensive loss				(43,804,000)	(43,343,000)
(Gain) loss on foreign currency exchange rates				(22,000)	(2,223,000)
Total assets				160,966,000	127,925,000
Operating lease, liability				19,662,000
Operating lease asset				13,203,000
Derivative liabilities		$ 41,000,000		$ 41,000,000
Assurance Type Warranty, Term				2 years
Capitalized Contract Cost, Amortization Period				5 years
Cash and cash equivalents				$ 270,000	45,353,000
The Joint Venture
Debt Instrument [Line Items]
Joint Ventures, Terms, Purchase Price Of Fixed Assets	R$ 2.5								$ 3,000,000.0
Equity method investment, ownership percentage	50.00%								50.00%
Joint Venture, Terms, Threshold Of Days For Cash Contribution	60 days
Joint Ventures, Terms, Aggregate Cash Contribution Due | R$	R$ 9.0
Joint Venture, Terms, Threshold Of Months For Contribution Of Supply Agreements	6 months
Joint Venture, Terms, Period Of Entitlement To Certain Priority Fixed Cumulative Dividends	10 years
Accounting Standards Update 2016-02
Debt Instrument [Line Items]
Total assets		25,700,000
Operating lease, liability		33,600,000
Operating lease asset		29,700,000
Accounting Standards Update 2017-11
Debt Instrument [Line Items]
Accumulated deficit		(8,500,000)
Increase (decrease) in derivative liabilities		41,000,000.0
Additional paid in capital		$ 32,500,000
Other Expense, Net
Debt Instrument [Line Items]
(Gain) loss on foreign currency exchange rates				$ (200,000)	$ 1,600,000
Machinery, Equipment, and Fixtures | Minimum
Debt Instrument [Line Items]
Property, plant and equipment, useful life				3 years
Machinery, Equipment, and Fixtures | Maximum
Debt Instrument [Line Items]
Property, plant and equipment, useful life				15 years
Building
Debt Instrument [Line Items]
Property, plant and equipment, useful life				15 years
Subsequent Event
Debt Instrument [Line Items]
Long-term debt			$ 60,000,000.0
Debt conversion, converted instrument, amount			75,000,000.0
Convertible Senior Notes, 6.0% Due in 2021
Debt Instrument [Line Items]
Debt instrument, face amount										$ 60,000,000.0
Interest rate per annum										6.00%	6.00%
The Naxyris Loan Agreement
Debt Instrument [Line Items]
Debt instrument, face amount							$ 24,400,000	$ 10,400,000
Interest rate per annum								12.00%
Total Raffinage Chimie, Nikko Chemicals Co. Ltd and Schottenfeld Group LLC | Subsequent Event
Debt Instrument [Line Items]
Debt instrument, face amount			$ 17,600,000

XML

Related Party Transactions (Tables)

12 Months Ended

Dec. 31, 2019

Related Party Transactions [Abstract]

Schedule of Related Party Debt

Related party debt was as follows:

	2019						2018
December 31, (in thousands)	Principal		Unaccreted Debt Discount		Net		Principal		Unaccreted Debt Discount		Net
DSM notes	$	33,000	$	(4,621)	$	28,379	$	25,000	$	(6,311)	$	18,689
Foris
Foris notes	115,351		(9,516)		105,835		—		—		—
2014 Rule 144A convertible notes	—		—		—		5,000		(181)		4,819
	115,351		(9,516)		105,835		5,000		(181)		4,819
Naxyris note	24,437		(822)		23,615		—		—		—
Temasek 2014 Rule 144A convertible note	—		—		—		10,000		(435)		9,565
Total 2014 Rule 144A convertible note	10,178		—		10,178		9,705		(422)		9,283
	$	182,966	$	(14,959)	$	168,007	$	49,705	$	(7,349)	$	42,356

Schedule of Related Party Revenues

The Company recognized revenue from related parties and from all other customers as follows:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Revenue from related parties:
DSM	$	10	$	49,051	$	4,120	$	53,181	$	18	$	5,958	$	4,735	$	10,711
Total	46		—		—		46		342		—		—		342
Novvi	—		—		—		—		—		—		—		—
Subtotal revenue from related parties	56		49,051		4,120		53,227		360		5,958		4,735		11,053
Revenue from all other customers	59,816		4,992		34,522		99,330		33,238		1,700		17,613		52,551
Total revenue from all customers	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Schedule of Related Party Accounts Receivables

Related party accounts receivable was as follows:

December 31, (In thousands)	2019		2018
DSM	$	3,868	$	1,071
Novvi	—		188
Total	—		90
Related party accounts receivable, net	$	3,868	$	1,349

XML

Related Party Transactions - Related Party Joint Venture (Details) - Nikko - USD ($) $ in Millions	1 Months Ended	12 Months Ended	36 Months Ended
	Dec. 31, 2016	Dec. 31, 2019	Dec. 31, 2019
First Aprinnova Loan
Related Party Transaction [Line Items]
Debt instrument, face amount	$ 0.5	$ 0.2	$ 0.2
Second Aprinnova Loan
Related Party Transaction [Line Items]
Debt instrument, face amount	1.5	0.2	0.2
Aprinnova Short Term Loan
Related Party Transaction [Line Items]
Debt instrument, face amount		$ 1.2	$ 1.2
Aprinnova JV
Related Party Transaction [Line Items]
Equity method investment, ownership percentage		50.00%	50.00%
Payments to acquire businesses, gross	10.0
Noncontrolling interest, period increase (decrease)		$ 0.3
Notes receivable, related parties	$ 3.9
Aprinnova JV | Maximum
Related Party Transaction [Line Items]
Proceeds from equity method investment, distribution, return of capital			$ 10.0

XML

Related Party Transactions - Related Party Accounts Receivable Narrative (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Contingent consideration	$ 3,303	$ 4,286
Accounts receivable, unbilled - related party	0	8,021
Accounts receivable, unbilled - related party | DSM International B.V.
Related Party Transaction [Line Items]
Accounts receivable, unbilled - related party	0	8,000
Contract assets, noncurrent - related party | DSM International B.V.
Related Party Transaction [Line Items]
Accounts receivable, unbilled - related party	$ 1,200	$ 1,200

XML

Label	Element	Value
Accounting Standards Update 2014-09 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ (762,000)
Accounting Standards Update 2014-09 [Member] | Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	(762,000)
Accounting Standards Update 2017-11 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	41,043,000
Accounting Standards Update 2017-11 [Member] | Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	8,531,000
Accounting Standards Update 2017-11 [Member] | Additional Paid-in Capital [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 32,512,000

XML

Basis of Presentation and Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Presentation and Significant Accounting Policies

Basis of Presentation and Summary of Significant Accounting Policies

Business Description

Amyris, Inc. and subsidiaries (collectively, Amyris or the Company) is a leading industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets. The Company's proven technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. The Company's biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. The Company has successfully used its technology to develop and produce many distinct molecules at commercial volumes.

Going Concern

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations for at least the next 12 months following the issuance of the financial statements. As of December 31, 2019, the Company had negative working capital of $86.7 million and an accumulated deficit of $1.8 billion.

As of December 31, 2019, the Company's debt (including related party debt), net of deferred discount and issuance costs of $20.3 million and a fair value adjustment of $15.4 million, totaled $261.8 million, of which $63.8 million is classified as current. However, $75.0 million of debt was converted into equity in January 2020; see Note 15, “Subsequent Events” for more information. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness, material adverse effect and cross default provisions. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding indebtedness. At December 31, 2019, the Company failed to meet certain covenants under several credit arrangements (which are discussed in Note 4, “Debt”), including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. In March 2020, these lenders provided permanent waivers to the Company for breaches of all past covenant violations and cross-default payment failures (discussed below), through March 13, 2020 under the respective credit agreements, and significantly reduced the minimum liquidity requirement and substantially increased the base of eligible assets to calculate the asset coverage requirement..

On January 31, 2020, the Company failed to pay Total Raffinage Chimie (Total), Nikko Chemicals Co. Ltd (Nikko) and certain affiliates of the Schottenfeld Group LLC (Schottenfeld) an aggregate of $17.6 million of maturing promissory notes, and previously on December 15, 2019 failed to pay Ginkgo $5.2 million of past due interest, past due partnership payments and the first installment of a waiver fee. These failures resulted in an event of default under the respective agreements and also triggered cross-defaults under other debt instruments (discussed above) that permitted each of the affected cross-default debt holders of such indebtedness to accelerate the amounts owing under such instruments. The Company subsequently received waivers from each of the affected cross-default debt holders to waive the right to accelerate due to the event specific cross-defaults. As a result, the indebtedness with respect to which the Company has obtained such waivers continues to be classified as long-term on the Company’s balance sheet. The indebtedness reflected by the Total and certain Ginkgo, Nikko and Schottenfeld amounts continues to be classified as a current liability on the Company’s balance sheet as the due date for these amounts was within one year of December 31, 2019.

Subsequent to December 31, 2019, the Company (i) obtained a waiver and forbearance agreement from Schottenfeld, (ii) amended the credit arrangements with Total and Nikko Notes to extend the maturity date of the original promissory notes, and (iii) entered into a waiver and amendment to the partnership agreement with Ginkgo to waive all past payment defaults under the Ginkgo Note and Ginkgo Partnership Agreement, and to extend the payment due date and modify the periodic partnership payment timing and amount. See Note 15, “Subsequent Events” for further information.

Although the Company obtained extensions to make these payments, it currently does not have sufficient funds to repay the amounts due under the Total, Nikko, Schottenfeld and Ginkgo credit arrangements, and while the Company intends to seek equity or debt financing, the proceeds of which would be used to repay Total, Nikko, Schottenfeld and Ginkgo, there can be no assurance that the Company will be able to obtain such financing on our expected timeline, or on acceptable terms, if at all.

Also, while the Company has been able to cure these defaults to date to avoid additional cross-acceleration, it may not be able to cure such a default promptly in the future.

Further, cash and cash equivalents of $0.3 million as of December 31, 2019 are not sufficient to fund expected future negative cash flows from operations and cash debt service obligations through March 2021. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that these financial statements are issued. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. In addition to repaying the Total, Nikko, Schottenfeld and Ginkgo amounts previously discussed, the Company's ability to continue as a going concern will depend, in large part, on its ability to raise additional proceeds through financings, achieve positive cash flows from operations during the 12 months from the date of this filing, and refinance or extend other existing debt maturities occurring later in 2020, all of which are uncertain and outside the control of the Company. Further, the Company's operating plan for 2020 contemplates a significant reduction in its net operating cash outflows as compared to the year ended December 31, 2019, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) reduced spending in general and administrative areas, and (iv) an increase in cash inflows from collaborations and grants. If the Company is unable to complete these actions, it expects to be unable to meet its operating cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and the Company may be forced to obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all, and/or liquidate its assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these financial statements. The Company has in the past, including in July 2019, had certain of its debt instruments accelerated for failure to make a payment when due. While we have been able to obtain permanent waivers or cure these defaults to date to avoid additional cross-acceleration, we may not be able to obtain waivers or cure such a default promptly in the future.

Basis of Consolidation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States (U.S. GAAP). The consolidated financial statements include the accounts of Amyris, Inc. and its wholly-owned and partially-owned subsidiaries in which the Company has a controlling interest after elimination of all significant intercompany accounts and transactions.

Investments and joint venture arrangements are assessed to determine whether the terms provide economic or other control over the entity requiring consolidation of the entity. Entities controlled by means other than a majority voting interest are referred to as variable-interest entities (VIEs) and are consolidated when Amyris has both the power to direct the activities of the VIE that most significantly impact its economic performance and the obligation to absorb losses or the right to receive benefits that could potentially be significant to the entity. For any investment or joint venture in which (i) the Company does not have a majority ownership interest, (ii) the Company possesses the ability to exert significant influence and (iii) the entity is not a VIE for which the Company is considered the primary beneficiary, the Company accounts for the investment or joint venture using the equity method. Equity investments in which the Company does not exert significant influence and that do not have readily determinable fair values are measured at cost, adjusted for changes from observable market transactions, less impairment (“adjusted cost basis”). The Company evaluates its investments for impairment by considering a variety of factors, including the earnings capacity of the related investments. Fair value measurements for the Company’s equity investments are classified within Level 3 of the fair value hierarchy based on the nature of the fair value inputs. Realized and unrealized gains or losses are recognized in other income or expense.

Raizen Joint Venture Agreement

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into a joint venture agreement relating to the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products. In connection with the formation of the joint venture, among other things, (i) the joint venture will construct a manufacturing facility on land owned by Raizen and leased to the joint venture (the Sweetener Plant), (ii) the Company will grant to the joint venture an exclusive, royalty-free, worldwide license to certain technology owned by the Company relevant to the joint venture’s business, and (iii) the Company and Raizen will enter into a shareholders agreement setting forth the rights and obligations of the parties with respect to, and the management of, the joint venture. The formation of the joint venture is subject to certain conditions, including certain regulatory approvals and the achievement of certain technological and economic milestones relating to the Company’s existing production of its alternative sweetener product. If such conditions are not satisfied by May 2020, the joint venture will automatically terminate. However, the termination date can be extended by mutual agreement of the parties. In addition, notwithstanding the satisfaction of the closing conditions, Raizen may elect not to

consummate the formation and operation of the joint venture, in which event, the Company will retain the right to construct and operate the Sweetener Plant.

Upon the closing of the joint venture, each party will make an initial capital contribution to the joint venture of 2.5 million Brazilian Real (R$2.5 million) and the joint venture will be owned 50% by the Company and 50% by Raizen. Within 60 days of the formation, the parties will make an aggregate cash contribution to the joint venture of USD $9.0 million to purchase certain fixed assets currently owned by the Company and located at the site of the Company’s former joint venture with Sao Martinho S.A. in Pradopolis, Brazil for USD $3.0 million, as well as to pay for costs related to the removal and transportation of such assets to the site of the Sweetener Plant. In addition, within six months of the formation, the Company will contribute to the joint venture its existing supply agreements related to its alternative sweetener product, subject to certain exceptions, in exchange for shares of dividend-bearing preferred stock in the joint venture, which will be entitled, for a period of 10 years commencing from the initial date of operation of the Sweetener Plant, to certain priority fixed cumulative dividends including, in the event that certain technological and economic milestones are met in any fiscal quarter, a percentage of the operating cash flow of the joint venture in such quarter.

The Company is evaluating the accounting treatment for its future interest in the joint venture under ASC 810, Consolidations and ASC 323, Equity Method and Joint Ventures and will conclude once the corporate governance and economic participation structure is finalized and the formation of the joint venture is consummated.

Use of Estimates and Judgements

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates, and such differences may be material to the consolidated financial statements. Significant estimates and judgements used in these consolidated financial statements are discussed in the relevant accounting policies below or specifically discussed in the Notes to Consolidated Financial Statements where such transactions are disclosed.

Significant Accounting Policies

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with an original or remaining maturity of three months or less at the date of purchase to be cash equivalents. Cash and cash equivalents are maintained with various financial institutions.

Inventories

Inventories, which consist of farnesene-derived products, flavors and fragrances ingredients and clean beauty products, are stated at the lower of actual cost or net realizable value and are categorized as finished goods, work in process or raw material inventories. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds their estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or net realizable value approach that is used to value inventory. Cost for farnesene-derived products and flavors and fragrances ingredients are computed on a weighted-average basis. Cost for clean beauty products are computed on a standard cost basis.

Property, Plant and Equipment, Net

Property, plant and equipment are recorded at cost. Depreciation and amortization are computed straight-line based on the estimated useful lives of the related assets, ranging from 3 to 15 years for machinery, equipment and fixtures, and 15 years for buildings. Leasehold improvements are amortized over their estimated useful lives or the period of the related lease, whichever is shorter.

The Company expenses costs for maintenance and repairs and capitalizes major replacements, renewals and betterments. For assets retired or otherwise disposed, both cost and accumulated depreciation are eliminated from the asset and accumulated depreciation accounts, and gains or losses related to the disposal are recorded in the statement of operations for the period.

Impairment

Long-lived assets that are held and used by the Company are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. Determination of recoverability of long-lived assets is based on an estimate of the undiscounted future cash flows resulting from the use of the asset and its eventual disposition. Measurement of an impairment loss for long-lived assets that management expects to hold and use is based on the difference between the fair value of the asset and its carrying value. Long-lived assets to be disposed of are reported at the lower of carrying amount or fair value less costs to sell.

Recoverable Taxes from Brazilian Government Entities

Recoverable taxes from Brazilian government entities represent value-added taxes paid on purchases in Brazil, which are reclaimable from the Brazilian tax authorities, net of reserves for amounts estimated not to be recoverable.

Fair Value Measurements

The carrying amounts of certain financial instruments, such as cash equivalents, short-term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities.

The Company measures the following financial assets and liabilities at fair value:

•Freestanding and bifurcated derivatives in connection with certain debt and equity financings; and

•Senior Convertible Notes Due 2022 and 6% Convertible Notes Due 2021 (see Note 3, "Fair Value Measurement" and Note 4, "Debt", for which the Company elected fair value accounting.

Fair value is based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation techniques are applied. These valuation techniques involve some level of management estimation and judgement, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

Changes to the inputs used in these valuation models can have a significant impact on the estimated fair value of the Senior Convertible Notes Due 2022, 6% Convertible Notes Due 2021 and the Company's embedded and freestanding derivatives. For example, a decrease (increase) in the estimated credit spread for the Company results in an increase (decrease) in estimated fair value. Conversely, a decrease (increase) in the stock price results in a decrease (increase) in estimated fair value.

The changes during 2019 and 2018 in the fair values of the bifurcated compound embedded derivatives are primarily related to the change in price of the Company's common stock and are reflected in the consolidated statements of operations as “Gain (loss) from change in fair value of derivative instruments”.

For debt instruments for which the Company has not elected fair value accounting, fair value is based on the present value of expected future cash flows and assumptions about the then-current market interest rates as of the reporting period and the creditworthiness of the Company. Most of the Company's debt is carried on the consolidated balance sheet on a historical cost basis net of unamortized discounts and premiums, because the Company has not elected the fair value option of accounting. However, for the Senior Convertible Notes Due 2022 and the 6% Notes Due 2021, the Company elected fair value accounting, so that balances reported for those debt instruments represent fair value as of the applicable balance sheet date; see Note 3, "Fair Value Measurement", for additional information. Changes in fair value of the Senior Convertible Notes Due 2022 and the 6% Convertible Notes Due 2021 are reflected in the consolidated statements of operations as “Gain (loss) from change in fair value of debt”.

For all debt instruments, including any for which the Company has elected fair value accounting, the Company classifies interest that has been accrued during each period as Interest expense on the consolidated statements of operations.

Derivatives

Embedded derivatives that are required to be bifurcated from the underlying debt instrument (i.e., host) are accounted for and valued as separate financial instruments. The Company has evaluated the terms and features of its convertible notes payable and convertible preferred stock and identified compound embedded derivatives requiring bifurcation and accounting at fair value, using the valuation techniques mentioned in the Fair Value Measurements section of this Note, because the economic and contractual characteristics of the embedded derivatives met the criteria for bifurcation and separate accounting due to the instruments containing conversion options, certain “make-whole interest” provisions, down-round conversion price adjustment provisions and/or conversion rate adjustments, and mandatory redemption features that are not clearly and closely related to the debt host instrument.

Prior to the adoption of ASU 2017-11, certain previously issued warrants with a fair value of $41 million issued in conjunction with the convertible debt and equity financings were freestanding financial instruments and classified as derivative liabilities as of December 31, 2019. Upon adoption of ASU 2017-11 on January 1, 2019, these freestanding instruments met the criteria to be accounted for within equity and the $41 million derivative liability balance was reclassified to stockholders’ equity.

During the third and fourth quarter of 2019, the Company issued warrants in connection with a debt financing that met the criteria of a freestanding instrument but did not qualify for equity accounting treatment. As a result, these warrants are accounting for at fair value until settled and are classified as derivative liabilities at December 31, 2019. See Note 6 “Stockholders’ Deficit” for further information.

Noncontrolling Interest

Noncontrolling interests represent the portion of net income (loss), net assets and comprehensive income (loss) that is not allocable to the Company, in situations where the Company consolidates its equity investment in a joint venture for which there are other owners. The amount of noncontrolling interest is comprised of the amount of such interests at the date of the Company's original acquisition of an equity interest in a joint venture, plus the other shareholders' share of changes in equity since the date the Company made an investment in the joint venture.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents, short-term investments and accounts receivable. The Company places its cash equivalents and investments (primarily certificates of deposits) with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:

As of December 31,	2019	2018
Customer A (related party)	19%	**
Customer B	21%	24%
Customer C	**	19%
Customer E	**	11%
Customer F	10%	**

______________

** Less than 10%

Customers representing 10% or greater of revenue were as follows:

Years Ended December 31,	Year First Customer	2019	2018
Customer A (related party)	2017	35%	17%
Customer B	2014	10%	18%
Customer C	2014	**	13%
Customer D	2014	**	13%
Customer G	2019	12%	*

______________

* Not a customer

** Less than 10%

Revenue Recognition

The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer, and transaction price is allocated utilizing stand-alone selling price. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does not incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators, among others, when determining if it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does not meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in Note 9, "Revenue Recognition".

The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to receive payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. For most of the Company's renewable products customers, supply agreements between the Company and each customer indicate when transfer of title occurs.

In some cases, the Company may make a payment to a customer. When that occurs, the Company evaluates whether the payment is for a distinct good or service receivable from the customer. If the fair value of the goods or services receivable is greater than or equal to the amount paid to the customer, then the entire payment is treated as a purchase. If, on the other hand, the fair value of goods or services is less than the amount paid, then the difference is treated as a reduction in transaction price of the Company's sales to the customer or a reduction of cumulative to-date revenue recognized from the customer in the period the payment is made or goods or services are received from the customer.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts may contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis.

The following is a description of the principal goods and services from which the Company generates revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does not have the ability to direct the product to a different customer. It is at this point that the Company has the right to receive payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do not include rights of return, except for direct-to-consumer products, for which the Company estimates sales returns subsequent to sale and reduces revenue accordingly. For renewable products other than direct-to-consumer, returns are accepted only if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception which requires the Company to estimate the revenue that is recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts, using the best evidence available at the time, derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends. Estimates are adjusted to actual or as new information becomes available.

When the Company’s intellectual property license is not the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts.

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services: The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to

scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaboration partners with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include one or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement, and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Generally, revenue is recognized using an input-based measure of progress towards the satisfaction of the performance obligations which can be labor hours expended or time-based in proportion to the estimated total project effort or total projected time to complete. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Certain performance obligations are associated with milestones agreed between the Company and its customer. Revenue generated from the performance of services in accordance with these milestones is recognized upon confirmation from the customer that the milestone has been achieved. In these cases, amounts recognized are constrained to the amount of consideration received upon achievement of the milestone.

The Company generally invoices its collaboration partners on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Contract liabilities arise from amounts received in advance of performing the research and development activities and are recognized as revenue in future periods as the performance obligations are satisfied.

Grants: The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect grant revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

The Company receives certain consideration from AICEP Portugal Global (AICEP), and entity funded by government of Portugal, under the Consortium Internal Regulatory Agreement and an AICEP Investment Contract (the “Agreements”) entered

into by Amyris (the “Company”) with Universidade Católica Portuguesa (UCP) Porto Campus. The Company considered this arrangement to be a government grant and accounts for the arrangement under International Accounting Standard 20 “Accounting for Government Grants and Disclosure of Government Assistance”. Grant revenue is recognized when there is reasonable assurance that monies will be received and that conditions attached to the grant have been met.

Cost of Products Sold

Cost of products sold includes the production costs of renewable products, which include the cost of raw materials, in-house manufacturing labor and overhead, amounts paid to contract manufacturers, including amortization of tolling fees, and period costs including inventory write-downs resulting from applying lower of cost or net realizable value inventory adjustments. Cost of products sold also includes certain costs related to the scale-up of production. Shipping and handling costs charged to customers are recorded as revenues. Outbound shipping costs incurred are included in cost of products sold. Such charges were not material for any of the periods presented.

The Company recognizes deferred cost of products sold as an asset on the balance sheet when a cost is incurred in connection with a revenue performance obligation that will not be fulfilled until a future period. The Company also recorded a deferred cost of products asset in 2018 and 2019 for the fair value of amounts paid to DSM under a supply agreement for manufacturing capacity to produce its sweetener product at the Brotas facility in Brazil. The deferred cost of products sold asset is expensed to cost of products sold on a units of production basis over the five-year term of the supply agreement. On a quarterly basis, the Company evaluates its future production volumes for its sweetener product and adjusts the unit cost to be expensed over the remaining estimated production volume. The Company also periodically evaluates the asset for recoverability based on changes business strategy and product demand trends over the term of the supply agreement.

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants, including internal research. Research and development costs consist of direct and indirect internal costs related to specific projects, as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Debt Extinguishment

The Company accounts for the income or loss from extinguishment of debt in accordance with ASC 470, Debt, which indicates that for all extinguishments of debt, including instances where the terms of a debt instrument are modified in a manner that significantly changes the underlying cash flows, the difference between the reacquisition consideration and the net carrying amount of the debt being extinguished should be recognized as gain or loss when the debt is extinguished. Losses from debt extinguishment are shown in the consolidated statements of operations under "Other income (expense)" as "Loss upon extinguishment of debt".

Stock-based Compensation

The Company accounts for stock-based employee compensation plans under the fair value recognition and measurement provisions of U.S. GAAP. Those provisions require all stock-based payments to employees, including grants of stock options and restricted stock units (RSUs), to be measured using the grant-date fair value of each award. The Company recognizes stock-based compensation expense net of expected forfeitures over each award's requisite service period, which is generally the vesting term. Expected forfeiture rates are estimated based on the Company's historical experience. Stock-based compensation plans are described more fully in Note 11, "Stock-based Compensation".

Income Taxes

The Company is subject to income taxes in the United States and foreign jurisdictions and uses estimates to determine its provisions for income taxes. The Company uses the asset and liability method of accounting for income taxes, whereby deferred tax asset or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. The Company recognizes a valuation allowance against its net deferred tax assets unless it is more likely than not that such deferred tax assets will be realized. This assessment requires judgement as to the likelihood and amounts of future taxable income by tax jurisdiction.

The Company applies the provisions of Financial Accounting Standards Board (FASB) guidance on accounting for uncertainty in income taxes. The Company assesses all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position’s sustainability, and the tax benefit to be recognized is measured at the largest amount of benefit that is greater than 50 percent likely of being realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and the Company will determine whether (i) the factors underlying the sustainability assertion have changed and (ii) the amount of the recognized tax benefit is still appropriate. The recognition and measurement of tax benefits requires significant judgement, and such judgements may change as new information becomes available.

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into U.S. dollars at the rates in effect at each balance sheet date, and revenue and expense amounts are translated at average rates during each period, with resulting foreign currency translation adjustments recorded in other comprehensive loss, net of tax, in the consolidated statements of stockholders’ deficit. As of December 31, 2019 and 2018, cumulative translation adjustment, net of tax, were $43.8 million and $43.3 million, respectively.

Where the U.S. dollar is the functional currency, remeasurement adjustments are recorded in other income (expense), net in the accompanying consolidated statements of operations. Net losses resulting from foreign exchange transactions were $0.2 million and $1.6 million for the years ended December 31, 2019 and 2018, respectively and are recorded in other income (expense), net in the consolidated statements of operations.

New Accounting Standards or Updates Recently Adopted

During the year ended December 31, 2019 the Company adopted the following Accounting Standards Updates (ASUs):

Leases In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) (ASU 2016-02). The standard requires the recognition of lease liabilities and right-of-use (ROU) assets on the balance sheet arising from lease transactions at the lease commencement date and the disclosure of key information about leasing arrangements. In July 2018, the FASB issued ASU 2018-11, Leases (Topic 842): Targeted Improvements, which provided entities the option to use the effective date as the date of initial application on transition to the new guidance. The Company elected this transition method, and as a result, the Company did not adjust comparative information for prior periods. The Company elected certain additional practical expedients permitted by the new guidance allowing the Company to carry forward historical accounting related to lease identification and classification for existing leases upon adoption.

The Company adopted this standard on January 1, 2019 using the modified retrospective approach and elected the package of practical expedients permitted under transition guidance, which allowed the Company to carry forward its historical assessments of: (1) whether contracts are or contain leases, (2) lease classification and (3) initial direct costs, where applicable. The Company did not elect the practical expedient allowing the use-of-hindsight which would require the Company to reassess the lease term of its leases based on all facts and circumstances through the effective date and did not elect the practical expedient pertaining to land easements as this is not applicable to the Company’s current contracts. The Company elected the post-transition practical expedient to not separate lease components from non-lease components for all leases of manufacturing equipment. The Company also elected a policy of not recording leases on its condensed consolidated balance sheets when the leases have a term of 12 months or less and the Company is not reasonably certain to elect an option to purchase the leased asset.

The Company's adoption of this standard had the effect of increasing assets and liabilities by $25.7 million, after considering prepaid and other current and noncurrent assets previously recorded on the condensed consolidated balance sheet but did not have a material impact on the condensed consolidated statements of operations or cash flows. The most significant impact relates to (1) the recognition of new ROU assets and lease liabilities on the balance sheet for the Company's operating leases; and (2) providing significant new disclosures about the Company's leasing activities.

Upon adoption, the Company recognized operating lease liabilities of $33.6 million, based on the present value of the remaining minimum rental payments under current leasing standards for existing operating leases. The Company also recognized ROU assets of $29.7 million, which represents the operating lease liability, adjusted for prepaid expenses and deferred rent. The difference between the operating lease ROU assets and lease liabilities reflects the net of advanced rent payments and deferred rent balances that were derecognized at the time of adoption.

Financial Instruments with "Down Round" Features In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features. The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update became effective in the first quarter of fiscal year 2019, and the Company adopted the standard using a modified retrospective approach. Since the adoption of ASU 2017-11 would have classified the warrants effected as equity at inception, the cumulative-effect adjustment should (i) record the issuance date value of the warrants as if they had been equity classified at the issuance date, (ii) reverse the effects of changes in the fair value of the warrants that had been recorded in the statement of operations of each period, and (iii) eliminate the derivative liabilities from the balance sheet. Upon adoption, the Company (i) recorded an increase of $32.5 million to additional paid-in capital, (ii) recorded a decrease to accumulated deficit of $8.5 million and (iii) decreased the warrant liability by $41.0 million.

Recent Accounting Standards or Updates Not Yet Effective

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement, which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for fair value measurements by removing, modifying or adding certain disclosures. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative arrangement is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. The ASU provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020 retroactively. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments—Credit Losses (Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to measure all expected credit losses for most financial assets held at the reporting date based on an expected loss model which includes historical experience, current conditions, and reasonable and supportable forecasts. Entities will now use forward-looking information to better form their credit loss estimates. ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand significant estimates and judgments used in estimating credit losses, as well as the credit quality and underwriting standards of an entity's portfolio. ASU 2016-13 will become effective for the Company beginning in the first quarter of fiscal year 2020. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments- Credit Losses. This ASU clarifies and addresses certain items related to amendments in ASU 2016-13. This new guidance is effective for the Company beginning on January 1, 2020. This new guidance is not expected to have a material impact on the Company’s consolidated financial statements.

Income Taxes In December 2019, the FASB issued ASU 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes, which simplifies the accounting for income taxes. This guidance will become effective for the Company in the first quarter of fiscal year 2021 on a prospective basis. The Company is currently evaluating the impact of the new guidance on its consolidated financial statements.

In January 2020, the FASB issued ASU 2020-01, Investments-Equity Securities (Topic 321), Investments-Equity Method and Joint Ventures (Topic 323), and Derivatives and Hedging (Topic 815)-Clarifying the Interactions between Topic 321, Topic 323, and Topic 815. The guidance provides clarification of the interaction of rules for equity securities, the equity method of accounting and forward contracts and purchase options on certain types of securities. This new guidance is effective for the

Company beginning on January 1, 2021. While the Company is currently assessing the impact of the new guidance, it is not expected to have a material impact on the Company’s consolidated financial statements.

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Mezzanine Equity

12 Months Ended

Dec. 31, 2019

Equity [Abstract]

Mezzanine Equity

Mezzanine Equity

Mezzanine equity at December 31, 2019 and 2018 is comprised of proceeds from common shares sold on May 10, 2016 to the Bill & Melinda Gates Foundation (the Gates Foundation). On April 8, 2016, the Company entered into a Securities Purchase Agreement with the Gates Foundation, pursuant to which the Company agreed to sell and issue 292,398 shares of its common stock to the Gates Foundation in a private placement at a purchase price per share of $17.10, the average of the daily closing price per share of the Company’s common stock on the Nasdaq Stock Market for the twenty consecutive trading days ending on April 7, 2016, for aggregate proceeds to the Company of approximately $5.0 million (the Gates Foundation Investment). The Securities Purchase Agreement includes customary representations, warranties and covenants of the parties.

In connection with the entry into the Securities Purchase Agreement, on April 8, 2016, the Company and the Gates Foundation entered into a Charitable Purposes Letter Agreement, pursuant to which the Company agreed to expend an aggregate amount not less than the amount of the Gates Foundation Investment to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria commencing in 2017. The Company is currently conducting the project. If the Company defaults in its obligation to use the proceeds from the Gates Foundation Investment as set forth above or defaults under certain other commitments in the Charitable Purposes Letter Agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party of, the Gates Foundation Investment shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, or (ii) an amount equal to $17.10 plus a compounded annual return of 10%. As of December 31, 2019, the Company's remaining research and development obligation under this arrangement was $0.4 million.

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Income Taxes - Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax Disclosure [Abstract]
Net operating loss carryforwards	$ 88,513	$ 57,921
Property, plant and equipment	8,239	9,269
Research and development credits	15,002	12,046
Foreign tax credit	0	0
Accruals and reserves	13,934	8,526
Stock-based compensation	6,164	6,496
Disallowed interest carryforward	7,072	2,359
Capitalized research and development costs	21,723	27,888
Intangible and others	2,503	3,114
Equity investments	304	156
Total deferred tax assets	163,454	127,775
Operating leases right-of-use assets	(2,643)
Debt discount and derivatives	(7,176)	(3,750)
Total deferred tax liabilities	(9,819)	(3,750)
Net deferred tax assets prior to valuation allowance	153,635	124,025
Less: valuation allowance	(153,635)	(124,025)	$ (81,086)
Net deferred tax assets	$ 0	$ 0

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Revenue Recognition

12 Months Ended

Dec. 31, 2019

Revenue from Contract with Customer [Abstract]

Revenue Recognition

Revenue Recognition

Disaggregation of Revenue

The following tables present revenue by primary geographical market, based on the location of the customer, as well as by major product and service:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Europe	$	10,092	$	54,043	$	6,674	$	70,809	$	7,576	$	7,658	$	14,172	$	29,406
United States	34,295		—		24,376		58,671		16,292		—		9,948		26,240
Asia	11,503		—		7,477		18,980		8,664		—		(2,333)		6,331
Brazil	3,612		—		115		3,727		381		—		561		942
Other	370		—		—		370		685		—		—		685
	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Significant Revenue Agreements

For the years ended December 31, 2019 and 2018, the Company recognized revenue in connection with significant revenue agreements and from all other customers as follows:

	2019								2018
Years Ended December 31, (In thousands)	Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL		Renewable Products		Licenses and Royalties		Grants and Collaborations		TOTAL
Revenue from significant revenue agreements with:
DSM (related party)	$	10	$	49,051	$	4,120	$	53,181	$	18	$	5,958	$	4,735	$	10,711
Firmenich	8,591		4,992		1,413		14,996		3,727		1,700		5,717		11,144
Lavvan	—		—		18,342		18,342		—		—		—		—
Givaudan	7,477		—		1,500		8,977		4,078		—		4,358		8,436
DARPA	—		—		5,504		5,504		—		—		8,436		8,436
Subtotal revenue from significant revenue agreements	16,078		54,043		30,879		101,000		7,823		7,658		23,246		38,727
Revenue from all other customers	43,794		—		7,763		51,557		25,775		—		(898)		24,877
Total revenue from all customers	$	59,872	$	54,043	$	38,642	$	152,557	$	33,598	$	7,658	$	22,348	$	63,604

Cannabinoid Agreement

On May 2, 2019, the Company consummated a research, collaboration and license agreement (the Cannabinoid Agreement) with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids, subject to certain closing conditions. Under the agreement, the Company would perform research and development activities and Lavvan would be responsible for the manufacturing and commercialization of the cannabinoids developed under the agreement. The Cannabinoid Agreement is being principally funded on a milestone basis, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. The Company could receive aggregate funding of up to $300 million over the term of the Cannabinoid Agreement if all of the milestones are achieved. Additionally, the Cannabinoid Agreement provides for profit share to the Company on Lavvan's gross profit margin once products are commercialized; these payments will be due for the next 20 years. On May 2, 2019, the parties consummated the transactions contemplated by the Cannabinoid Agreement, including the formation of a special purpose entity to hold certain intellectual property created during the collaboration (the Cannabinoid Collaboration IP), the licensing of certain Company intellectual property to Lavvan, the licensing of the Cannabinoid Collaboration IP to the Company and Lavvan, and the granting by the Company to Lavvan of a lien on the Company background intellectual property being licensed to Lavvan under the Cannabinoid Agreement, which lien would be subordinated to the lien on such intellectual property under the Foris LSA (see Note 4, “Debt”).

The Cannabinoid Agreement is accounted for as a revenue contract under ASC 606, with the total transaction price estimated and updated on a quarterly basis, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligations. The Company concluded the agreement contained a single performance obligation of research and development services provided

continuously over time. The Company estimated the total unconstrained transaction price to be $145 million, based on a high probability of achieving certain underlying milestones. As of December 31, 2019, the Company has constrained $181.0 million of variable consideration related to milestones that have not met the criteria under ASC 606 necessary to be included in the transaction price. The Company concluded that the performance obligation is delivered over time and that revenue recognition is based on an input measure of progress of hours incurred compared to total estimated hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, with cumulative adjustments to revenue recorded as necessary. The Company recognized $18.3 million of collaboration revenue under the Cannabinoid Agreement for the year ended December 31, 2019 based on proportional performance delivered to date. At December 31, 2019, $8.3 million of the collaboration revenues recognized in the year ended December 31, 2019 were recorded as a contract asset. See the "Contract Assets and Liabilities" section below for further information regarding this contract asset.

Firmenich Agreements

In July 2017, the Company and Firmenich entered into the Firmenich Collaboration Agreement Agreement (for the development and commercialization of multiple renewable flavors and fragrances molecules), pursuant to which the parties agreed to exclude certain molecules from the scope of the agreement and to amend certain terms connected with the supply and use of such molecules when commercially produced. In addition, the parties agreed to (i) fix at a 70/30 basis (70% for Firmenich) the ratio at which the parties will share profit margins from sales of two molecules; (ii) set at a 70/30 basis (70% for Firmenich) the ratio at which the parties will share profit margins from sales of a distinct form of compound until Firmenich receives $15.0 million more than the Company in the aggregate from such sales, after which time the parties will share the profit margins 50/50 and (iii) a maximum Company cost of a compound where a specified purchase volume is satisfied, and alternative production and margin share arrangements in the event such Company cost cap is not achieved.

In August 2018, the Company and Firmenich entered into the Firmenich Amended and Restated Supply Agreement, which incorporates all previous amendments and new changes and supersedes the September 2014 supply agreement. With this Amended and Restated Supply Agreement, the parties agreed on the molecules to be supplied under the agreement and the commercial specifications of these products, and made some adjustments to the pricing of the molecules.

Pursuant to the Firmenich Collaboration Agreement, the Company agreed to pay a one-time success bonus to Firmenich of up to $2.5 million if certain commercialization targets are met. Such targets have not yet been met as of December 31, 2019. The one-time success bonus will expire upon termination of the Firmenich Collaboration Agreement, which has an initial term of 10 years and will automatically renew at the end of such term (and at the end of any extension) for an additional 3-year term unless otherwise terminated. At December 31, 2019, the Company had a $0.7 million liability associated with this one-time success bonus that has been recorded as a reduction to the associated collaboration revenue.

Givaudan Agreements

In September 2018, Amyris and Givaudan, entered into a Collaboration Agreement for the development and commercialization of molecules for use and sale in the cosmetics and flavors markets (collectively the “Collaboration Markets”). Under Collaboration Agreement, the parties will collaborate to develop, produce and commercialize. Under the agreement, the Company granted Givaudan exclusive access to specified intellectual property for the development and commercialization of such molecules in the Collaboration Markets in exchange for research and development funding. Funding, including payment terms, will be based on milestones and milestone-based payments, to be mutually agreed upon by the parties on a project by project basis. The Company is currently working on development and commercialization of two significant molecules. The Company also manufactures and supplies a certain compound that was developed by the Company under a prior (expired) collaboration agreement with Givaudan. The supply agreement was entered into in September 2018 and has a five-year term with successive one-year renewals until terminated by either party.

Following the research and development phase of a project, if Givaudan elects to proceed with commercialization, a supply agreement will be negotiated for each compound. The significant terms for each supply agreement are set forth in the Collaboration Agreement including the price at which the molecules are to be supplied. The price for each compound will be negotiated and agreed upon by both parties at a future time. Under the Collaboration Agreement, following commercial development of the agreed upon compound, the Company will manufacture the compound and Givaudan will perform any required downstream polishing, distribution, sales and marketing. The collaboration work and supply of the molecules is exclusively limited to the Cosmetics Actives Market and the Flavors Market.

DSM July and September 2017 Collaboration and Licensing Agreements

In July and September 2017, the Company entered into three separate collaboration agreements with DSM (DSM Collaboration Agreements) to jointly develop three new molecules in the Health & Wellness (DSM Ingredients) market using the Company’s technology, which the Company would produce and DSM would commercialize. Pursuant to the DSM Collaboration Agreements, DSM will, subject to certain conditions, provide funding for the development of the DSM Ingredients and, upon commercialization, the parties would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredients from the Company at prices agreed by the parties. The development services will be directed by a joint steering committee with equal representation by DSM and the Company. In addition, the parties will share profit margin from DSM’s sales of products that incorporate the DSM Ingredients subject to the DSM Collaboration Agreements.

In connection with the entry into the DSM Collaboration Agreements, the Company and DSM also entered into certain license arrangements (DSM License Agreements) providing DSM with certain rights to use the technology underlying the development of the DSM Ingredients to produce and sell products incorporating the DSM Ingredients. Under the DSM License Agreements, DSM paid the Company $9.0 million for a worldwide, exclusive, perpetual, royalty-free license to produce and sell products incorporating one of the DSM Ingredients in the Health & Wellness field.

December 2017 DSM Agreements

In December 2017, the Company entered into a series of agreements with DSM (December 2017 DSM Agreements) which are described below. The December 2017 DSM Agreements were evaluated as a combined transaction for accounting purposes in conjunction with the sales of the Brotas 1 facility discussed more fully in Note 10, "Related Party Transactions" and Note 12, "Divestiture".

DSM November 2017 Intellectual Property License Agreement

In November 2017, in connection with the Company's divestiture of its Brotas, Brazil production facility (see Note 12, "Divestiture"), the Company and DSM entered into a license agreement covering certain intellectual property of the Company useful in the performance of certain commercial supply agreements assigned by the Company to DSM relating to products currently manufactured at the Brotas facility (DSM November 2017 Intellectual Property License Agreement). In December 2017, DSM paid the Company an upfront license fee of $27.5 million. In accounting for the Divestiture with DSM, a multiple-element arrangement, the license of intellectual property to DSM was identified as revenue deliverable with standalone value and qualified as a separate unit of accounting. The Company performed an analysis to determine the fair value for of the license, and allocated the non-contingent consideration based on the relative fair value. The Company determined that the license had been fully delivered, and, as such, license revenue of $54.6 million was recognized for the period ended December 31. 2017.

On November 19, 2018, the Company and DSM entered into a letter agreement (November 2018 DSM Letter Agreement), pursuant to which the Company agreed (i) to cause the removal of certain existing liens on intellectual property owned by the Company and licensed to DSM and (ii) if such liens were not removed prior to December 15, 2018, to issue to DSM shares of the Company’s common stock with a value equal to $5.0 million. On December 14, 2018, the Company entered into an amendment to the GACP Term Loan Facility to remove such lien, and the November 2018 DSM Letter Agreement was thereby terminated.

DSM Value Sharing Agreement

In December 2017, in conjunction with the Company's divestiture of its Brotas, Brazil production facility (see Note 12, "Divestiture" and Note 10, "Related Party Transactions"), the Company and DSM entered into a value sharing agreement (Value Sharing Agreement), pursuant to which DSM agreed to make certain royalty payments to the Company representing a portion of the profit on the sale of products produced using farnesene purchased under the Nenter Supply Agreement realized by Nenter and paid to DSM in accordance with the Nenter Supply Agreement. In addition, pursuant to the Value Sharing Agreement, DSM agreed to guarantee certain minimum annual royalty payments totaling $33.1 million over the first three calendar years of the Value Sharing Agreement, subject to future offsets in the event that the royalty payments to which the Company would otherwise have been entitled under the Value Sharing Agreement for such years fall below certain milestones. The nonrefundable minimum annual royalty payments were determined to be fixed and determinable and were included as part of the total arrangement consideration subject to allocation in the December 2017 multiple-element divestiture transaction with DSM. At closing, DSM paid the Company a nonrefundable royalty payment of $15.0 million under the Value Sharing Agreement and paid two additional future nonrefundable minimum annual royalty payments totaling $18.1 million related to 2019 and 2020 royalties. In June 2018, the Company received the 2019 non-refundable minimum royalty payment of $9.3 million (net of a $0.7 million early payment discount) and in March 2019, the Company received the 2020 payment of

$7.4 million (net of a $0.7 million early payment discount). During 2018, the Company and DSM amended the Value Sharing Agreement to (i) provide for the use of estimates in calculating quarterly royalty payments (subject to true-up), (ii) modify how the guaranteed minimum annual royalty payment for 2018 will be offset against value payments accruing during 2018 and (iii) accelerate the minimum annual royalty payment for 2019 from December 31, 2018 to June 30, 2018 in exchange for a fee of $750,000. For the year ended December 31, 2018, the Company recognized $7.9 million of revenue in connection with the DSM Value Sharing Agreement.

In April 2019, the Company assigned to DSM, and DSM assumed, all of the Company’s rights and obligations under the December 2017 DSM Value Sharing Agreement, as amended, for aggregate consideration to the Company of $57.0 million, which included $7.4 million received on March 29, 2019 for the third and final annual royalty payment due under the original agreement. On April 16, 2019, the Company received net cash of $21.7 million, with the remaining $27.9 million used by the Company to offset past due trade payables (including interest) under the 2017 Supply Agreement (discussed below), the obligation under the November 2018 Securities Purchase Agreement, and manufacturing capacity fees under the provisions of Amendment No. 1 to the 2017 Supply Agreement (see Note 10, "Related Party Transactions" for a description of these agreements).

The original Value Sharing Agreement was accounted for as a single performance obligation in connection with a license with fixed and determinable consideration and variable consideration that was accounted for pursuant to the sales-based royalty scope exception. The April 16, 2019 assignment of the December 2017 DSM Value Sharing Agreement was accounted for as a contract modification under ASC 606, resulting in additional fixed and determinable consideration of $37.1 million and variable consideration of $12.5 million in the form of a stand-ready obligation to refund some or all of the $12.5 million consideration if certain criteria outlined in the assignment agreement are not met by December 2021. The Company periodically updates its estimate of amounts to be retained and reduces the refund liability and records additional license and royalty revenue as the criteria are met. The effect of the contract modification on the transaction price, and on the Company’s measure of progress toward complete satisfaction of the performance obligation was recognized as an adjustment to revenue at the date of the contract modification on a cumulative catch-up basis. As a result, the Company recognized $37.1 million of license and royalty in the second quarter of 2019, due to fully satisfying the performance obligation at the modification date.The Company also recognized an additional $3.6 million of previously deferred royalty revenue under the December 2017 DSM Value Sharing Agreement, as the remaining underlying performance obligation was fully satisfied through the April 16, 2019 assignment of the agreement to DSM. The Company recorded an additional $8.8 million of license and royalty revenue in the fourth quarter of 2019 related to a change in the estimated refund liability.

DSM Performance Agreement

In December 2017, in connection with the Company's divestiture of its Brotas, Brazil production facility (see Note 12, "Divestiture"), the Company and DSM entered into a performance agreement (Performance Agreement), pursuant to which the Company will provide certain research and development services to DSM relating to the development of the technology underlying the farnesene-related products to be manufactured at the Brotas facility in exchange for related funding, including certain bonus payments in the event that specific performance metrics are achieved. The Company will record the bonus payments as earned revenue upon the transfer of the developed technology to DSM. If the Company does not meet the established metrics under the Performance Agreement, the Company will be required to pay $1.8 million to DSM. The Performance Agreement will expire in December 2020, subject to the right of each of the parties to terminate for uncured material breach by the other party or in the event the other party is subject to bankruptcy proceedings, liquidation, dissolution or similar proceedings or other specified events.

DSM December 2017 Supply Agreement and November 2018 Supply Agreement Amendment

On November 19, 2018, the Company and DSM entered into an amendment (Supply Agreement Amendment) to the supply agreement, dated December 28, 2017 (Supply Agreement), by and between the Company and DSM. Under the Supply Agreement, DSM agreed to manufacture and supply to the Company certain products useful in the Company’s business, at prices and on production and delivery terms and specifications set forth in the Supply Agreement, which prices are based upon DSM’s manufacturing cost plus an agreed margin. The Supply Agreement originally provided that it would expire (i) with respect to non-farnesene related products, on the date that the Company’s planned new specialty ingredients manufacturing facility in Brazil is fully operational and meets its production targets, but in any event no later than December 31, 2021 and (ii) with respect to farnesene related products, on December 28, 2037, subject in each case to earlier termination in certain circumstances. Pursuant to the Supply Agreement Amendment, (i) the outside expiration date of the Supply Agreement with respect to non-farnesene related products was extended to December 31, 2022, with specified pricing terms added for products manufactured during 2022, (ii) DSM committed to produce certain non-farnesene related products for the Company for two months of each calendar year during the term of the Supply Agreement and (iii) the Company agreed to (A) pay DSM a cash

fee totaling $15.5 million, payable in installments during 2018 and 2019, (B) issue 1,643,991 shares of the Company's common stock to DSM, and (C) pay DSM a cash fee of $7.3 million, payable on or before March 29, 2019, plus, if the closing price of the Common Stock on the trading day immediately preceding the date of such payment is less than $4.41 per share, an amount equal to such deficiency multiplied by 1,643,991.

In addition, on April 16, 2019 the Company and DSM entered into amendments to the 2017 Supply Agreement and the 2017 Performance Agreement, as well as the Quota Purchase Agreement relating to the December 2017 sale of Amyris Brasil to DSM (see Note 12, “Divestiture”), pursuant to which (i) DSM agreed to reduce certain manufacturing costs and fees paid by the Company related to the production of farnesene under the Supply Agreement through 2021, as well as remove the priority of certain customers over the Company with respect to production capacity at the Brotas, Brazil facility, (ii) the Company agreed to provide DSM rights to conduct certain process and downstream recovery improvements under the Performance Agreement at facilities other than the Brotas, Brazil facility in exchange for DSM providing the Company with a license to such improvements and (iii) the Company released DSM from its obligation to provide manufacturing and support services under the Quota Purchase Agreement in connection with the Company’s planned new manufacturing facility, which is no longer to be located at the Brotas, Brazil location.

DARPA Technology Investment Agreement

In September 2015, the Company entered into a technology investment agreement (TIA) with The Defense Advanced Research Projects Agency (DARPA), under which the Company, with the assistance of specialized subcontractors, is working to create new research and development tools and technologies for strain engineering and scale-up activities. The agreement is being funded by DARPA on a milestone basis. Under the TIA, the Company and its subcontractors could collectively receive DARPA funding of up to $35.0 million over the program’s four year term if all of the program’s milestones are achieved. In conjunction with DARPA’s funding, the Company and its subcontractors are obligated to collectively contribute approximately $15.5 million toward the program over its four year term (primarily by providing specified labor and/or purchasing certain equipment). For the DARPA agreement, the Company recognizes revenue using an output-based measure of progress of the milestones completed relative to remaining milestones, once acknowledged by DARPA.

Contract Assets and Liabilities

When a contract results in revenue being recognized in excess of the amount the Company has invoiced or has the right to invoice to the customer, a contract asset is recognized. Contract assets are transferred to accounts receivable, net when the rights to the consideration become unconditional.

Contract liabilities consist of payments received from customers, or such consideration that is contractually due, in advance of providing the product or performing services such that control has not passed to the customer.

Trade receivables related to revenue from contracts with customers are included in accounts receivable on the consolidated balance sheets, net of the allowance for doubtful accounts. Trade receivables are recorded at the point of renewable product sale or in accordance with the contractual payment terms for licenses and royalties, and grants and collaborative research and development services for the amount payable by the customer to the Company for sale of goods or the performance of services, and for which the Company has the unconditional right to receive payment.

Contract Balances

The following table provides information about accounts receivable and contract liabilities from contracts with customers:

December 31, (In thousands)	2019		2018
Accounts receivable, net	$	16,322	$	16,003
Accounts receivable - related party, net	$	3,868	$	1,349
Accounts receivable, unbilled - related party	$	—	$	8,021
Contract assets	$	8,485	$	—
Contract assets, noncurrent - related party	$	1,203	$	1,203
Contract liabilities	$	1,353	$	8,236
Contract liabilities, noncurrent(1)	$	1,449	$	1,587

______________

⁽¹⁾The balances in contract liabilities, noncurrent are included in other noncurrent liabilities on the consolidated balance sheets.

Unbilled receivables relate to the Company’s right to consideration from DSM for (i) minimum future royalties and (ii) a material right arising from a customer option for a future transfer of technology. The Company’s right to cash receipt for these minimum royalty amounts occurs on or before December 31, 2019, and the right to cash receipt for the customer option occurs on or before December 31, 2020.

Contract liabilities, current decreased by $6.9 million at December 31, 2019 resulting from collaboration and royalty amounts recognized as revenue during the year ended December 31, 2019 that was included in contract liabilities at the beginning of the period.

Remaining Performance Obligations

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of December 31, 2019.

(In thousands)	As of December 31, 2019
2020	$	56,719
2021	52,313
2022	30,483
2023 and thereafter	—
Total from all customers	$	139,515

In accordance with the disclosure provisions of ASC 606, the table above excludes estimated future revenues for performance obligations that are part of a contract that has an original expected duration of one year or less or a performance obligation with variable consideration that is recognized using the sales-based royalty exception for licenses of intellectual property. Additionally, $181.0 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

XML

Geographical Information - Long-lived Assets by Geography (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Segment Reporting Information [Line Items]
Long-lived assets	$ 28,930	$ 17,049
United States
Segment Reporting Information [Line Items]
Long-lived assets	13,799	10,404
Brazil
Segment Reporting Information [Line Items]
Long-lived assets	14,277	6,447
Europe
Segment Reporting Information [Line Items]
Long-lived assets	$ 854	$ 198

XML

Debt - Ginkgo Note, Partnership Agreement and Note Amendment (Details) - USD ($) $ in Millions			1 Months Ended
	Mar. 31, 2020	Dec. 15, 2019	Nov. 30, 2017	Nov. 30, 2019	Oct. 01, 2019	Sep. 29, 2019
Ginkgo Partnership Agreement
Debt Conversion [Line Items]
Debt instrument, face amount			$ 12.0
Debt instrument, fee			0.8
Debt Instrument, Total Amount			12.7
Contractual obligation, present value			6.1
Reduction in licenses and royalties revenue			13.1
Notes payable and other liabilities			$ 13.1
Interest rate per annum			10.50%
Notes payable			$ 7.0
Debt instrument, term			2 years
Debt Instrument, Renewal Terms			1 year
Ginkgo Partnership Agreement | Long-term Debt
Debt Conversion [Line Items]
Debt instrument, unamortized discount			$ 5.0
Ginkgo Partnership Agreement | Long Term Debt over Five Year Term
Debt Conversion [Line Items]
Debt instrument, unamortized discount			$ 6.6
Debt Discount, Term			5 years
Secured Promissory Note in Connection with Termination of Ginkgo Collaboration Agreement
Debt Conversion [Line Items]
Interest rate per annum					12.00%	10.50%
Debt instrument, cash waiver fee amount payable						$ 1.3
Debt instrument, periodic payment		$ 0.5	$ 0.5
Debt instrument				$ 5.2
Secured Promissory Note in Connection with Termination of Ginkgo Collaboration Agreement | Subsequent Event
Debt Conversion [Line Items]
Debt instrument, periodic payment	$ 0.8

XML

Stockholders' Deficit - Additional Information (Details)																									1 Months Ended						3 Months Ended	12 Months Ended
	Jan. 31, 2020 $ / shares shares	Jan. 14, 2020 USD ($) $ / shares shares	Nov. 14, 2019 USD ($) $ / shares shares	Oct. 28, 2019 USD ($) $ / shares shares	Oct. 24, 2019 $ / shares shares	Oct. 11, 2019 $ / shares shares	Sep. 10, 2019 USD ($) $ / shares shares	Aug. 28, 2019 USD ($) $ / shares shares	Aug. 14, 2019 USD ($) $ / shares shares	Jul. 24, 2019 USD ($) $ / shares	Jul. 08, 2019 USD ($) $ / shares shares	Jun. 24, 2019 USD ($) $ / shares shares	May 15, 2019 USD ($) $ / shares shares	May 14, 2019 USD ($) $ / shares shares	May 10, 2019 USD ($) $ / shares shares	May 03, 2019 USD ($) $ / shares shares	Apr. 29, 2019 USD ($) $ / shares shares	Apr. 26, 2019 USD ($) $ / shares shares	Apr. 16, 2019 USD ($) $ / shares shares	Mar. 29, 2019 USD ($)	Nov. 20, 2018 USD ($) $ / shares shares	Nov. 19, 2018 USD ($) shares	Aug. 07, 2017 USD ($) $ / shares shares	Aug. 03, 2017 USD ($) $ / shares shares	Jan. 31, 2020 USD ($) $ / shares shares	Nov. 30, 2019 USD ($) $ / shares shares	Oct. 31, 2019 USD ($)	Dec. 31, 2018 USD ($) $ / shares shares	Aug. 31, 2017	May 31, 2017 shares	Sep. 30, 2018 USD ($) shares	Dec. 31, 2019 USD ($) $ / shares shares	Dec. 31, 2018 USD ($) $ / shares shares	Jan. 13, 2020 shares	Nov. 15, 2019	Nov. 08, 2019 USD ($)	Oct. 10, 2019 $ / shares	Sep. 30, 2019 shares	Aug. 17, 2019 $ / shares	Jul. 26, 2019 USD ($)	Jul. 10, 2019 USD ($) $ / shares shares	Jul. 09, 2019 $ / shares	Mar. 28, 2019 USD ($) $ / shares	Jan. 01, 2019 USD ($)	Dec. 10, 2018 USD ($)	Dec. 06, 2018
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																						1,643,991
Issuance of Series A preferred stock for cash | $																																$ 14,221,000	$ 1,415,000
Warrants not settleable in cash, fair value disclosure | $																																$ 6,900,000
Additional Warrants Issued (in shares) | shares																																45,130,273
Issuance of common stock upon exercise of warrants (in shares) | shares																																(2,649,982)
Proceeds from exercise of warrants, net of issuance costs | $																																$ 1,000	$ 57,767,000
Derivative liabilities | $																																$ 41,000,000												$ 41,000,000
Stock price (in dollars per share)																												$ 3.34				$ 3.09	$ 3.34										$ 2.10
Preferred stock, shares outstanding, ending balance | shares																												14,656				8,280	14,656
Adjustments to adjustments additional paid in capital, other | $																															$ 6,800,000
Warrants and rights outstanding | $								$ 8,700,000
Preferred stock, beneficial ownership limitation							6.99%
Preferred stock (in dollars per share)																												$ 0.0001				$ 0.0001	$ 0.0001
Interest expense | $																																$ 58,665,000	$ 42,703,000
Fair value adjustment of debt | $										$ 900,000
Percent of composite trading volume																																10.00%
Debt instrument, fair value | $																												$ 149,300,000				$ 194,800,000	$ 149,300,000
Warrants exercised, net settled (in shares) | shares																																2,500,000
Common Stock
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																																3,610,944	205,168
Issuance of common stock upon exercise of warrants (in shares) | shares																																(2,515,174)	(20,891,038)
Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																									3.21
Stock price volatility | July Foris Credit Agreement
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																									1.24
Measurement Input, Risk Free Interest Rate | July Foris Credit Agreement
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																									0.0182
Measurement Input, Exercise Price | July Foris Credit Agreement
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																									2.87
Measurement Input, Expected Term | July Foris Credit Agreement
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																									0.9
Measurement Input, Expected Dividend Rate | July Foris Credit Agreement
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																									0
Series B Preferred Stock
Class of Stock [Line Items]
Preferred stock, shares outstanding, ending balance | shares					6,376.28
Series B Preferred Stock | Common Stock
Class of Stock [Line Items]
Conversion of series B preferred shares into common shares (in shares) | shares																																1,012,071
Series D Preferred Stock
Class of Stock [Line Items]
Preferred stock, stated value																								$ 1,000
Preferred stock, conversion price per share to common stock																								4.26
Preferred stock, shares outstanding, ending balance | shares																												8,280				8,280	8,280
Common stock, dividends, per share, declared																								$ 0.0001
Dividends, preferred stock, total | $																																$ 0
Preferred stock, beneficial ownership limitation																																9.99%
Convertible Preferred Stock
Class of Stock [Line Items]
Preferred stock, dividend rate					17.38%
Preferred stock (in dollars per share)					$ 0.0001
Preferred stock, beneficial ownership limitation, percent					4.99%
Preferred stock, percent of shares outstanding after conversion, maximum					9.99%
Common Stock
Class of Stock [Line Items]
Conversion of series B preferred shares into common shares (in shares) | shares					1,000,000.0
DSM Supply Agreement
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																						1,643,991,000,000
Issuance of Series A preferred stock for cash | $																				$ 7,300,000		$ 6,100,000
Shares issued (in dollars per share)																																											$ 4.41
Class of warrant or right, term																					181 days
Subsequent Event
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)	$ 2.87	$ 2.87																							$ 2.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	1,200,000																								1,200,000									4,877,386
Issuance of common stock upon exercise of warrants (in shares) | shares	(25,326,095)	(4,877,386)
Proceeds from exercise of warrants, net of issuance costs | $		$ 14,000,000.0
Debt conversion, converted instrument, amount | $																									$ 75,000,000.0
Subsequent Event | Foris Ventures, LLC
Class of Stock [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	10,200,000																								10,200,000
Subsequent Event | Common Stock
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares		7,500,000
DSM International B.V.
Class of Stock [Line Items]
Designated holder maximum common stock ownership																													33.00%
DSM International B.V. | Designated Director One
Class of Stock [Line Items]
Designated director, minimum beneficial ownership level																													4.50%
DSM International B.V. | Designated Director Two
Class of Stock [Line Items]
Designated director, minimum beneficial ownership level																							10.00%
DSM International B.V. | Series B Convertible Preferred Stock
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																$ 2.87
Issuance of common stock for cash (in shares) | shares																							25,000
Stock price (in dollars per share)																							$ 1,000
Proceeds from issuance of convertible preferred stock | $																							$ 25,900,000
Vivo Capital LLC
Class of Stock [Line Items]
Proceeds from issuance of common stock | $																	$ 4,500,000
Foris Ventures, LLC
Class of Stock [Line Items]
Proceeds from issuance of common stock | $																		$ 15,000,000.0
Non-affiliated Investors
Class of Stock [Line Items]
Proceeds from issuance of common stock | $																	1,300,000	8,200,000
Private Placement
Class of Stock [Line Items]
Proceeds from issuance of common stock | $																$ 5,000,000.0	$ 5,800,000	$ 23,200,000
Beneficial common stock ownership maximum percentage																19.99%
Private Placement | DSM
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																					1,643,991
Shares issued (in dollars per share)																					$ 3.68
Derivative liabilities | $																					$ 1,200,000											$ 1,800,000											$ 3,800,000
Gain (loss) from fair value adjustment in collaboration agreement | $																																600,000
Private Placement | Vivo Capital LLC
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																	900,000
Shares issued (in dollars per share)																	$ 4.76
Private Placement | Other Non-affiliated Investors
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																1,200,000	300,000	2,000,000.0
Shares issued (in dollars per share)																$ 4.02	$ 4.02	$ 4.02
Class of warrant or right, term																2 years
Private Placement | Foris Ventures, LLC
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																		2,800,000	6,700,000
Shares issued (in dollars per share)																		$ 5.12	$ 2.87
Proceeds from issuance of common stock | $																			$ 20,000,000.0
Securities Purchase Agreement | Vivo Capital LLC
Class of Stock [Line Items]
Proceeds from issuance of common stock | $																								$ 24,800,000
Securities Purchase Agreement | Vivo Capital LLC | Series D Convertible Preferred Stock
Class of Stock [Line Items]
Issuance of common stock for cash (in shares) | shares																								12,958
Stock price (in dollars per share)																								$ 1,000
Convertible Senior Notes, 6.0% Due in 2021
Class of Stock [Line Items]
Debt instrument, face amount | $																																													$ 60,000,000.0
Interest rate per annum																																													6.00%	6.00%
August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Debt conversion, original debt | $											$ 5,100,000
Debt conversion, converted instrument (in shares) | shares											1,800,000
Exercise price of warrants or rights (in dollars per share)											$ 2.87
Warrants not settleable in cash, fair value disclosure | $											$ 1,900,000
Shares issued (in dollars per share)											$ 3.30
Debt conversion, converted instrument, shares issued, value | $											$ 5,900,000
Class of warrant or right, term											2 years
Rule 144A Convertible Notes | Other Non-affiliated Investors
Class of Stock [Line Items]
Debt conversion, original debt | $														$ 5,000,000.0	$ 13,500,000
Debt conversion, converted instrument (in shares) | shares														1,100,000	3,500,000
Debt conversion, warrants issued | shares															1,400,000
Exercise price of warrants or rights (in dollars per share)															$ 5.02
Debt instrument, term															2 years
Rule 144A Convertible Notes | Foris Ventures, LLC
Class of Stock [Line Items]
Debt conversion, original debt | $														$ 5,000,000.0
Rule 144A Convertible Notes | Maxwell (Mauritius) Pte Ltd
Class of Stock [Line Items]
Debt conversion, original debt | $													$ 10,000,000.0
Debt conversion, converted instrument (in shares) | shares													2,500,000
Convertible Senior Notes, 6 Percent Due in 2021
Class of Stock [Line Items]
Debt conversion, original debt | $																												$ 60,000,000.0					$ 57,918,000
Interest expense | $												$ 4,400,000																$ 5,300,000
Debt instrument, face amount | $																																				$ 66,000,000.0
Debt conversion, converted instrument, amount | $																																15,000,000
Interest rate per annum																												6.00%					6.00%		6.00%	6.00%
The Naxyris Loan Agreement
Class of Stock [Line Items]
Debt instrument, face amount | $				$ 24,400,000					$ 10,400,000
Interest rate per annum									12.00%
August Foris Credit Agreement
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)								$ 3.90
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares								4,900,000						400,000				3,900,000
Warrants and rights outstanding | $								$ 5,200,000
Class of warrant or right, term								2 years
Beneficial common stock ownership maximum percentage								19.99%
Adjustments to additional paid-in capital warrant exercised | $								$ 1,100,000
Class of warrant or right, cashless exercise term								6 months
August Foris Credit Agreement | Foris Ventures, LLC
Class of Stock [Line Items]
Warrants and rights outstanding | $								$ 8,700,000
Debt instrument, unamortized discount | $								$ 6,800,000
Debt instrument, percent of face amount								100.00%
Warrants and rights outstanding, relative fair value | $								$ 5,200,000
Interest rate per annum								12.00%
August Foris Credit Agreement | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								3.67
August Foris Credit Agreement | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								0.94
August Foris Credit Agreement | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								0.0150
August Foris Credit Agreement | Measurement Input, Exercise Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								3.90
August Foris Credit Agreement | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								2.0						1.7
August Foris Credit Agreement | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								0
August Foris Credit Agreement | Minimum | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								0.98
August Foris Credit Agreement | Maximum | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input								1
Schottenfeld November 2019 Credit and Security Agreement
Class of Stock [Line Items]
Debt conversion, original debt | $			$ 400,000
Exercise price of warrants or rights (in dollars per share)			$ 3.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares			2,000,000.0
Debt instrument, term			2 years
Debt instrument, unamortized discount | $			$ 6,800,000
Debt conversion, converted instrument, amount | $			$ 50,000,000
Interest rate per annum			12.00%
Schottenfeld November 2019 Credit and Security Agreement | Maximum
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)			$ 3.90
Senior Convertible Notes Due 2022
Class of Stock [Line Items]
Debt conversion, original debt | $																																$ 10,000,000
Interest rate per annum										5.00%																						15.00%			5.00%
Senior Convertible Notes Due 2022 | Convertible Debt
Class of Stock [Line Items]
Debt conversion, original debt | $																																$ 10,000,000
Senior Convertible Notes Due 2022 | Minimum
Class of Stock [Line Items]
Debt instrument, percent of face amount																																110.00%
Senior Convertible Notes Due 2022 | Maximum
Class of Stock [Line Items]
Debt instrument, percent of face amount																																115.00%
Senior Convertible Notes Due 2022 | Subsequent Event | Convertible Debt
Class of Stock [Line Items]
Debt conversion, original debt | $		$ 10,000,000
Debt conversion, converted instrument (in shares) | shares		2,742,160
Debt instrument, term		18 months
Debt instrument, face amount | $		$ 51,000,000
Debt instrument, fair value | $		$ 4,200,000
Cost approach borrowing rate		9.75%
May 2017 Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																												$ 2.87					$ 2.87
Additional Warrants Issued (in shares) | shares																																	6,078,156
Class of warrant or right, term																														5 years
May 2017 Warrants, Warrant 1
Class of Stock [Line Items]
Additional Warrants Issued (in shares) | shares																														14,768,380
Class of warrant or right, dilution period																														3 years
May 2017 dilution warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																$ 0.0015
Additional Warrants Issued (in shares) | shares																																4,795,924
Issuance of common stock upon exercise of warrants (in shares) | shares																																(1,758,009)
Dilution Warrants
Class of Stock [Line Items]
Proceeds from exercise of warrants, net of issuance costs | $																																$ 0
Preferred stock effective conversion price																																$ 2.87
Class of warrant or right, exercises during the period | shares																																2,600,000
DSM Warrants | DSM International B.V.
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																							$ 6.30
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																							3,968,116
Class of warrant or right, term																							5 years
DSM Dilution Warrant | DSM International B.V.
Class of Stock [Line Items]
Preferred stock effective conversion price																							$ 2.87
Class of warrant or right, term																							5 years
August 2017 Vito Dilution Warrants
Class of Stock [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares																															(4,678)
Designated holder maximum common stock ownership																								33.00%
Minimum beneficial ownership level to designate a director																								4.50%
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Stock [Line Items]
Class of warrant or right, stock ownership percentage, restriction on ability to exercise													4.99%
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Foris Ventures, LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)								$ 3.90						$ 4.56
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors
Class of Stock [Line Items]
Warrants not settleable in cash, fair value disclosure | $													$ 5,900,000
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													0.96
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													0
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Minimum | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													4.27
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Minimum | Measurement Input, Strike Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													4.56
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Minimum | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													0.0220
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Maximum | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													4.54
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Maximum | Measurement Input, Strike Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													5.02
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Maximum | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input													0.0226
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Foris Ventures, LLC
Class of Stock [Line Items]
Debt conversion, converted instrument (in shares) | shares														1,100,000
Debt conversion, warrants issued | shares														400,000
Exercise price of warrants or rights (in dollars per share)								3.90						$ 4.56
Class of warrant or right, term														2 years
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Rule 144A Convertible Notes | Other Non-affiliated Investors
Class of Stock [Line Items]
Debt conversion, warrants issued | shares															1,400,000
Exercise price of warrants or rights (in dollars per share)															$ 5.02
Issuance of common stock for cash (in shares) | shares													7,100,000
Issuance of Series A preferred stock for cash | $													$ 30,800,000
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares													1,700,000
Warrants not settleable in cash, fair value disclosure | $													$ 3,800,000
Class of warrant or right, term															2 years
Class of warrant or right, cashless exercise term													6 months
Interest rate per annum													6.50%
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | August Foris Credit Agreement | Foris Ventures, LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)								3.90						$ 4.56
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares														400,000
Warrants Issued For August 2013 Convertible Notes | Wolverine | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input											3.33
Warrants Issued For August 2013 Convertible Notes | Wolverine | Measurement Input, Strike Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input											2.87
Warrants Issued For August 2013 Convertible Notes | Wolverine | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input											0.94
Warrants Issued For August 2013 Convertible Notes | Wolverine | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input											0.0188
Warrants Issued For August 2013 Convertible Notes | Wolverine | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input											0
Warrants Issued For August 2013 Convertible Notes | August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Debt conversion, warrants issued | shares											1,100,000
Warrants not settleable in cash, fair value disclosure | $											$ 1,900,000
Private Placement, April 16, 2019 | Foris Ventures, LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																			$ 2.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																			5,400,000
Class of warrant or right, term																			2 years
Private Placement, April 26, 2019 | Foris Ventures, LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)								3.90										$ 5.12
Private Placement, April 26, 2019 | Other Non-affiliated Investors
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																		$ 5.02
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																		1,600,000
Class of warrant or right, term																		2 years
Private Placement, April 26, 2019 | Foris Ventures, LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																		$ 5.12
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																		4,000,000.0
Class of warrant or right, term																		2 years
Private Placement, April 26, 2019 | August Foris Credit Agreement | Foris Ventures, LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)								$ 3.90										$ 5.12
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																		3,900,000
Private Placement April 29, 2019 | Vivo Capital LLC
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																	$ 4.76
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																	1,200,000
Class of warrant or right, term																	2 years
Private Placement April 29, 2019 | Other Non-affiliated Investors
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																	$ 5.02
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																	300,000
Class of warrant or right, term																	2 years
Private Placement May 3, 2019 | Other Non-affiliated Investors
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																$ 5.02
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																1,000,000.0
Class of warrant or right, term																6 months
Cash and Dilution Warrants and Temasek Funding Warrant
Class of Stock [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																																						8,100,000
July Foris Credit Agreement
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																							$ 7.52		$ 2.87	$ 7.52
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																																									4,900,000
Debt instrument, unamortized discount | $																																									$ 4,000,000.0
July Foris Credit Agreement | Foris Ventures, LLC
Class of Stock [Line Items]
Long-term line of credit | $																																								$ 8,000,000.0	16,000,000
Debt instrument, face amount | $																																									$ 8,000,000.0
Interest rate per annum																																									12.50%
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)												$ 5.12
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares												200,000	2,000,000.0
Class of warrant or right, term													2 years
Debt instrument, percent of face amount												4.99%
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												2.0
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												0
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Minimum | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												3.55
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Minimum | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												0.94
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Minimum | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												0.0172
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Maximum | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												4.39
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Maximum | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												0.96
Warrants Issued in Exchange for 6 Percent Convertible Notes Due 2021 | Maximum | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input												0.0216
Convertible Senior Notes, 6 Percent Due in 2021
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)										$ 2.87			$ 5.12
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares													2,000,000.0
Class of warrant or right, term													2 years
Convertible Senior Notes, 6 Percent Due in 2021 | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input										0.93
Convertible Senior Notes, 6 Percent Due in 2021 | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input										0.0186
Convertible Senior Notes, 6 Percent Due in 2021 | Measurement Input, Exercise Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input										2.87
Convertible Senior Notes, 6 Percent Due in 2021 | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input										1.8
Convertible Senior Notes, 6 Percent Due in 2021 | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input										0
Investors Warrants
Class of Stock [Line Items]
Warrants and rights outstanding | $							$ 7,900,000
Investors Warrants | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input							4.56
Investors Warrants | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input							0.0167
Investors Warrants | Measurement Input, Exercise Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input							3.90
Investors Warrants | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input							2
Investors Warrants | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input							0
Investors Warrants | Minimum | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input							0.94
Investors Warrants | Investor Credit Agreements
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)							$ 3.90
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares							3,200,000
Preferred stock, beneficial ownership limitation							9.99%
Class of warrant or right, term							2 years
Stock repurchase program, period in force							60 days
Warrants and rights outstanding, term							120 days
Warrants or rights outstanding, reduction in exercise price							10.00%
Warrants or rights outstanding, additional reduction in exercise price							5.00%
Warrant, failure of registration, period							90 days
Class of warrant or right, cashless exercise term							6 months
Investors Warrants | Investor Credit Agreements | Minimum
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)							$ 3.31
Investors Warrants | Investor Credit Agreements | Maximum
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)							3.90
Foris Loan And Security Amendment
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)						$ 2.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares						2,000,000.0
Class of warrant or right, term						2 years
Foris Loan And Security Amendment | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																					3.65
Adjustments to additional paid-in capital warrant exercised | $																											$ 4,100,000
Foris Loan And Security Amendment | Measurement Input, Strike Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																					2.87
Foris Loan And Security Amendment | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																					0.94
Foris Loan And Security Amendment | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																					0.0163
Foris Loan And Security Amendment | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																																					0
November 2019 Foris warrant
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																										$ 3.87						$ 3.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares																										1,000,000.0
Additional Warrants Issued (in shares) | shares																																1,000,000
Issuance of common stock upon exercise of warrants (in shares) | shares																																0
Class of warrant or right, term																										2 years
Beneficial common stock ownership maximum percentage						19.99%
Class of warrant or right, cashless exercise term																										6 months
November 2019 Foris warrant | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																										4.00
Adjustments to additional paid-in capital warrant exercised | $																										$ 2,100,000
November 2019 Foris warrant | Measurement Input, Strike Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																										3.87
November 2019 Foris warrant | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																										0.94
November 2019 Foris warrant | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																										0.0163
November 2019 Foris warrant | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input																										0
LSA Amendment Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares									1,400,000
Beneficial common stock ownership maximum percentage									19.99%
Adjustments to additional paid-in capital warrant exercised | $									$ 2,900,000
Class of warrant or right, cashless exercise term									6 months
LSA Amendment Warrants | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									3.59
LSA Amendment Warrants | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									0.94
LSA Amendment Warrants | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									0.0158
LSA Amendment Warrants | Measurement Input, Exercise Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									2.87
LSA Amendment Warrants | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									2.0
LSA Amendment Warrants | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									0
Naxyris LSA warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																$ 2.87
Additional Warrants Issued (in shares) | shares																																2,000,000
Issuance of common stock upon exercise of warrants (in shares) | shares																																0
Naxyris LSA warrants | The Naxyris Loan Agreement
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)									$ 2.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares									2,000,000.0
Warrants and rights outstanding | $									$ 4,000,000.0
Class of warrant or right, term									2 years
Warrants and rights outstanding, relative fair value | $									$ 3,000,000.0
Naxyris LSA warrants | The Naxyris Loan Agreement | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									3.59
Naxyris LSA warrants | The Naxyris Loan Agreement | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									0.94
Naxyris LSA warrants | The Naxyris Loan Agreement | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									0.0158
Naxyris LSA warrants | The Naxyris Loan Agreement | Measurement Input, Exercise Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									2.87
Naxyris LSA warrants | The Naxyris Loan Agreement | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									2.0
Naxyris LSA warrants | The Naxyris Loan Agreement | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input									0
October 2019 Naxyris warrant
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)				$ 3.87																												$ 3.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares				2,000,000.0
Additional Warrants Issued (in shares) | shares																																2,000,000
Issuance of common stock upon exercise of warrants (in shares) | shares																																0
Warrants and rights outstanding | $				$ 3,600,000
Class of warrant or right, term				2 years
Warrants and rights outstanding, relative fair value | $				$ 2,800,000
October 2019 Naxyris warrant | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input				3.69
October 2019 Naxyris warrant | Measurement Input, Strike Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input				3.87
October 2019 Naxyris warrant | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input				0.94
October 2019 Naxyris warrant | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input				0.0164
October 2019 Naxyris warrant | Measurement Input, Expected Term
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input				2.0
October 2019 Naxyris warrant | Measurement Input, Expected Dividend Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input				0
Schottenfeld November 2019 Credit and Security Agreement
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)							$ 3.87
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares							2,000,000.0
Warrants and rights outstanding | $			$ 4,000,000.0
Class of warrant or right, term							2 years
Schottenfeld November 2019 Credit and Security Agreement | Fair value of common stock on issue date
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input			3.89
Schottenfeld November 2019 Credit and Security Agreement | Measurement Input, Risk Free Interest Rate
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input			0.0158
Schottenfeld November 2019 Credit and Security Agreement | Measurement Input, Exercise Price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input			3.87
Schottenfeld November 2019 Credit and Security Agreement | Minimum | Stock price volatility
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input			0.95
Schottenfeld November 2019 Credit and Security Agreement | Investor Credit Agreements | Maximum
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)							$ 3.87
April 6th 2019 PIPE Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																$ 3.9
April 29 2021 PIPE Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																4.76
APril 2019 PIPE Warrants Due May 3 2021
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																5.02
September 2019 Investor Credit Agreement Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																3.87
November 2019 Investor Credit Agreement Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																3.9
May 2019 Note Exchange Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																2.87
June 2019 Note Exchange Warrants
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																5.12
May 2019 6.5% Note Exchange Warrants, Due May 2021
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																3.9
May 2019 6.5% Note Exchange Warrants, Due May 14, 2021
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																5.02
August 2018 Warrant Exercise Agreements, Due May 17, 2020
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																2.87
August 2018 Warrant Exercise Agreements, Due May 20, 2020
Class of Stock [Line Items]
Exercise price of warrants or rights (in dollars per share)																																$ 7.52

XML

Debt - Nikko Notes (Details)				1 Months Ended			6 Months Ended	12 Months Ended
	Mar. 12, 2020 USD ($)	Apr. 01, 2019 USD ($)	Feb. 01, 2019 USD ($)	Jan. 31, 2020 USD ($)	Feb. 28, 2017 USD ($)	Dec. 31, 2016 USD ($)	May 01, 2020 USD ($)	Dec. 31, 2019 USD ($) instrument	Feb. 28, 2020 USD ($)	Dec. 19, 2019	Nov. 30, 2019 USD ($)	Oct. 31, 2019 USD ($)	Jul. 29, 2019 USD ($)
Subsequent Event
Debt Conversion [Line Items]
Debt conversion, converted instrument, amount				$ 75,000,000.0
Repayments of debt	$ 500,000
Aprinnova JV | Nikko Notes
Debt Conversion [Line Items]
Debt instrument, face amount					$ 1,500,000			$ 1,300,000			$ 1,300,000	$ 1,300,000	$ 3,900,000
Debt conversion, converted instrument, amount						$ 3,500,000
Debt instrument, term			7 years			13 years
Interest rate per annum			5.00%			5.00%				2.75%
First priority lien on interests owned by the company						10.00%							10.00%
Repayments of debt					500,000,000
Debt instrument, periodic payment, principal					$ 4			$ 700,000,000
Debt instrument, number of promissory notes | instrument								3
Due from joint ventures			$ 200,000
Debt instrument, periodic payment		$ 7,200,000
Aprinnova JV | Nikko Notes | Subsequent Event
Debt Conversion [Line Items]
Debt instrument, face amount									$ 1,300,000
Debt instrument, periodic payment, principal							$ 100,000,000

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Debt - Schottenfeld September 2019 Credit Agreements (Details) - USD ($) $ / shares in Units, shares in Millions		12 Months Ended
	Sep. 10, 2019	Dec. 31, 2019	Aug. 14, 2019
Debt Conversion [Line Items]
Fair value adjustments of warrants		$ (4,800,000)
Schottenfeld September 2019 Credit Agreements
Debt Conversion [Line Items]
Debt instrument, face amount			$ 12,500,000
Debt instrument, percent of face amount	100.00%
Fair value of embedded derivative liability	$ 300,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	3.2
Exercise price of warrants or rights (in dollars per share)	$ 3.90
Fair value adjustments of warrants	$ 7,900,000
Interest rate per annum	12.00%
Class of warrant or right, term	2 years

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Debt - Foris LSA Amendments, Additional Loan and Warrant Issuance (Details) - USD ($) $ / shares in Units, shares in Millions					12 Months Ended
	Nov. 27, 2019	Oct. 10, 2019	Jul. 10, 2019	May 10, 2019	Dec. 31, 2019	Dec. 31, 2018	Oct. 11, 2019	Jul. 09, 2019	Jan. 01, 2019
Debt Conversion [Line Items]
Fair value adjustments of warrants					$ (4,800,000)
Loss upon extinguishment of debt					(44,208,000)	$ (17,424,000)
Debt instrument, fair value					194,800,000	149,300,000
Accretion of debt discount					11,665,000	$ 16,602,000
Derivative liabilities					41,000,000				$ 41,000,000
Foris LSA Amendments
Debt Conversion [Line Items]
Exercise price of warrants or rights (in dollars per share)	$ 3.87							$ 2.87
Debt instrument, term		2 years
Fair value adjustments of warrants	$ 2,100,000		$ 4,100,000
Foris Ventures, LLC
Debt Conversion [Line Items]
Derivative liabilities					$ 19,000,000
Foris LSA Amendments | Foris Ventures, LLC
Debt Conversion [Line Items]
Debt instrument, additional face amount	10,000,000.0	$ 10,000,000.0					$ 10,000,000.0
Debt instrument, face amount	$ 91,000,000.0	$ 81,000,000.0
Debt conversion, warrants issued	1.0			2.0
Fair value adjustments of warrants	$ 2,100,000
Loss upon extinguishment of debt	12,800,000
Debt instrument, unamortized discount	8,700,000
Debt instrument, fair value	4,100,000
Accretion of debt discount	3,500,000
Derivative liabilities	$ 1,400,000
Class of warrant or right, term	2 years

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Debt - Loss on Debt Extinguishment of 6% Convertible Notes Due 2021 (Details) - USD ($) $ in Thousands	1 Months Ended	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2019	Dec. 31, 2018
Extinguishment of Debt [Line Items]
Loss on debt extinguishment		$ (44,208)	$ (17,424)
Convertible Senior Notes, 6 Percent Due in 2021
Extinguishment of Debt [Line Items]
Debt conversion, original debt	$ 60,000		$ 57,918
Less: principal paid in cash during 2019		(13,395)
Less: principal converted to common stock during 2019		(15,000)
Loss on change in fair value during 2019		18,303
Accrued interest		3,168
Carrying value of registration rights liability		5,757
Net carrying value at extinguishment		56,751
Total reacquisition price		58,640
Loss on debt extinguishment		$ (1,889)

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Fair Value Measurement - Convertible Debt (Details) - Long-term Debt $ in Thousands	2 Months Ended
	Dec. 31, 2019 USD ($)
Servicing Liability at Fair Value, Amount [Roll Forward]
Fair value, beginning balance	$ 54,425
Less: Gain from change in fair value	3,801
Fair value, ending balance	$ 50,624

XML

Fair Value Measurement - Fair Value Measurement Inputs and Valuation Techniques (Details)	Dec. 31, 2019
Measurement Input, Expected Dividend Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000
Minimum | Fair value of common stock on issue date
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	3.09
Minimum | Stock price volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	94
Minimum | Measurement Input, Risk Free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	1.58
Maximum | Fair value of common stock on issue date
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	4.76
Maximum | Stock price volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	105
Maximum | Measurement Input, Risk Free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	1.67

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Balance Sheet Details - Right-of-use Assets and Related Lease Liabilities (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2019 USD ($)
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Cash paid for operating lease liabilities, in thousands	$ 17,809
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$ 33,264
Weighted-average remaining lease term	3 years 4 months 6 days
Weighted-average discount rate	18.10%
New finance lease	$ 7,700

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Balance Sheet Details - Inventories (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials	$ 3,255	$ 3,901
Work in process	7,204	539
Finished goods	17,311	5,253
Total inventories	$ 27,770	$ 9,693

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Balance Sheet Details - Other Noncurrent Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Liability for unrecognized tax benefit	$ 7,204	$ 6,582
Liability in connection with acquisition of equity-method investment	5,249	0
Ginkgo partnership payments obligation, net of current portion	4,492	6,185
Refund liability	3,750	0
Contract liabilities, net of current portion	1,449	1,587
Accrued Rent, Noncurrent	0	6,440
Contract termination fees, net of current portion	0	1,530
Long-term portion		195
Other	880	673
Total other noncurrent liabilities	$ 23,024	$ 23,192

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Net Loss Per Share Attributable to Common Stockholders - Antidilutive Securities Excluded From Computation of Earnings Per Share (Details) - shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Class of Stock [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	85,932,619	53,332,381
Period-end common stock warrants
Class of Stock [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	59,204,650	25,986,370
Convertible Promissory Notes
Class of Stock [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	13,381,238	13,703,162
Period-end stock options to purchase common stock
Class of Stock [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	5,620,419	5,392,269
Period-end restricted stock units
Class of Stock [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	5,782,651	5,294,848
Period-end preferred shares on an as-converted basis
Class of Stock [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,943,661	2,955,732

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Consolidated Statements of Stockholders' Deficit and Mezzanine Equity - USD ($) $ in Thousands	Total	Preferred Stock	Common Stock	Additional Paid-in Capital	AOCI Attributable to Parent	Retained Earnings	Noncontrolling Interest	Mezzanine Equity, Common Stock	Series D Preferred Stock	Series D Preferred Stock Additional Paid-in Capital	Series B Preferred Stock Preferred Stock	Series B Preferred Stock Common Stock
Beginning Balance (in shares) at Dec. 31, 2017		22,171	45,637,433
Beginning Balance at Dec. 31, 2017	$ (217,088)	$ 0	$ 5	$ 1,114,546	$ (42,156)	$ (1,290,420)	$ 937	$ 5,000
Issuance of common stock upon exercise of warrants (in shares)			20,891,038
Issuance of common stock upon exercise of warrants	62,154		$ 2	62,152
Settlement of derivatives liability upon exercise of warrants	108,670			108,670
Issuance of common stock in private placement, net of issuance costs of $0			205,168
Issuance of common stock in private placement, net of issuance costs of $0	1,415			1,415
Issuance of common stock in private placement - related party, net of issuance costs (in shares)			1,643,991
Issuance of common stock in private placement - related party, net of issuance costs	6,050			6,050
Issuance of common stock upon conversion of preferred stock (in shares)		(7,515)	1,548,480
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock									$ 6,852	$ 6,852
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock									$ (6,852)	$ (6,852)
Issuance of common stock upon conversion of debt (in shares)			5,674,926
Issuance of common stock upon conversion of debt	42,369		$ 1	42,368
Issuance of common stock for settlement of debt interest payments (in shares)			238,898
Issuance of common stock for settlement of debt interest payments	1,800			1,800
Issuance of common stock upon exercise of stock options (in shares)			70,807
Issuance of common stock upon exercise of stock options	288			288
Issuance of common stock upon ESPP purchase (in shares)			246,230
Issuance of common stock upon ESPP purchase	777			777
Issuance of common stock upon restricted stock settlement (in shares)			407,858
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	(260)			(260)
Stock-based compensation	9,190			9,190
Foreign currency translation adjustment	(1,187)				(1,187)
Net loss attributable to Amyris, Inc.	(230,235)				0	(230,235)
Ending Balance (in shares) at Dec. 31, 2018		14,656	76,564,829
Ending Balance at Dec. 31, 2018	$ (216,819)	$ 0	$ 8	1,346,996	(43,343)	(1,521,417)	937	5,000
Issuance of common stock upon exercise of warrants (in shares)	2,649,982		2,515,174
Issuance of common stock upon exercise of warrants	$ 1			1
Issuance of common stock in private placement, net of issuance costs of $0			3,610,944
Issuance of common stock in private placement, net of issuance costs of $0	14,221			14,221
Issuance of common stock in private placement - related party, net of issuance costs (in shares)			10,478,338
Issuance of common stock in private placement - related party, net of issuance costs	39,500		$ 1	39,499
Issuance and modification of common stock warrants	34,964			34,964
Deemed dividend to preferred shareholder on issuance and modification of common stock warrants	$ (34,964)			(34,964)
Issuance of common stock upon exercise of stock options (in shares)	7,445		3,612
Issuance of common stock upon exercise of stock options	$ 27			27
Issuance of common stock upon ESPP purchase (in shares)			318,490
Issuance of common stock upon ESPP purchase	1,078			1,078
Issuance of common stock upon restricted stock settlement (in shares)			1,631,582
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	(1,102)			(1,102)
Issuance of common stock and warrants upon conversion of debt principal and accrued interest (in shares)			14,107,637
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	62,861		$ 2	62,859
Issuance of warrants in connection with related party debt issuance	20,121			20,121
Issuance of warrants in connection with related party debt modification	4,932			4,932
Issuance of warrants in connection with debt accounted for at fair value	5,358			5,358
Stock-based compensation	12,554			12,554
Fair Value of pre-delivery shares issued to lenders (in shares)			7,500,000
Fair value of pre-delivery shares issued to lenders	4,215		$ 1	4,214
Fair value of bifurcated embedded conversion feature in connection with debt modification	398
Conversion of series B preferred shares into common shares (in shares)											(6,376)	1,012,071
Distribution to non-controlling interests	(328)						(328)
Foreign currency translation adjustment	(461)				(461)
Net loss attributable to Amyris, Inc.	(242,767)					(242,767)
Ending Balance (in shares) at Dec. 31, 2019		8,280	117,742,677
Ending Balance at Dec. 31, 2019	$ (255,168)	$ 0	$ 12	$ 1,543,668	$ (43,804)	$ (1,755,653)	$ 609	$ 5,000

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Debt - Long-term Debt Instruments (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Debt Instrument [Line Items]
2020	$ 113,875
2021	97,085
2022	128,995
2023	37,334
2024	398
Thereafter	1,870
Total future minimum payments	379,557
Less: amount representing interest	(82,095)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	297,462
Less: current portion of debt principal	(74,551)
Noncurrent portion of debt principal	222,911
Deferred discount and issuance costs	20,314	$ 17,142
Convertible Debt
Debt Instrument [Line Items]
2020	43,384
2021	40,177
2022	0
2023	0
2024	0
Thereafter	0
Total future minimum payments	83,561
Less: amount representing interest	(17,561)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	66,000
Less: current portion of debt principal	(31,800)
Noncurrent portion of debt principal	34,200
Deferred discount and issuance costs	0	3,350
Loans Payable and Credit Facilities
Debt Instrument [Line Items]
2020	26,324
2021	3,342
2022	15,177
2023	13,011
2024	398
Thereafter	1,870
Total future minimum payments	60,122
Less: amount representing interest	(11,626)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	48,496
Less: current portion of debt principal	(21,193)
Noncurrent portion of debt principal	27,303
Related Party Convertible Notes
Debt Instrument [Line Items]
2020	10,437
2021	0
2022	0
2023	0
2024	0
Thereafter	0
Total future minimum payments	10,437
Less: amount representing interest	(259)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	10,178
Less: current portion of debt principal	(10,178)
Noncurrent portion of debt principal	0
Deferred discount and issuance costs	0	$ 1,038
Related Party Loans Payable and Credit Facilities
Debt Instrument [Line Items]
2020	33,730
2021	53,566
2022	113,818
2023	24,323
2024	0
Thereafter	0
Total future minimum payments	225,437
Less: amount representing interest	(52,649)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	172,788
Less: current portion of debt principal	(11,380)
Noncurrent portion of debt principal	$ 161,408

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Debt Notes - Notes Conversion into Common Stock (Details) - USD ($) $ / shares in Units, $ in Thousands				3 Months Ended	12 Months Ended
	May 15, 2019	May 14, 2019	May 10, 2019	Dec. 31, 2019	Dec. 31, 2019	Dec. 31, 2018	Aug. 28, 2019
Debt Conversion [Line Items]
Loss upon extinguishment of debt					$ (44,208)	$ (17,424)
Warrants and rights outstanding							$ 8,700
Class of warrant or right, outstanding				65,755,629	65,755,629	26,891,512
Rule 144A Convertible Notes Converted to Common Stock
Debt Conversion [Line Items]
Debt conversion, original debt					$ 29,100
Debt conversion, converted instrument (in shares)					7,100,000
Debt conversion, converted instrument, amount					$ 30,800
Debt issuance costs				$ 400	400
Warrants Issued in Connection with Rule 144A Convertible Notes Conversion
Debt Conversion [Line Items]
Warrants and rights outstanding				$ 3,800	$ 3,800
Class of warrant or right, outstanding				1,700,000	1,700,000
Warrants Issued in Connection with Rule 144A Convertible Notes Conversion | Foris Ventures, LLC
Debt Conversion [Line Items]
Debt conversion, warrants issued		400,000
Exercise price of warrants or rights (in dollars per share)		$ 4.56					$ 3.90
Debt instrument, term		2 years
Rule 144A Convertible Notes
Debt Conversion [Line Items]
Loss upon extinguishment of debt				$ (5,900)
Other Non-affiliated Investors | Rule 144A Convertible Notes
Debt Conversion [Line Items]
Debt conversion, original debt		$ 5,000	$ 13,500
Debt conversion, converted instrument (in shares)		1,100,000	3,500,000
Debt conversion, warrants issued			1,400,000
Exercise price of warrants or rights (in dollars per share)			$ 5.02
Debt instrument, term			2 years
Maxwell (Mauritius) Pte Ltd | Rule 144A Convertible Notes
Debt Conversion [Line Items]
Debt conversion, original debt	$ 10,000
Debt conversion, converted instrument (in shares)	2,500,000

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Consolidated Balance Sheets (Parentheticals) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
Accounts receivable, allowance	$ 45	$ 642
Accounts receivable, related party, allowance	0	0
Debt, current portion — instruments measured at fair value	24,392	57,918
Long term debt, net of current portion — instruments measured at fair value	$ 26,232	$ 0
Preferred stock (in dollars per share)	$ 0.0001	$ 0.0001
Preferred Stock, Shares Authorized	5,000,000	5,000,000
Preferred Stock, Shares Issued	8,280	14,656
Preferred stock, shares outstanding	8,280	14,656
Common Stock, Par or Stated Value Per Share	$ 0.0001	$ 0.0001
Common Stock, Shares Authorized	250,000,000	250,000,000
Common stock issued (in shares)	117,742,677	76,564,829
Common Stock, Shares, Outstanding	117,742,677	76,564,829

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Revenue Recognition - Additional Information (Details) - USD ($)				1 Months Ended								3 Months Ended		12 Months Ended
	May 02, 2019	Apr. 16, 2019	Nov. 19, 2018	Apr. 30, 2019	Mar. 31, 2019	Sep. 30, 2018	Aug. 31, 2018	Jun. 30, 2018	Dec. 31, 2017	Jul. 31, 2017	Sep. 30, 2015	Dec. 31, 2019	Jun. 30, 2019	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Sep. 30, 2017
Disaggregation of Revenue [Line Items]
Revenue														$ 152,557,000	$ 63,604,000
Contract assets												$ 8,485,000		8,485,000	0
Issuance of common stock for cash (in shares)			1,643,991
Decrease in contract liabilities														6,872,000	(3,158,000)
Revenue, remaining performance obligation, constrained variable consideration												181,000,000.0		181,000,000.0
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue														54,043,000	7,658,000
Technology Investment Agreement with DARPA
Disaggregation of Revenue [Line Items]
Maximum DARPA funding to be received if all milestones are achieved											$ 35,000,000.0
Collective obligation due											$ 15,500,000
Collaboration agreement period											4 years
Lavvan | The Cannabinoid Agreement
Disaggregation of Revenue [Line Items]
Agreement amount	$ 300,000,000
Research and development funding that could be received	$ 300,000,000
Profit sharing to be received, period	20 years
Estimated total unconstrained transaction price	$ 145,000,000
Variable consideration related to milestones												181,000,000.0		181,000,000.0
Contract assets												8,300,000		8,300,000
Firmenich | Collaborative Arrangement | Flavors and Fragrances Compounds
Disaggregation of Revenue [Line Items]
Sales margin collaborator percentage split										70.00%
Firmenich | Master Collaboration Agreement | Flavors and Fragrances Compounds
Disaggregation of Revenue [Line Items]
Sales margin collaborator percentage split										70.00%
Return required for collaboration partner before adjusting split on sales margin										$ 15,000,000.0
Success bonus										$ 2,500,000
Supply agreement, renewable terms							10 years
Collaboration agreement, automatic renewal term							3 years
Contingent consideration liability												700,000		700,000
Givaudan International, SA | Collaborative Arrangement
Disaggregation of Revenue [Line Items]
Supply agreement, renewable terms						5 years
Collaboration agreement, automatic renewal term						1 year
DSM International B.V.
Disaggregation of Revenue [Line Items]
Consideration transferred				$ 57,000,000.0
Final annual royalty payment due under original agreement				7,400,000
Proceeds from Customers		$ 21,700,000
Offset of past due trade payables		$ 27,900,000
Cumulative catch-up adjustment to revenue												8,800,000	$ 37,100,000	37,100,000
Contract with customer, liability				$ 12,500,000								$ 12,500,000		12,500,000
Revenue recognized														3,600,000
Performance agreement, contingent obligation															$ 1,800,000
DSM International B.V. | License
Disaggregation of Revenue [Line Items]
Revenue																$ 54,600,000
Upfront license fee received									$ 27,500,000
DSM International B.V. | Collaborative Arrangement
Disaggregation of Revenue [Line Items]
Receivable from collaborators																	$ 9,000,000.0
DSM International B.V. | DSM November 2018 Letter Agreement
Disaggregation of Revenue [Line Items]
Common stock, value reserved for future issuance			$ 5,000,000.0
DSM International B.V. | DSM Value Sharing Agreement
Disaggregation of Revenue [Line Items]
Revenue														7,900,000
Receivable from collaborators									$ 33,100,000							33,100,000
Nonrefundable royalty payment received					$ 7,400,000			$ 9,300,000								15,000,000.0
Additional royalty payments received																$ 18,100,000
Royalty payment received, net of early payment discount					$ 700,000			$ 700,000
Agreement, accelerated payment fee														$ 750,000
DSM International B.V. | DSM November 2018 Supply Agreement Amendment
Disaggregation of Revenue [Line Items]
Cash reservation fee, payable			$ 15,500,000
Issuance of common stock for cash (in shares)			1,643,991
Cash fee			$ 7,300,000
Contingent fee, share price trigger (in dollars per share)			$ 4.41

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Stock-based Compensation - Employee Service Share-based Compensation, Allocation of Recognized Period Costs (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Compensating Balances [Line Items]
Share-based payment arrangement, expense	$ 12,554	$ 9,190
Research and Development Expense
Compensating Balances [Line Items]
Share-based payment arrangement, expense	2,900	1,797
Selling, General and Administrative Expenses
Compensating Balances [Line Items]
Share-based payment arrangement, expense	$ 9,654	$ 7,393

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Fair Value Measurement (Tables)

12 Months Ended

Dec. 31, 2019

Fair Value Disclosures [Abstract]

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis

As of December 31, 2019 and 2018, the Company’s financial liabilities measured and recorded at fair value on a recurring basis were classified within the fair value hierarchy as follows:

December 31, (In thousands)	2019								2018
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Senior Convertible Notes Due 2022	$	—	$	—	$	50,624	50,624		$	—	$	—	$	—	$	—
6% Convertible Notes Due 2021	—		—		—		—		—		—		57,918		57,918
Embedded derivatives bifurcated from debt instruments	—		—		2,832		2,832		—		—		—		—
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		6,971		6,971		—		—		42,796		42,796
Total liabilities measured and recorded at fair value	$	—	$	—	$	60,427	$	60,427	$	—	$	—	$	100,714	$	100,714

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation

For the year ended December 31, 2019, the Company recorded a $3.8 million gain from change in fair value of debt in connection with the initial issuance and subsequent fair value remeasurement of the Senior Convertible Notes Due 2022, as follows:

In thousands
Fair value at November 14, 2019	$	54,425
Less: Gain from change in fair value	(3,801)
Fair value at December 31, 2019	$	50,624

Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt and equity instruments – either freestanding or compound embedded – measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Equity-related Derivative Liability		Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2018	$	41,272	$	1,524	$	42,796
Derecognition upon adoption of ASU 2017-11	(39,513)		(1,524)		(41,037)
Fair value of derivative liabilities issued during the period	—		15,158		15,158
Change in fair value of derivative liabilities	2,039		(4,816)		(2,777)
Derecognition on extinguishment	(3,798)		(539)		(4,337)
Balance at December 31, 2019	$	—	$	9,803	$	9,803

Fair Value Measurement Inputs and Valuation Techniques

Input assumptions for these freestanding instruments are as follows:

Input assumptions for liability classified warrants:	Range
Fair value of common stock on issue date	$3.09 – $4.76
Expected volatility	94% - 105%
Risk-free interest rate	1.58% - 1.67%
Dividend yield	0.0	%

The market-based assumptions and estimates used in valuing the compound embedded and freestanding derivative liabilities include amounts in the following ranges/amounts:

December 31,	2019	2018
Risk-free interest rate	1.6% - 1.7%	2.5% - 3.0%
Risk-adjusted discount yield	20.0% - 27.0%	17.2% - 27.3%
Stock price volatility	45%	45.0% - 85.0%
Probability of change in control	5.0%	0.0%
Stock price	$3.09	$3.34
Credit spread	18.4% - 25.4%	14.6% - 24.9%
Estimated conversion dates	2022 - 2023	2019 - 2025

Fair Value of Consideration

The fair value of the consideration transferred to DSM under the combined arrangement totaled $33.3 million and was allocated as follows (in thousands):

Element	Fair Value Allocation
Manufacturing capacity reservation fee	$	24,395
Legal settlement and consent waiver	6,764
Working capital adjustment	2,145
Total fair value of consideration transferred	$	33,304

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Stock-based Compensation - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Number of Stock Options
Outstanding (in shares)	5,390,270
Grants in period, (in shares)	530,140	4,337,119
Exercised (in shares)	(7,445)
Forfeited or expired (in shares)	(292,546)
Outstanding (in shares)	5,620,419	5,390,270
Vested or expected to vest (in shares)	5,037,260
Exercisable shares (in shares)	1,314,113
Weighted- average Exercise Price
Outstanding, weighted average exercise price (in dollars per share)	$ 11.55
Weighted average exercise price (in dollars per share)	3.83
Weighted average exercise price, exercises in period (in dollars per share)	3.60
Weighted average exercise price, forfeitures in period (in dollars per share)	17.18
Outstanding, weighted average exercise price (in dollars per share)	10.27	$ 11.55
Weighted average exercise price, vested and expected to vest (in dollars per share)	10.88
Weighted average exercise price, exercisable (in dollars per share)	$ 27.46
Weighted average remaining contractual term	7 years 9 months 18 days	8 years 6 months
Weighted average remaining contractual term, vested and expected to vest	7 years 8 months 12 days
Weighted average remaining contractual term, exercisable	6 years 1 month 6 days
Options, outstanding, intrinsic value	$ 24	$ 29
Aggregate intrinsic value, vested and expected to vest	23
Intrinsic value, exercisable	$ 10

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Stock-based Compensation

12 Months Ended

Dec. 31, 2019

Compensation Related Costs [Abstract]

Share-based Compensation

Stock-based Compensation

Stock-based Compensation Expense Related to All Plans

Stock-based compensation expense related to all employee stock compensation plans, including options, restricted stock units and ESPP, was as follows:

Years Ended December 31, (In thousands)	2019		2018
Research and development	$	2,900	$	1,797
Sales, general and administrative	9,654		7,393
Total stock-based compensation expense	$	12,554	$	9,190

Plans

2010 Equity Incentive Plan

The Company's 2010 Equity Incentive Plan (2010 Equity Plan) became effective on September 27, 2010 and will terminate in 2020. The 2010 Equity Plan provides for the granting of common stock options, restricted stock awards, stock bonuses, stock appreciation rights, restricted stock units (RSUs) and performance awards. It allows for time-based or performance-based vesting for the awards. Options granted under the 2010 Equity Plan may be either incentive stock options (ISOs) or non-statutory stock options (NSOs). ISOs may be granted only to Company employees (including officers and directors who are also employees). NSOs may be granted to Company employees, non-employee directors and consultants. The Company will be able to issue no more than 2,000,000 shares pursuant to the grant of ISOs under the 2010 Equity Plan. Options under the 2010 Equity Plan may be granted for periods of up to ten years. All options issued to date have had a ten-year life. Under the plan, the exercise price of any ISOs and NSOs may not be less than 100% of the fair market value of the shares on the date of grant. The exercise price of any ISOs and NSOs granted to a 10% stockholder may not be less than 110% of the fair value of the underlying stock on the date of grant. The options and RSUs granted to-date generally vest over three to five years.

As of December 31, 2019 and 2018, options were outstanding to purchase 5,589,315 and 5,339,214 shares, respectively, of the Company's common stock granted under the 2010 Equity Plan, with weighted-average exercise prices per share of $8.89 and $9.62, respectively. In addition, as of December 31, 2019 and 2018, restricted stock units representing the right to receive 5,782,651 and 5,294,803 shares, respectively, of the Company's common stock granted under the 2010 Equity Plan were

outstanding. As of December 31, 2019 and 2018, 3,815,625 and 2,359,750 shares, respectively, of the Company’s common stock remained available for future awards that may be granted under the 2010 Equity Plan.

The number of shares reserved for issuance under the 2010 Equity Plan increases automatically on January 1 of each year starting with January 1, 2011, by a number of shares equal to 5% of the Company’s total outstanding shares as of the immediately preceding December 31. However, the Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors retains the discretion to reduce the amount of the increase in any particular year.

In May 2018, shareholders approved amendments to the 2010 Equity Plan to (i) increase the number of shares of common stock available for grant and issuance thereunder by 9.0 million shares and (ii) increase the annual per-participant award limit thereunder to 4.0 million shares. Subsequent to the amendments, the total number of shares available for grant was 9,280,000, not including the annual evergreen increases.

2005 Stock Option/Stock Issuance Plan

In 2005, the Company established its 2005 Stock Option/Stock Issuance Plan (2005 Plan) which provided for the granting of common stock options, restricted stock units, restricted stock and stock purchase rights awards to employees and consultants of the Company. The 2005 Plan allowed for time-based or performance-based vesting for the awards. Options granted under the 2005 Plan were ISOs or NSOs. ISOs were granted only to Company employees (including officers and directors who are also employees). NSOs were granted to Company employees, non-employee directors, and consultants.

All options issued under the 2005 Plan had a ten-year life. The exercise prices of ISOs and NSOs granted under the 2005 Plan were not less than 100% of the estimated fair value of the shares on the date of grant, as determined by the Board of Directors. The exercise price of an ISO and NSO granted to a 10% stockholder could not be less than 110% of the estimated fair value of the underlying stock on the date of grant as determined by the Board. The options generally vested over 5 years.

As of December 31, 2019 and 2018, options to purchase 31,104 and 52,389 shares, respectively, of the Company’s common stock granted under the 2005 Plan remained outstanding, and as a result of the adoption of the 2010 Equity Plan discussed above, zero shares of the Company’s common stock remained available for future awards issuance under the 2005 Plan. The options outstanding under the 2005 Plan as of December 31, 2019 and 2018 had a weighted-average exercise price per share of $259.19 and $185.93, respectively.

2010 Employee Stock Purchase Plan

The 2010 Employee Stock Purchase Plan (2010 ESPP) became effective on September 27, 2010. The 2010 ESPP is designed to enable eligible employees to purchase shares of the Company’s common stock at a discount. Offering periods under the 2010 ESPP generally commence on each May 16 and November 16, with each offering period lasting for one year and consisting of two six-month purchase periods. The purchase price for shares of common stock under the 2010 ESPP is the lesser of 85% of the fair market value of the Company’s common stock on the first day of the applicable offering period or the last day of each purchase period. During the life of the 2010 ESPP, the number of shares reserved for issuance increases automatically on January 1 of each year, starting with January 1, 2011, by a number of shares equal to 1% of the Company’s total outstanding shares as of the immediately preceding December 31. However, the Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors retains the discretion to reduce the amount of the increase in any particular year. In May 2018, shareholders approved an amendment to the 2010 ESPP to increase the maximum number of shares of common stock that may be issued over the term of the ESPP by 1 million shares. No more than 1,666,666 shares of the Company’s common stock may be issued under the 2010 ESPP and no other shares may be added to this plan without the approval of the Company’s stockholders.

2018 CEO Performance-based Stock Options

In May 2018, the Company granted its chief executive officer performance-based stock options (PSOs) to purchase 3,250,000 shares. PSOs are equity awards with the final number of PSOs that may vest determined based on the Company’s performance against pre-established EBITDA milestones and Amyris stock price milestones. The EBITDA milestones are measured from the grant date through December 31, 2021, and the stock price milestones are measured from the grant date through December 31, 2022. The PSOs vest in four tranches contingent upon the achievement of both the EBITDA milestones and stock price milestones for each respective tranche, and the chief executive officer’s continued employment with the Company. Over the measurement periods, the number of PSOs that may be issued and the related stock-based compensation expense that is recognized is adjusted upward or downward based upon the probability of achieving the EBITDA milestones.

Depending on the probability of achieving the EBITDA milestones and stock price milestones and certification of achievement of those milestones for each vesting tranche by the Company’s Board of Directors or Compensation Committee, the PSOs issued could be from zero to 3,250,000 stock options, with an exercise price of $5.08 per share.

Stock-based compensation expense for this award is recognized using a graded-vesting approach over the service period beginning at the grant date through December 31, 2022, as the Company’s management has determined that certain EBITDA milestones are probable of achievement over the next four years as of December 31, 2019, The Company utilized a Monte Carlo simulation to estimate the grant date fair value of each tranche of the award which totaled $5.1 million. For the years ended December 31, 2019 and 2018, the Company recognized $0 and $0.7 million, respectively, of compensation expense for this award. The assumptions used to estimate the fair value of this award with performance and market vesting conditions were as follows:

Stock Option Award with Performance and Market Vesting Conditions:
Fair value of the Company’s common stock on grant date	$	5.08
Expected volatility	70		%
Risk-free interest rate	2.75		%
Dividend yield	0.0		%

Stock Option Activity

Stock option activity is summarized as follows:

Year ended December 31,	2019		2018
Options granted	530,140		4,337,119
Weighted-average grant-date fair value per share	$	3.83	$	5.18
Compensation expense related to stock options (in millions)	$	2.0	$	2.6
Unrecognized compensation costs as of December 31 (in millions)	$	4.5	$	8.5

The Company expects to recognize the December 31, 2019 balance of unrecognized costs over a weighted-average period of 3.8 years. Future option grants will increase the amount of compensation expense to be recorded in these periods.

Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes-Merton option pricing model. The fair value of employee stock options is amortized on a ratable basis over the requisite service period of the awards. The fair value of employee stock options and employee stock purchase plan rights was estimated using the following weighted-average assumptions:

Years Ended December 31,	2019	2018
Expected dividend yield	—%	—%
Risk-free interest rate	1.8%	2.8%
Expected term (in years)	6.9	6.9
Expected volatility	84%	80%

The expected life of options is based primarily on historical share option exercise experience of the employees for options granted by the Company. All options are treated as a single group in the determination of expected life, as the Company does not currently expect substantially different exercise or post-vesting termination behavior among the employee population. The risk-free interest rate is based on the U.S. Treasury yield for a term consistent with the expected life of the awards in effect at the time of grant. Expected volatility is based on the historical volatility of the Company's common stock. The Company has no history or expectation of paying dividends on common stock.

Stock-based compensation expense associated with options is based on awards ultimately expected to vest. At the time of an option grant, the Company estimates the expected future rate of forfeitures based on historical experience. These estimates are revised, if necessary, in subsequent periods if actual forfeiture rates differ from those estimates. If the actual forfeiture rate

is lower than estimated the Company will record additional expense and if the actual forfeiture is higher than estimated the Company will record a recovery of prior expense.

The Company’s stock option activity and related information for the year ended December 31, 2019 was as follows:

	Number of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding - December 31, 2018	5,390,270	$	11.55	8.5	$	29
Options granted	530,140	$	3.83
Options exercised	(7,445)	$	3.60
Options forfeited or expired	(292,546)	$	17.18
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Vested or expected to vest after December 31, 2019	5,037,260	$	10.88	7.7	$	23
Exercisable at December 31, 2019	1,314,113	$	27.46	6.1	$	10

The aggregate intrinsic value of options exercised under all option plans was $0 and $0.2 million for the years ended December 31, 2019 and 2018, respectively, determined as of the date of option exercise.

Restricted Stock Units Activity and Expense

During the years ended December 31, 2019 and 2018, 2,996,660 and 5,452,664 RSUs, respectively, were granted with weighted-average service-inception date fair value per unit of $3.96 and $5.36, respectively. The Company recognized RSU-related stock-based compensation expense of $10.2 million and $6.4 million, respectively, for the years ended December 31, 2019 and 2018. As of December 31, 2019 and 2018, unrecognized RSU-related compensation costs totaled $22.3 million and $23.8 million, respectively.

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant.

The Company’s RSU and restricted stock activity and related information for the year ended December 31, 2019 was as follows:

	Number of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life (in years)
Outstanding - December 31, 2018	5,294,803	$	5.50	1.4
Awarded	2,996,660	$	3.96
Vested	(1,891,931)	$	5.51
Forfeited	(616,881)	$	4.84
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Vested or expected to vest after December 31, 2019	5,338,558	$	4.78	1.6

ESPP Activity and Expense

During the years ended December 31, 2019 and 2018, 318,490 and 246,230 shares, respectively, of the Company's common stock were purchased under the 2010 ESPP. At December 31, 2019 and 2018, 263,797 and 199,463 shares, respectively, of the Company’s common stock remained reserved for issuance under the 2010 ESPP.

During the years ended December 31, 2019 and 2018, the Company also recognized ESPP-related stock-based compensation expense of $0.4 million and $0.2 million, respectively.

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Income Taxes - Components of Benefit (Provision) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Current:
Federal	$ 621	$ 0
State	0	0
Foreign	8	0
Total current provision	629	0
Deferred:
Federal	0	0
State	0	0
Foreign	0	0
Total deferred benefit	0	0
Total provision for income taxes	$ 629	$ 0

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Subsequent Events

12 Months Ended

Dec. 31, 2019

Subsequent Events [Abstract]

Subsequent Events

Subsequent Events

Warrants Exercises for Cash

On January 13, 2020 Foris Ventures, LLC (Foris), an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock, delivered to the Company an irrevocable notice of cash exercise with respect to a warrant to purchase 4,877,386 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to a warrant issued by the Company on August 17, 2018. On January 14, 2020, the Company received approximately $14.0 million from Foris in connection with the warrant exercise representing 4,877,386 shares of common stock.

On March 11, 2020 Foris provided to the Company a notice of cash exercise to purchase 5,226,481 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to the PIPE Rights (discussed in the January 2020 Private Placement section below) issued by the Company on January 31, 2020. On March 12, 2020, the Company received approximately $15.0 million from Foris in connection with the PIPE Rights exercise.

Exchange of Senior Convertible Notes Due 2022

On January 14, 2020, the Company completed the exchange, pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), of the Company’s Senior Convertible Notes Due 2022 (or the Prior Notes) for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes due 2022), (ii) an aggregate of 2,742,160 shares of Common Stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of Common Stock, (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of Common Stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, (v) accrued and unpaid interest on the Senior Convertible Notes Due 2022 (payable on or prior to January 31, 2020) and (vi) cash fees in an aggregate amount of $1.0 million (payable on or prior to January 31, 2020).

The New Notes have substantially similar terms as the Prior Notes, except that (i) the Company would not be required to redeem the New Notes in an aggregate principal amount of $10 million on December 31, 2019, (ii) the Company would only be required to redeem the New Notes in an aggregate amount of $10 million following the receipt by the Company of at least $80 million of aggregate net cash proceeds from one or more financing transactions, and at a price of 107% of the amount being redeemed, (iii) the financing activity requirement was reduced such that the Company would only be required to raise aggregate net cash proceeds of $50 million from one or more financing transactions by January 31, 2020, (iv) the Company would have until January 31, 2020 to comply with certain covenants related to the repayment, conversion or exchange into equity or amendment of certain outstanding indebtedness of the Company, and (v) the deadline for the Company to seek the Stockholder Approval would be extended from January 31, 2020 to March 15, 2020.

On February 18, 2020, the Company and the Holders entered into separate waiver and forbearance agreements, (the W&F Agreements), pursuant to which the Holders agreed to, for 60 days following the date of the W&F Agreement, except in case of early termination of the W&F Agreement or, solely with respect to the Stockholder Approval if the other defaults described below have been cured on or prior to the date that is 60 days following the date of the W&F Agreement, until May 31, 2020 (the W&F Period), and in each case subject to certain conditions to effectiveness contained in the W&F Agreement, (i) forbear from exercising certain of their rights and remedies with respect to certain defaults by the Company, including, but not limited to, the Company's failure, on or before January 31, 2020, (A) to receive aggregated net cash proceeds of not less than $50 million from one or more financing transactions, (B) to repay in full or convert into equity all indebtedness outstanding under the Schottenfeld September Credit Agreement and the Schottenfeld November Credit and Security Agreement or amend all such indebtedness outstanding to fit within the definition of permitted indebtedness of the New Notes, and certain other events of default, and (ii) waive any event of default for (A) violations of the minimum liquidity covenant since December 31, 2019 and (B) failure to obtain the Stockholder Approval prior to March 15, 2020.

In addition, pursuant to the W&F Agreements, the Company and the Holders agreed that (i) the New Note amortization payment due on March 1, 2020 (the Amortization Payment) shall be in the aggregate amount of $10.0 million (split proportionally among the Holders) and that the Company shall elect to pay such amortization payment in shares of Common Stock in accordance with the terms of the New Note, provided however, that: (A) the Amortization Stock Payment Price (as defined in the New Note) shall be $3.00, (B) the Amortization Share Payment Period (as defined in the New Note) with respect to the Amortization Payment will end on April 30, 2020 rather than March 31, 2020; and (C) in the event that Holder does not elect to receive the full Amortization Share Amount (as defined in the New Note) during such Amortization Share Payment Period, then the Amortization Payment shall be automatically reduced by the portion of such Amortization Payment not received by the Holder, (ii) there shall be no amortization payment due on April 1, 2020, and (iii) the amortization payment due on May 1, 2020 shall be in the aggregate amount of $8.9 million (split proportionally among the Holders).

On February 24, 2020, a Holder of the Rights notified the Company about the exercise of the Rights for the issuance of an aggregate of 2,484,321 shares of common stock, which were issued by the Company according to the terms of the Senior Convertible Notes Due 2022.

January 2020 Warrant Amendments and Exercises, Debt Equitization and PIPE

As described below in further detail, on January 31, 2020, the Company completed a series of transactions that resulted in the Company (i) receiving $28.3 million in cash, (ii) reducing its aggregate debt principal by $60.0 million and accrued interest by approximately $10.0 million, (iii) issuing an aggregate of (A) 25,326,095 shares of common stock as a result of the exercise of outstanding warrants, and (B) 13,989,973 new shares of common stock in private placements, and (iv) issuing rights to purchase an aggregate of 18,649,961 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months.

Warrant Amendments

On January 31, 2020, the Company entered into separate warrant amendment agreements (the Warrant Amendments) with Foris and certain other holders (the Warrant Holders) of the Company’s outstanding warrants to purchase shares of the Company’s common stock, pursuant to which the exercise price of certain warrants (the Amended Warrants) held by the Warrant Holders totaling 1.2 million shares and Foris totaling 10.2 million shares was reduced to $2.87 per share upon the exercise of the Amended Warrant.

Warrant Exercises by Certain Holders

In connection with the entry into the Warrant Amendments, on January 31, 2020 the Warrant Holders delivered to the Company irrevocable notices of cash exercise with respect to their Amended Warrants, representing an aggregate of 1,160,929 shares of Common Stock (the Warrant Amendment Shares), and the Company issued to the Holders rights to purchase an aggregate of 1,160,929 shares of Common Stock, at an exercise price of $2.87 per share, for an exercise term of twelve months

from the January 31, 2020 issuance (the Rights). The Company received net proceeds of $3.3 million from the exercise of the Amended Warrants and issued to the Holders the Warrant Amendment Shares.

Warrant Exercise, Common Stock Purchase and Debt Equitization by Foris – Related Party

On January 31, 2020, the Company and Foris entered into a warrant exercise agreement (the Exercise Agreement) pursuant to which (i) Foris (A) exercised all of its then outstanding common stock purchase warrants (the Foris Warrants), totaling 19,287,780 shares of Common Stock (the Foris Warrant Shares), at a weighted average exercise price of approximately $2.84 per share (following the Warrant Amendments noted above) for an aggregate exercise price of $54.8 million (the Exercise Price), and (B) purchased 5,279,171 shares of Common Stock (the Foris Shares), at $2.87 per share for a total purchase price of $15.2 million (Purchase Price), (ii) Foris paid the Exercise Price and the Purchase Price through the cancellation of $70 million of principal and accrued interest owed by the Company to Foris under the Foris $19 million Note and the Foris LSA (as discussed in Note 4, "Debt") and (iii) the Company issued to Foris the Foris Shares and an additional right to purchase 8,778,230 shares of Common Stock at a purchase price of $2.87 per share, for a period of 12 months from the Exercise Agreement.

January 2020 Private Placement

On January 31, 2020 the Company entered into separate Security Purchase Agreements (the Purchase Agreements) with certain accredited investors (the Investors), including Foris, for the issuance and sale of an aggregate of 8,710,802 shares of Common Stock (the PIPE Shares) and rights to purchase an aggregate of 8,710,802 shares of Common Stock (the PIPE Rights) at a purchase price of $2.87 per share, for a period of 12 months for an aggregate purchase price of $25 million.

Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan

In February 2020, the Company's Board of Directors (the Board) approved increases to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (the Equity Plan) and 2010 Employee Stock Purchase Plan (the Purchase Plan). These shares in connection with the Equity Plan represented an automatic annual increase in the number of shares available for grant and issuance under the Equity Plan of 5,887,133 shares and under the Purchase Plan of 588,713 shares. These increases correspond to approximately 5.0% and 0.5%, respectively, of the total outstanding shares of the Company’s common stock as of December 31, 2019. These automatic increases are effective as of January 1, 2020.

Schottenfeld Forbearance Agreement

The Company and Schottenfeld Opportunities Fund II, L.P. (Schottenfeld) and certain of its affiliates (collectively, the Lenders) are parties (i) to certain Credit Agreements, each dated September 10, 2019 (collectively, the September Credit Agreements) and (ii) to a Credit and Security Agreement, dated November 14, 2019 (the CSA, and collectively with the September Credit Agreements, the Credit Agreements), pursuant to which the Company issued to the Lenders certain notes (the September Notes and the November Notes, respectively, and collectively, the Schottenfeld Notes) and warrants (the September Warrants and the November Warrants, respectively, and collectively, the Shottenfeld Warrants) to purchase shares (the Warrant Shares) of the Company’s common stock. See Not 4, “Debt” for further information.

On February 28, 2020, the Company entered into a forbearance agreement with the Lenders, pursuant to which the Lenders would forbear, for 60 days from the date of the Forbearance Agreement, unless terminated earlier (the Forbearance Period), to exercise certain rights under the Credit Agreement as a result of the Company’s defaults under the Credit Agreements and related Schottenfeld Notes, including the failure of the Company to (i) to pay all principal and accrued interest on the November Notes at the maturity date, (ii) the failure to pay on or before December 31, 2019, all accrued and unpaid interest through December 31, 2019 on the September Notes, and (iii) the failure, on or before December 15, 2019, to convert or exchange at least $60 million, but not less than 100%, of certain junior outstanding indebtedness into equity in the Company, and certain other events of default. Under the forbearance agreement the Company agreed to (i) pay a late fee of 5% on any obligations under the November Notes not paid in full on or before the last day of the Forbearance Period; (ii) pay on or prior to the earliest to occur of April 19, 2020 or the last day of the Forbearance Period, (A) all interest due pursuant to the November Notes and the September Notes, plus all interest accruing on such unpaid interest, plus all interest accrued on account of the November Notes and the September Notes from the date of the Forbearance Agreement through the date of such payment, and (B) a forbearance fee in the amount of $150,000; (iii) pay, upon signature of the Forbearance Agreement, $150,000 as a partial payment of the interest that has accrued pursuant to the November Notes and the September Notes as of the date of the Forbearance Agreement; (iv) amended the Schottenfeld Warrants to (A) reduce the exercise price of each Schottenfeld Warrant to $2.87 per share, and (B) with respect to the November Warrants, extend the deadline to register the Warrant Shares for resale by the holders thereof.

Ginkgo Waiver Agreement

On March 11, 2020, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Waiver Agreement and Amendment to Partnership Agreement (the Ginkgo Waiver), pursuant to the terms of (i) the Ginkgo promissory note dated October 20, 2017, issued by the Company to Ginkgo (as amended, the Ginkgo Note), (ii) the Ginkgo Partnership Agreement, dated October 20, 2017, by and between the Company and Ginkgo, and (iii) the Waiver Agreement and Amendment to Ginkgo Note, dated September 29, 2019, by and between the Company and Ginkgo.

Ginkgo agreed to (i) waive the Company’s failure (a) to pay past due interest and partnership payments, including interest thereon of $6.7 million, and (b) to comply with a reporting covenant prior to March 31, 2020, (iii) to make a prior waiver fee payment of $0.5 million on December 15, 2019, (ii) waive any cross defaults due to events of default under other debt obligations by the Company, and (iii) amend payments on the Ginkgo Partnership Agreement beginning on March 31, 2020 to a monthly payment of $0.5 million through and including October 31, 2021.

Total Note Extension Agreement

On March 11, 2020, the Company and Total Raffinage Chimie (Total) entered into a Senior Convertible Note Maturity Extension Agreement that resulted in the reissuance of the December 20, 2019 promissory note under which the Company owed Total $10.2 million plus accrued interest. Under the terms of the Senior Convertible Note Maturity Extension Agreement, the Company paid Total $1.5 million to satisfy all accrued but unpaid interest and to reduce the principal balance of the reissued note by $1.1 million. The reissued note has (i) a maturity date of March 31, 2020, (ii) a $9.1 million principal amount due, (iii) accrues interest at a rate of 12.0% per annum maturity date and (iv) terms substantially identical to the December 20, 2019 promissory note.

Nikko Amendment to Loan Agreement

On March 12, 2020, the Company and Nikko Chemicals Co. Ltd. (Nikko), entered into an amendment to the Loan Agreement dated December 19, 2019, under which the Company borrowed $4.5 million from Nikko (the Nikko Loan). Under the terms of the amendment, the Company paid Nikko $0.5 million to reduce the principal balance of the Loan Agreement to $4.0 million, the maturity date of the amended Loan Agreement was extended to March 31, 2020, with an increase in the interest rate to 8.0% per annum, and other terms substantially identical to the December 19, 2019 Nikko Loan.

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Fair Value Measurement

12 Months Ended

Dec. 31, 2019

Fair Value Disclosures [Abstract]

Fair Value Measurement

Fair Value Measurement

Assets and liabilities are measured and reported at fair value based on the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The fair value hierarchy prioritizes the inputs to valuation techniques used to measure fair value. An asset's or liability's classification level is based on the lowest level of input that is significant to the fair value measurement. Assets and liabilities carried at fair value are valued and disclosed in one of the following three levels of the valuation hierarchy:

•Level 1: Quoted market prices in active markets for identical assets or liabilities.

•Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

•Level 3: Unobservable inputs that are not corroborated by market data.

Liabilities Measured and Recorded at Fair Value on a Recurring Basis

As of December 31, 2019 and 2018, the Company’s financial liabilities measured and recorded at fair value on a recurring basis were classified within the fair value hierarchy as follows:

December 31, (In thousands)	2019								2018
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Senior Convertible Notes Due 2022	$	—	$	—	$	50,624	50,624		$	—	$	—	$	—	$	—
6% Convertible Notes Due 2021	—		—		—		—		—		—		57,918		57,918
Embedded derivatives bifurcated from debt instruments	—		—		2,832		2,832		—		—		—		—
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		6,971		6,971		—		—		42,796		42,796
Total liabilities measured and recorded at fair value	$	—	$	—	$	60,427	$	60,427	$	—	$	—	$	100,714	$	100,714

The Company did not hold any financial assets to be measured and recorded at fair value on a recurring basis as of December 31, 2019 and 2018. Also, there were no transfers between the levels during 2019 or 2018.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgements and consider factors specific to the asset or liability. The method of determining the fair value of compound embedded derivative liabilities is described subsequently in this note. Market risk associated with compound embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

At December 31, 2019 and December 31, 2018, the carrying value of certain financial instruments, such as cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable and other current accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable.

Changes in fair value of derivative liabilities are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of derivative instruments".

Changes in the fair value of debt that is accounted for at fair value are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of debt".

Senior Convertible Notes Due 2022

On November 15, 2019, the Company issued $66.0 million of Senior Convertible Notes Due 2022 and elected the fair value option of accounting for this debt instrument (see Note 4, "Debt" for details). At December 31, 2019, the contractual outstanding principal of the Senior Convertible Notes Due 2022 was $66.0 million and the fair value was $50.6 million. The Company measured the fair value using a binomial lattice model (which is discussed in further detail below) with the following inputs: (i) 233% discount yield, (ii) 45% equity volatility, (iii) 25% / 75% probability of principal repayment in cash or stock, respectively and (iv) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year.

In connection with the issuance of the Senior Convertible Notes Due 2022, the Company was required to pre-deliver 7.5 million shares of common stock (the Pre-Delivery Shares) to the note holders, which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the note holders to sell, trade or hold, subject to certain limitations, for as long as the Senior Convertible Notes Due 2022 are outstanding. However, the Company may elect or be required to apply the value of the pre-delivered shares to satisfy periodic principal and interest payments or other repayment events. Within ten business days following redemption or repayment of in full the Senior Convertible Notes Due 2022 and the satisfaction or discharge by the Company of all outstanding Company obligations under the Senior Convertible Notes Due 2022, the noteholders shall deliver 7.5 million shares of the Company’s common stock to the Company, less any shares used to satisfy any accrued interest or principal amortization payments under such notes.

The Company concluded the Pre-Delivery Shares provision meets the criteria of freestanding instrument that is legally detachable and separately exercisable from the Senior Convertible Notes Due 2022 and should be classified in equity as the common shares issued are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the Pre-Delivery Shares within equity and will not subsequently remeasure to fair value at each reporting period, unless new events trigger a requirement for the shares to be reclassified to an asset or liability. The Company measured the issue date fair value of the Pre-Delivery Shares under an expected borrowing cost approach using a 9.75% annual borrowing rate over a 19-month estimated repayment term for the Senior Convertible Notes Due 2022. The resulting $4.2 million fair value was recorded in equity as additional paid in capital with an offset to the fair value of the Senior Convertible Notes Due 2022. See Note 6, “Stockholders’ Deficit” for further information regarding the issuance of the common stock.

For the year ended December 31, 2019, the Company recorded a $3.8 million gain from change in fair value of debt in connection with the initial issuance and subsequent fair value remeasurement of the Senior Convertible Notes Due 2022, as follows:

In thousands
Fair value at November 14, 2019	$	54,425
Less: Gain from change in fair value	(3,801)
Fair value at December 31, 2019	$	50,624

A binomial lattice model was used to determine if the Senior Convertible Notes Due 2022 would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible note will be converted early if the conversion value is greater than the holding value and (ii) the convertible note will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible note is called, the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible note. Using this lattice method, the Company valued the Senior Convertible Notes Due 2022 using the "with-and-without method", where the fair value of the Senior Convertible Notes Due 2022 including the embedded and freestanding features is defined as the "with", and the fair value of the Senior Convertible Notes Due 2022 excluding the embedded and freestanding features is defined as the "without". This method estimates the fair value of the Senior Convertible Notes Due 2022 by looking at the difference in the values of Senior Convertible Notes Due 2022 with the embedded and freestanding derivatives and the fair value of Senior Convertible Notes Due 2022 without the embedded and freestanding features. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company remeasures the fair value of the debt instrument and records the change as a gain or loss from change in fair value of debt in the statement of operations for each reporting period.

6% Convertible Notes Due 2021

On December 10, 2018, the Company issued $60.0 million of 6% Convertible Notes Due 2021 (see Note 4, "Debt" for details) and elected the fair value option of accounting for this debt instrument. The notes were extinguished in November 2019. The Company recorded a $23.2 million loss from change in fair value of debt in the year ended December 31, 2019 prior to extinguishing the debt.

Derivative Liabilities Recognized in Connection with the Issuance of Debt and Equity Instruments

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt and equity instruments – either freestanding or compound embedded – measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Equity-related Derivative Liability		Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2018	$	41,272	$	1,524	$	42,796
Derecognition upon adoption of ASU 2017-11	(39,513)		(1,524)		(41,037)
Fair value of derivative liabilities issued during the period	—		15,158		15,158
Change in fair value of derivative liabilities	2,039		(4,816)		(2,777)
Derecognition on extinguishment	(3,798)		(539)		(4,337)
Balance at December 31, 2019	$	—	$	9,803	$	9,803

As of December 31, 2019, the $3.8 million derivative liability recorded in connection with the November 2018 Securities Purchase Agreement with DSM was settled and extinguished through a cash payment in April 2019.

During the second half of 2019, the Company issued four debt instruments with an embedded mandatory redemption feature and two freestanding liability classified warrants with conversion rate adjustment and antidilution provisions. See Note 4, “Debt” for a description of the transactions and the initial accounting treatment for these debt related derivatives. There is no current observable market for these types of derivatives and the Company determined the fair value of the embedded mandatory redemption feature using a probability weighted discounted cash flow model measuring the fair value of the debt instrument both with and without the embedded feature, which is discussed in more detail below; and the freestanding liability warrants using a Black-Scholes-Merton option pricing model, which is also discussed in more detail below.

The collective fair value of the four embedded derivatives totaled $2.5 million at issuance date and were recorded as a derivative liability and a debt discount against the underlying debt instruments. In the fourth quarter of 2019, the Company modified certain key terms in two of the four underlying debt instruments, resulting in a debt extinguishment of the two instruments. Consequently, the collective fair value of the two embedded derivative liabilities totaling $0.5 million were written off against the loss on debt extinguishment and the $0.7 million collective fair value of the two new embedded mandatory redemption features were recorded as derivative liabilities at the date of debt modification. The collective fair value of the four embedded derivative liabilities totaled $2.8 million at December 31, 2019.

The freestanding liability warrants issued on September 10, 2019 and November 14, 2019 had an initial fair value of $7.9 million and $4.0 million, respectively and were recorded as a derivative liability and a debt discount. The warrants will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations as a gain or loss on change in fair value of derivative liabilities. At December 31, 2019 the warrants derivative had a fair value of $6.9 million. For the year ended December 31, 2019, the Company recorded a $4.8 million gain from change in fair value of debt-related embedded derivative liabilities.

Valuation Methodology and Approach to Measuring the Derivative Liabilities

The liabilities associated with the Company’s freestanding and compound embedded derivatives outstanding at December 31, 2019 and 2018 represent the fair value of freestanding equity instruments, mandatory redemption features embedded in certain debt instruments and antidilution provisions in some of the Company's debt warrant instruments. See Note 4, "Debt", and Note 6, "Stockholders' Deficit" for further information regarding these host instruments. There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the freestanding instrument or embedded derivatives using the Black-Scholes-Merton option pricing model, a probability weighted discounted cash flow analysis, or a Monte Carlo simulation.

The Company uses the Black-Scholes-Merton option pricing model to determine the fair value of its liability classified warrants issued in 2019. Input assumptions for these freestanding instruments are as follows:

Input assumptions for liability classified warrants:	Range
Fair value of common stock on issue date	$3.09 – $4.76
Expected volatility	94% - 105%
Risk-free interest rate	1.58% - 1.67%
Dividend yield	0.0	%

The Company uses a probability weighted discounted cash flow model to measure the fair value of the mandatory redemption features embedded in the four debt instruments issued in the second half of 2019. The model is designed to measure and determine if the debt instruments would be called or held at each decision point. Within the model, the following assumption is made: the underlying debt instrument will be called early if the change in control redemption value is greater than the holding value. If the underlying debt instrument is called, the holder will maximize their value by finding the optimal decision between (i) redeeming at the redemption price and (ii) holding the instrument until maturity. Using this assumption, the Company valued the embedded derivatives on a "with-and-without method", where the fair value of each underlying debt instrument including the embedded derivative is defined as the "with", and the fair value of each underlying debt instrument excluding the embedded derivatives is defined as the "without". This method estimates the fair value of the embedded derivatives by comparing the fair value differential between the with and without mandatory redemption feature. The model incorporates the mandatory redemption price, time to maturity, risk-free interest rate, estimated credit spread and estimated probability of a change in control default event.

The Company used a Monte Carlo simulation valuation model to determine the fair value of the May 2017 and August 2017 Cash and Dilution Warrants through December 31, 2018. Upon adoption of ASU 2017-11 on January 1, 2019, the fair value of these warrants was reclassified to equity as they no longer met the criteria for derivative liability accounting. Monte Carlo simulation combines a random number generator based on a probability distribution and additional inputs of volatility, time to expiration to generate a stock price and other uncertainties. The generated stock price at the time of expiration is then used to calculate the value of the option. The model then calculates results tens of thousands of times, each time using a different set of random values from the probability functions. The resulting Monte Carlo simulation valuation is based on the average of all the calculated results.

The market-based assumptions and estimates used in valuing the compound embedded and freestanding derivative liabilities include amounts in the following ranges/amounts:

December 31,	2019	2018
Risk-free interest rate	1.6% - 1.7%	2.5% - 3.0%
Risk-adjusted discount yield	20.0% - 27.0%	17.2% - 27.3%
Stock price volatility	45%	45.0% - 85.0%
Probability of change in control	5.0%	0.0%
Stock price	$3.09	$3.34
Credit spread	18.4% - 25.4%	14.6% - 24.9%
Estimated conversion dates	2022 - 2023	2019 - 2025

Changes in valuation assumptions can have a significant impact on the valuation of the embedded and freestanding derivative liabilities and debt that the Company elects to account for at fair value. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. Certain of the convertible notes, shares of convertible preferred stock and warrants also include conversion or exercise price adjustment features and, for example, certain issuances of common stock by the Company at prices lower than the current conversion or exercise price result in a reduction of the conversion price of such notes or convertible preferred stock, or a reduction in the exercise price of, or an increase in the number of shares subject to, such warrants, which increases the value of the embedded and freestanding derivative liabilities and debt measured at fair value; see Note 4, "Debt" for details.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable and credit facilities are recorded at carrying value, which is representative of fair value at the date of acquisition. The Company estimates the fair value of these instruments using observable market-based inputs (Level 2). The carrying amount (the total amount of net debt presented on the balance sheet) of the Company's debt at December 31, 2019 and at December 31, 2018, excluding the debt instruments recorded at fair value, was $195.8 million and $151.8 million, respectively. The fair value of such debt at December 31, 2019 and at December 31, 2018 was $194.8 million and $149.3 million,

respectively, and was determined by (i) discounting expected cash flows using current market discount rates estimated for certain of the debt instruments and (ii) using third-party fair value estimates for the remaining debt instruments.

Assets and Liabilities Measured and Recorded at Fair Value on a Non-Recurring Basis

On November 19, 2018, the Company amended its supply agreement with DSM, as discussed in Note 9, “Revenue Recognition” to secure production capacity at the Brotas facility in exchange for future cash payments totaling $22.7 million, the issuance of 1,643,991 shares common stock valued at $6.1 million on the date of issuance and a further cash payment for the difference between the fair value of the common stock and $7.3 million on March 29, 2019. In addition, the Company modified certain warrants held by DSM which resulted in the transfer of $2.9 million of value to DSM and paid $1.8 million to settle certain obligations to DSM related to the 2017 sale of the Brotas facility. The Company also entered into other transactions contemporaneously with the amended supply agreement as discussed in Note 10, “Related Party Transactions”. This series of transactions with DSM in November 2018 was accounted for as a combined transaction in which the Company determined and allocated the fair value of the consideration to each element. The fair value of the consideration transferred to DSM under the combined arrangement totaled $33.3 million and was allocated as follows (in thousands):

Element	Fair Value Allocation
Manufacturing capacity reservation fee	$	24,395
Legal settlement and consent waiver	6,764
Working capital adjustment	2,145
Total fair value of consideration transferred	$	33,304

The fair value of these elements is based on Level 3 inputs, which considered the lowest level of input that is significant to the fair value measurement of these elements. To determine the fair value of the manufacturing capacity reservation fee, the Company used a discounted cash flow model under a cost savings valuation approach based on a competing manufacturing quote for similar capacity, location and timing. The Company used a discount rate of 22.5% and a tax rate of 0% to discount the gross cash flows. The fair value of the legal settlement for failure to obtain consent from DSM prior to executing the August 2018 Vivo Warrant transaction was determined by calculating the difference between the fair values of the warrants held by Vivo prior to and after the August 2018 Vivo Warrant transaction using a combination of a Monte Carlo simulation and the Black-Scholes-Merton option pricing model. The fair value of the working capital adjustment was determined to equal the difference between the preliminary estimate for working capital upon closing the Brotas facility sale and the final working capital amounts transferred.

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Net Loss Per Share Attributable to Common Stockholders

12 Months Ended

Dec. 31, 2019

Earnings Per Share [Abstract]

Net Loss per Share Attributable to Common Stockholders

Net Loss per Share Attributable to Common Stockholders

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, convertible preferred stock, convertible promissory notes and common stock warrants, using the treasury stock method or the as converted method, as applicable. For the year ended December 31, 2018, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss were the same for those years.

The Company follows the two-class method when computing net loss per common share when shares are issued that meet the definition of participating securities. The two-class method requires income available to common stockholders for the period to be allocated between common stock and participating securities based upon their respective rights to receive dividends as if all income for the period had been distributed. The two-class method also requires losses for the period to be allocated between common stock and participating securities based on their respective rights if the participating security contractually participates in losses. The Company’s convertible preferred stock are participating securities as they contractually entitle the holders of such shares to participate in dividends and contractually require the holders of such shares to participate in the Company’s losses.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders:

Years Ended December 31, (In thousands, except shares and per share amounts)	2019		2018
Numerator:
Net loss attributable to Amyris, Inc.	$	(242,767)	$	(230,235)
Less deemed dividend to preferred shareholder on issuance and modification of common stock warrants	(34,964)		—
Less deemed dividend related to proceeds discount upon conversion of Series D preferred stock	—		(6,852)
Add: losses allocated to participating securities	7,380		13,991
Net loss attributable to Amyris, Inc. common stockholders, basic	(270,351)		(223,096)
Adjustment to losses allocated to participating securities	137		—
Gain from change in fair value of derivative instruments	(4,963)		—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(275,177)	$	(223,096)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	101,370,632		60,405,910
Basic loss per share	$	(2.67)	$	(3.69)
Weighted-average shares of common stock outstanding	101,370,632		60,405,910
Effect of dilutive common stock warrants	(74,057)		—
Weighted-average common stock equivalents used in computing net income (loss) per share of common stock, diluted	101,296,575		60,405,910
Diluted loss per share	$	(2.72)	$	(3.69)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

Years Ended December 31,	2019	2018
Period-end common stock warrants	59,204,650	25,986,370
Convertible promissory notes(1)	13,381,238	13,703,162
Period-end stock options to purchase common stock	5,620,419	5,392,269
Period-end restricted stock units	5,782,651	5,294,848
Period-end preferred shares on an as-converted basis	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted net loss per share	85,932,619	53,332,381

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect at the respective year-end. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

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Income Taxes - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax Contingency [Line Items]
Additions	$ 29,610,000	$ 42,939,000
Income tax penalties and interest accrued	600,000	0
Unrecognized tax benefits that would impact effective tax rate	0	$ 0	$ 0
Domestic Tax Authority | Internal Revenue Service (IRS)
Income Tax Contingency [Line Items]
Operating loss carryforwards	411,300,000
Domestic Tax Authority | Internal Revenue Service (IRS) | Research Tax Credit Carryforward
Income Tax Contingency [Line Items]
Tax credit carryforward, amount	3,300,000
State and Local Jurisdiction
Income Tax Contingency [Line Items]
Operating loss carryforwards	158,100,000
State and Local Jurisdiction | California Franchise Tax Board | Research Tax Credit Carryforward
Income Tax Contingency [Line Items]
Tax credit carryforward, amount	15,200,000
Foreign Tax Authority
Income Tax Contingency [Line Items]
Operating loss carryforwards	$ 22,000,000.0

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Income Taxes (Tables)

12 Months Ended

Dec. 31, 2019

Income Tax Disclosure [Abstract]

Schedule of Income before Income Tax, Domestic and Foreign

The components of loss before income taxes are as follows:

Years Ended December 31, (In thousands)	2019		2018
United States	$	(227,614)	$	(218,109)
Foreign	(14,524)		(12,125)
Loss before income taxes	$	(242,138)	$	(230,234)

Schedule of Components of Income Tax Expense (Benefit)

The components of the provision for income taxes are as follows:

Years Ended December 31, (In thousands)	2019		2018
Current:
Federal	$	621	$	—
State	—		—
Foreign	8		—
Total current provision	629		—
Deferred:
Federal	—		—
State	—		—
Foreign	—		—
Total deferred benefit	—		—
Total provision for income taxes	$	629	$	—

Schedule of Effective Income Tax Rate Reconciliation

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:

Years Ended December 31,	2019		2018
Statutory tax rate	(21.0)	%	(21.0)	%
Federal R&D credit	(0.7)	%	(0.6)	%
Derivative liability	4.7	%	4.3	%
Nondeductible interest	1.0	%	1.0	%
Other	2.4	%	(0.1)	%
Foreign losses	0.9	%	0.9	%
Change in valuation allowance	13.0	%	15.5	%
Effective income tax rate	0.3	%	—	%

Schedule of Deferred Tax Assets and Liabilities

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows:

December 31, (In thousands)	2019		2018
Net operating loss carryforwards	$	88,513	$	57,921
Property, plant and equipment	8,239		9,269
Research and development credits	15,002		12,046
Foreign tax credit	—		—
Accruals and reserves	13,934		8,526
Stock-based compensation	6,164		6,496
Disallowed interest carryforward	7,072		2,359
Capitalized research and development costs	21,723		27,888
Intangible and others	2,503		3,114
Equity investments	304		156
Total deferred tax assets	163,454		127,775
Operating leases right-of-use assets	(2,643)		—
Debt discount and derivatives	(7,176)		(3,750)
Total deferred tax liabilities	(9,819)		(3,750)
Net deferred tax assets prior to valuation allowance	153,635		124,025
Less: valuation allowance	(153,635)		(124,025)
Net deferred tax assets	$	—	$	—

Summary of Valuation Allowance

Activity in the deferred tax assets valuation allowance is summarized as follows:

(In thousands)	Balance at Beginning of Year		Additions		Reductions / Charges		Balance at End of Year
Deferred tax assets valuation allowance:
Year ended December 31, 2019	$	124,025	$	29,610	$	—	$	153,635
Year ended December 31, 2018	$	81,086	$	42,939	$	—	$	124,025

Schedule of Unrecognized Tax Benefits Roll Forward

A reconciliation of the beginning and ending amounts of unrecognized tax benefits is as follows:

(In thousands)
Balance at December 31, 2017	$	28,833
Increases in tax positions for prior period	55
Increases in tax positions during current period	1,239
Balance at December 31, 2018	30,127
Increases in tax positions for prior period	—
Increases in tax positions during current period	1,411
Balance at December 31, 2019	$	31,538

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Stock-based Compensation (Details)		1 Months Ended	12 Months Ended
	Sep. 28, 2010 shares	May 31, 2018 shares	Dec. 31, 2019 USD ($) instrument $ / shares shares	Dec. 31, 2018 USD ($) $ / shares shares	Dec. 31, 2005
Compensating Balances [Line Items]
Outstanding awards (in shares)			5,620,419	5,390,270
Weighted average exercise price (in dollars per share) | $ / shares			$ 10.27	$ 11.55
Performance-based stock options, grant date fair value | $			$ 5,100,000
Share-based payment arrangement, expense | $			12,554,000	$ 9,190,000
Exercises in period, intrinsic value | $			$ 0	200,000
Issuance of common stock upon exercise of stock options (in shares)			7,445
Chief Executive Officer
Compensating Balances [Line Items]
Purchasable shares under performance based options		3,250,000
Fair value of the Company’s common stock on grant date (in dollars per share) | $ / shares			$ 5.08
Performance-based Stock Options
Compensating Balances [Line Items]
Fair value of the Company’s common stock on grant date (in dollars per share) | $ / shares			$ 5.08
Share-based payment arrangement, expense | $			$ 0	700,000
Share-based Payment Arrangement, Option
Compensating Balances [Line Items]
Share-based payment arrangement, expense | $			$ 2,000,000.0	$ 2,600,000
Period for recognition			3 years 9 months 18 days
Period-end restricted stock units
Compensating Balances [Line Items]
Outstanding, RSUs (in shares)			5,782,651	5,294,803
Grants in period (in shares)			2,996,660	5,452,664
Share-based payment arrangement, expense | $			$ 10,200,000	$ 6,400,000
Weighted average grant date fair value, grants in period (in dollars per share) | $ / shares			$ 3.96	$ 5.36
Share-based payment arrangement, nonvested award, cost not yet recognized, amount | $			$ 22,300,000	$ 23,800,000
Minimum | Chief Executive Officer
Compensating Balances [Line Items]
Performance-based stock options contingently available for issuance			0
Minimum | Period-end restricted stock units
Compensating Balances [Line Items]
Award vesting period			3 years
Maximum | Chief Executive Officer
Compensating Balances [Line Items]
Performance-based stock options contingently available for issuance			3,250,000
Maximum | Period-end restricted stock units
Compensating Balances [Line Items]
Award vesting period			5 years
Stock Options and Stock Issuance Plans, 2005
Compensating Balances [Line Items]
Minimum percent of exercise price to fair market value on grant date					100.00%
Minimum percent of shareholder triggering higher exercise price					10.00%
Minimum percent of exercise price to fair market value on grant date of ten percent or greater shareholder of company					110.00%
Award vesting period					5 years
Outstanding awards (in shares)			31,104	52,389
Weighted average exercise price (in dollars per share) | $ / shares			$ 259.19	$ 185.93
Number of shares available for grant (in shares)			0
Share-based Compensation Arrangement by Share-based Payment Award, Expiration Period			10 years
Equity Incentive Plan, 2010
Compensating Balances [Line Items]
Number of shares authorized (in shares)	2,000,000
Period available to grant	10 years
Minimum percent of exercise price to fair market value on grant date	100.00%
Minimum percent of shareholder triggering higher exercise price	10.00%
Minimum percent of exercise price to fair market value on grant date of ten percent or greater shareholder of company	110.00%
Outstanding awards (in shares)			5,589,315	5,339,214
Weighted average exercise price (in dollars per share) | $ / shares			$ 8.89	$ 9.62
Number of shares available for grant (in shares)		9,280,000	3,815,625	2,359,750
Number of additional shares authorized (in shares)		9,000,000.0
Maximum number of shares per employee		4,000,000.0
Percentage of outstanding shares			5.00%
Employee Stock Purchase Plan, 2010
Compensating Balances [Line Items]
Number of shares authorized (in shares)		1,666,666
Number of shares available for grant (in shares)			263,797	199,463
Number of additional shares authorized (in shares)		1,000,000
Purchase price of common stock, percent	85.00%
Percentage of outstanding shares	1.00%
Share-based payment arrangement, expense | $			$ 400,000	$ 200,000
Share-Based Compensation Arrangement By Share-based Payment Award, Consecutive Offering Period			1 year
Share-Based Compensation Arrangement By Share-based Payment Award, Number Of Purchase Periods | instrument			2
Share-Based Compensation Arrangement By Share-based Payment Award, Purchase Period			6 months
Common Stock
Compensating Balances [Line Items]
Issuance of common stock upon exercise of stock options (in shares)			3,612	70,807

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Net Loss Per Share Attributable to Common Stockholders (Tables)

12 Months Ended

Dec. 31, 2019

Earnings Per Share [Abstract]

Schedule of Earnings Per Share, Basic and Diluted

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders:

Years Ended December 31, (In thousands, except shares and per share amounts)	2019		2018
Numerator:
Net loss attributable to Amyris, Inc.	$	(242,767)	$	(230,235)
Less deemed dividend to preferred shareholder on issuance and modification of common stock warrants	(34,964)		—
Less deemed dividend related to proceeds discount upon conversion of Series D preferred stock	—		(6,852)
Add: losses allocated to participating securities	7,380		13,991
Net loss attributable to Amyris, Inc. common stockholders, basic	(270,351)		(223,096)
Adjustment to losses allocated to participating securities	137		—
Gain from change in fair value of derivative instruments	(4,963)		—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(275,177)	$	(223,096)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	101,370,632		60,405,910
Basic loss per share	$	(2.67)	$	(3.69)
Weighted-average shares of common stock outstanding	101,370,632		60,405,910
Effect of dilutive common stock warrants	(74,057)		—
Weighted-average common stock equivalents used in computing net income (loss) per share of common stock, diluted	101,296,575		60,405,910
Diluted loss per share	$	(2.72)	$	(3.69)

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:

Years Ended December 31,	2019	2018
Period-end common stock warrants	59,204,650	25,986,370
Convertible promissory notes(1)	13,381,238	13,703,162
Period-end stock options to purchase common stock	5,620,419	5,392,269
Period-end restricted stock units	5,782,651	5,294,848
Period-end preferred shares on an as-converted basis	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted net loss per share	85,932,619	53,332,381

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect at the respective year-end. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

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Related Party Transactions - Related Party DSM Transactions (Details) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Working capital		$ 86,700
Contract liabilities	$ 8,236	1,353	$ 8,236
Payments for legal settlements			6,800
DSM International B.V.
Related Party Transaction [Line Items]
Contract with customer, liability		34,700
Contract with customer, liability, fair value adjustment	1,400	33,300
Legal fees		6,800
Working capital		2,100
Contract liabilities	1,204	1,204	1,204
Post-closing working capital adjustment payment recorded as loss on divestiture		2,100
Royalty | DSM International B.V.
Related Party Transaction [Line Items]
Maximum borrowing capacity	25,000		25,000
Manufactured Product, Other | DSM International B.V.
Related Party Transaction [Line Items]
Contract with customer, liability		24,400
Manufacturing capacity, fair value			24,400
Contract liabilities	$ 3,300	14,100	$ 3,300
Additional deferred cost of products sold		$ 7,000

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Balance Sheet Details - Additional Information (Details) - USD ($) $ in Thousands		1 Months Ended	12 Months Ended
	Jan. 01, 2019	Oct. 31, 2019	Dec. 31, 2019	Dec. 31, 2018	Apr. 30, 2019	Nov. 30, 2018
Condensed Balance Sheet Statements, Captions [Line Items]
Deferred cost of products sold - related party			$ 16,492	$ 3,317
Deferred cost of products sold, amortization			900	0
Depreciation and amortization			4,581	4,921
Gain (loss) on disposition of assets			(212)	(941)
Rent expense				5,800
Operating lease asset			13,203
Operating lease, liability			19,662
Operating lease, expense			16,400
Lease, cost			7,000
Acquisition of right-of-use assets under operating leases	$ 29,700		3,551	0
Finance lease right-of-use asset accumulated amortization			1,700
Other asset impairment charges			200	3,900
Consideration transferred		$ 10,800
Unsecured debt		$ 10,800
Contract liabilities			1,353	8,236
Contract with customer, refund liability			$ 3,800
Capitalized Contract Cost, Amortization Period			5 years
Licenses and Royalties
Condensed Balance Sheet Statements, Captions [Line Items]
Increase (decrease) in revenue			$ 8,800
DSM International B.V.
Condensed Balance Sheet Statements, Captions [Line Items]
Contract with customer, liability			$ 12,500		$ 12,500
Accounting Standards Update 2016-02
Condensed Balance Sheet Statements, Captions [Line Items]
Operating lease asset	29,700
Operating lease, liability	$ 33,600
Minimum
Condensed Balance Sheet Statements, Captions [Line Items]
Lessee, operating lease, remaining lease term			1 year
Lessee, operating lease, renewal term			1 year
Maximum
Condensed Balance Sheet Statements, Captions [Line Items]
Lessee, operating lease, remaining lease term			5 years
Lessee, operating lease, renewal term			5 years
DSM International B.V.
Condensed Balance Sheet Statements, Captions [Line Items]
Manufacturing capacity reservation fee, current						$ 24,400
Deferred cost of products sold - related party			$ 7,000	3,300
Payments of reservation capacity fees			14,100
Contract liabilities			1,204	1,204
Contract with customer, liability			$ 34,700
Other Expense, Net
Condensed Balance Sheet Statements, Captions [Line Items]
Loss on divestiture				$ (900)

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Related Party Transactions - Related Party Revenues (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Revenues	$ 152,557	$ 63,604
Customers Other Than Related Parties
Related Party Transaction [Line Items]
Revenues	99,330	52,551
DSM International B.V.
Related Party Transaction [Line Items]
Revenues	53,181	10,711
Total
Related Party Transaction [Line Items]
Revenues	46	342
Novvi LLC
Related Party Transaction [Line Items]
Revenues	0	0
Related Parties
Related Party Transaction [Line Items]
Revenues	53,227	11,053
Renewable Products
Related Party Transaction [Line Items]
Revenues	59,872	33,598
Renewable Products | Customers Other Than Related Parties
Related Party Transaction [Line Items]
Revenues	59,816	33,238
Renewable Products | DSM International B.V.
Related Party Transaction [Line Items]
Revenues	10	18
Renewable Products | Total
Related Party Transaction [Line Items]
Revenues	46	342
Renewable Products | Novvi LLC
Related Party Transaction [Line Items]
Revenues	0	0
Renewable Products | Related Parties
Related Party Transaction [Line Items]
Revenues	56	360
Licenses and Royalties
Related Party Transaction [Line Items]
Revenues	54,043	7,658
Licenses and Royalties | Customers Other Than Related Parties
Related Party Transaction [Line Items]
Revenues	4,992	1,700
Licenses and Royalties | DSM International B.V.
Related Party Transaction [Line Items]
Revenues	49,051	5,958
Licenses and Royalties | Total
Related Party Transaction [Line Items]
Revenues	0	0
Licenses and Royalties | Novvi LLC
Related Party Transaction [Line Items]
Revenues	0	0
Licenses and Royalties | Related Parties
Related Party Transaction [Line Items]
Revenues	49,051	5,958
Grants and Collaborations
Related Party Transaction [Line Items]
Revenues	38,642	22,348
Grants and Collaborations | Customers Other Than Related Parties
Related Party Transaction [Line Items]
Revenues	34,522	17,613
Grants and Collaborations | DSM International B.V.
Related Party Transaction [Line Items]
Revenues	4,120	4,735
Grants and Collaborations | Total
Related Party Transaction [Line Items]
Revenues	0	0
Grants and Collaborations | Novvi LLC
Related Party Transaction [Line Items]
Revenues	0	0
Grants and Collaborations | Related Parties
Related Party Transaction [Line Items]
Revenues	$ 4,120	$ 4,735

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Fair Value Measurement - Financial Assets and Liabilities (Details) - USD ($) $ in Millions	Dec. 31, 2019	Nov. 14, 2019	Sep. 10, 2019	Dec. 31, 2018
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term and short-term debt	$ 195.8	$ 4.0	$ 7.9	$ 151.8
Debt instrument, fair value	$ 194.8			$ 149.3

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Fair Value Measurement - Fair Value, Assets, and Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	$ 26,232	$ 0
Fair Value, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	2,832	0
Freestanding derivative instruments issued in connection with other debt and equity instruments	6,971	42,796
Total liabilities measured and recorded at fair value	60,427	100,714
Fair Value, Recurring | Senior Convertible Notes Due 2022
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	50,624	0
Fair Value, Recurring | Convertible 6% Notes Due 2021
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	0	57,918
Fair Value, Inputs, Level 1 | Fair Value, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	0	0
Freestanding derivative instruments issued in connection with other debt and equity instruments	0	0
Total liabilities measured and recorded at fair value	0	0
Fair Value, Inputs, Level 1 | Fair Value, Recurring | Senior Convertible Notes Due 2022
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	0	0
Fair Value, Inputs, Level 1 | Fair Value, Recurring | Convertible 6% Notes Due 2021
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	0
Fair Value, Inputs, Level 2 | Fair Value, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	0	0
Freestanding derivative instruments issued in connection with other debt and equity instruments	0	0
Total liabilities measured and recorded at fair value	0	0
Fair Value, Inputs, Level 2 | Fair Value, Recurring | Senior Convertible Notes Due 2022
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	0	0
Fair Value, Inputs, Level 2 | Fair Value, Recurring | Convertible 6% Notes Due 2021
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	0
Fair Value, Inputs, Level 3 | Fair Value, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	2,832	0
Freestanding derivative instruments issued in connection with other debt and equity instruments	6,971	42,796
Total liabilities measured and recorded at fair value	60,427	100,714
Fair Value, Inputs, Level 3 | Fair Value, Recurring | Senior Convertible Notes Due 2022
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	50,624	0
Fair Value, Inputs, Level 3 | Fair Value, Recurring | Convertible 6% Notes Due 2021
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long term debt, net of current portion — instruments measured at fair value	$ 0	$ 57,918

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Fair Value Measurement - Reconciliation for Compound Embedded Derivative Liability (Details) - Fair Value, Inputs, Level 3 $ in Thousands	12 Months Ended
	Dec. 31, 2019 USD ($)
Derivative Liability, Equity-related
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	$ 41,272
Derecognition upon adoption of ASU 2017-11	(39,513)
Fair value of derivative liabilities issued during the period	0
Change in fair value of derivative liabilities	2,039
Derecognition on extinguishment	(3,798)
Fair value, ending balance	0
Derivative Liability, Debt-related
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	1,524
Derecognition upon adoption of ASU 2017-11	(1,524)
Fair value of derivative liabilities issued during the period	15,158
Change in fair value of derivative liabilities	(4,816)
Derecognition on extinguishment	(539)
Fair value, ending balance	9,803
Derivative Financial Instruments, Liabilities
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	42,796
Derecognition upon adoption of ASU 2017-11	(41,037)
Fair value of derivative liabilities issued during the period	15,158
Change in fair value of derivative liabilities	(2,777)
Derecognition on extinguishment	(4,337)
Fair value, ending balance	$ 9,803

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Mezzanine Equity (Details) - USD ($) $ / shares in Units, $ in Thousands			12 Months Ended
	Nov. 19, 2018	Apr. 08, 2016	Dec. 31, 2019	Dec. 31, 2018	Mar. 28, 2019
Schedule of Capitalization, Equity [Line Items]
Issuance of common stock for cash (in shares)	1,643,991
Stock price (in dollars per share)			$ 3.09	$ 3.34	$ 2.10
Proceeds from issuance of common stock in private placements, net of issuance costs			$ 14,221	$ 1,415
Gates Foundation Purchase Agreement
Schedule of Capitalization, Equity [Line Items]
Issuance of common stock for cash (in shares)		292,398
Stock price (in dollars per share)		$ 17.10
Proceeds from issuance of common stock in private placements, net of issuance costs		$ 5,000
Compound annual return (as a percent)		10.00%
Research and development obligation, remaining amount			$ 400

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Debt - DSM $25 Million Note (Details) - DSM Credit Agreement - USD ($)	Dec. 28, 2017	Dec. 31, 2018	Oct. 31, 2016
Extinguishment of Debt [Line Items]
Maximum borrowing capacity	$ 25,000,000.0	$ 25,000,000.0
Proceeds from long-term lines of credit	25,000,000.0
Debt issuance costs	$ 8,000,000.0
Interest rate per annum	10.00%
Unsecured Debt
Extinguishment of Debt [Line Items]
Maximum borrowing capacity			$ 25,000,000.0

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Debt - Naxyris LSA (Details) - USD ($) $ / shares in Units, shares in Millions			1 Months Ended
	Oct. 28, 2019	Aug. 14, 2019	Oct. 31, 2019	Aug. 28, 2019
Debt Conversion [Line Items]
Warrants and rights outstanding				$ 8,700,000
The Naxyris Loan Agreement
Debt Conversion [Line Items]
Debt instrument, fee		$ 500,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	2.0	2.0
Exercise price of warrants or rights (in dollars per share)	$ 3.87	$ 2.87
Warrants and rights outstanding	$ 3,600,000	$ 4,000,000.0
Debt instrument, unamortized discount		400,000
Debt issuance costs, gross		300,000
Debt issuance costs		$ 4,500,000
Class of warrant or right, term	2 years	2 years
The Naxyris Loan Agreement
Debt Conversion [Line Items]
Debt instrument, face amount	$ 24,400,000	$ 10,400,000
Debt instrument, fee		$ 400,000
Interest rate per annum		12.00%
Debt instrument, failure to pay fee rate		6.00%
Basis spread on variable rate		0.25%	5.00%
Loan and Security Agreement Amendment and Waiver | The Naxyris Loan Agreement
Debt Conversion [Line Items]
Fair value of embedded derivative liability		$ 300,000
Warrants and rights outstanding		$ 3,000,000.0		$ 2,800,000
Debt instrument, unamortized discount	$ 4,000,000.0

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Debt - Nikko Loan Agreements and Notes (Details) - USD ($) $ in Thousands									12 Months Ended
	Dec. 19, 2019	Dec. 09, 2019	Nov. 20, 2019	Oct. 31, 2019	Jul. 29, 2019	Feb. 01, 2019	Aug. 03, 2017	Dec. 19, 2016	Dec. 31, 2019	Dec. 31, 2018
Debt Instrument [Line Items]
Long-term debt, gross									$ 297,462	$ 228,921
Nikko $5.0M Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt					$ 5,000
Long-term debt, gross									5,000
Interest rate per annum					500.00%
Nikko $4.5M Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt	$ 4,500
Long-term debt, gross									4,500
Interest rate per annum	275.00%
Nikko $3.9M Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt								$ 3,900
Long-term debt, gross									2,862
Interest rate per annum								500.00%
Nikko $1.5M Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt							$ 1,500
Long-term debt, gross									900
Interest rate per annum							275.00%
Nikko $450K Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt		$ 450
Long-term debt, gross									450
Interest rate per annum		275.00%
Nikko $350K Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt			$ 350
Long-term debt, gross									350
Interest rate per annum			275.00%
Nikko $200K Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt						$ 200
Long-term debt, gross									171
Interest rate per annum						500.00%
Nikko $500K Note | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt				$ 500
Long-term debt, gross									84
Interest rate per annum				275.00%
Nikko Loan Agreements and Notes | Nikko Notes Payable
Debt Instrument [Line Items]
Debt conversion, original debt									16,400
Long-term debt, gross									$ 14,317

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Income Taxes - Uncertain Tax Benefits (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Beginning balance	$ 30,127	$ 28,833
Increases in tax positions for prior period	0	55
Increases in tax positions during current period	1,411	1,239
Ending balance	$ 31,538	$ 30,127

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Debt

12 Months Ended

Dec. 31, 2019

Debt Disclosure [Abstract]

Debt

Debt

	2019								2018
December 31, (In thousands)	Principal		Unaccreted Debt (Discount) Premium		Fair Value Adjustment		Net		Principal		Unaccreted Debt (Discount) Premium		Fair Value Adjustment		Net
Convertible notes payable
Senior convertible notes due 2022	$	66,000	$	—	$	(15,376)	$	50,624	$	—	$	—	$	—	$	—
6% convertible notes due 2021	—		—		—		—		60,000		—		(2,082)		57,918
2015 Rule 144A convertible notes	—		—		—		—		37,887		(2,413)		—		35,474
2014 Rule 144A convertible notes	—		—		—		—		24,004		(867)		—		23,137
August 2013 financing convertible notes	—		—		—		—		4,415		(70)		—		4,345
	66,000		—		(15,376)		50,624		126,306		(3,350)		(2,082)		120,874
Related party convertible notes payable
2014 Rule 144A convertible notes	10,178		—		—		10,178		24,705		(1,038)		—		23,667
	10,178		—		—		10,178		24,705		(1,038)		—		23,667
Loans payable and credit facilities
Schottenfeld notes	20,350		(1,315)		—		19,035		—		—		—		—
Nikko notes	14,318		(901)		—		13,417		4,598		(1,047)		—		3,551
Ginkgo note	12,000		(3,139)		—		8,861		12,000		(4,047)		—		7,953
Other loans payable	1,828		—		—		1,828		312		—		—		312
GACP term loan facility	—		—		—		—		36,000		(1,349)		—		34,651
	48,496		(5,355)		—		43,141		52,910		(6,443)		—		46,467
Related party loans payable
Foris notes	115,351		(9,516)		—		105,835		—		—		—		—
DSM notes	33,000		(4,621)		—		28,379		25,000		(6,311)		—		18,689
Naxyris note	24,437		(822)		—		23,615		—		—		—		—
	172,788		(14,959)		—		157,829		25,000		(6,311)		—		18,689
Total debt	$	297,462	$	(20,314)	$	(15,376)	261,772		$	228,921	$	(17,142)	$	(2,082)	209,697
Less: current portion							(63,805)								(147,677)
Long-term debt, net of current portion							$	197,967							$	62,020

Future minimum payments under the debt agreements as of December 31, 2019 are as follows:

Years ending December 31 (In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020	$	43,384	$	26,324	$	10,437	$	33,730	$	113,875
2021	40,177		3,342		—		53,566		97,085
2022	—		15,177		—		113,818		128,995
2023	—		13,011		—		24,323		37,334
2024	—		398		—		—		398
Thereafter	—		1,870		—		—		1,870
Total future minimum payments	83,561		60,122		10,437		225,437		379,557
Less: amount representing interest(1)	(17,561)		(11,626)		(259)		(52,649)		(82,095)
Less: future conversion of accrued interest to principal	—		—		—		—		—
Present value of minimum debt payments	66,000		48,496		10,178		172,788		297,462
Less: current portion of debt principal	(31,800)		(21,193)		(10,178)		(11,380)		(74,551)
Noncurrent portion of debt principal	$	34,200	$	27,303	$	—	$	161,408	$	222,911

______________

⁽¹⁾ Excluding net debt discount of $20.3 million that will be amortized to interest expense over the term of the debt.

August 2013 Financing Convertible Note

On January 14, 2019, Wolverine Flagship Fund Trading Limited (Wolverine) agreed to waive payment of the August 2013 Financing Convertible Note held by Wolverine at its January 15, 2019 maturity until July 15, 2019 in exchange for a fee, payable on or prior to July 15, 2019, of $0.6 million. The due date of the waiver fee was extended to October 13, 2019 and was subsequently paid on October 29, 2019. The Company concluded that the maturity date extension represented a debt modification, and the fee was accounted for as additional debt discount to be amortized over the remaining term.

On July 8, 2019, $5.1 million principal balance of the convertible note and unpaid interest was exchanged for 1.8 million shares of common stock with a total fair value of $5.9 million or $3.30 per share and a warrant to purchase 1.1 million shares of common stock with a fair value of $1.9 million. The Company recorded a $2.7 million loss on debt extinguishment for the difference between the carrying value of the debt and the sum of the fair values of the common stock and warrant. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of the common stock and warrant issued in connection with this exchange.

2015 Rule 144A Convertible Notes Extinguishment

On April 16, 2019, the Company repaid in cash the $37.9 million outstanding principal, as well as accrued and unpaid interest, under its 9.50% Convertible Senior Notes due 2019 (the 2015 Rule 144A Convertible Notes). This repayment did not result in an extinguishment gain or loss.

2014 Rule 144A Convertible Notes

In May 2019, the Company exchanged a portion of its 6.50% Convertible Senior Notes (the 2014 Rule 144A Convertible Notes), representing $38.2 million aggregate principal amount of 2014 Rule 144A Convertible Notes, for shares of common stock, warrants to purchase common stock and a new senior convertible note as described below and repaid the remaining $10.5 million of the 2014 Rule 144A Convertible Notes in cash at maturity.

Notes Conversion into Common Stock

On May 10, 2019, the Company exchanged $13.5 million aggregate principal amount of 2014 Rule 144A Convertible Notes held by certain non-affiliated investors, including accrued and unpaid interest thereon, for an aggregate of 3.5 million shares of common stock and warrants to purchase an aggregate of 1.4 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, in a private exchange.

On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of 2014 Rule 144A Convertible Notes held by Foris, including accrued and unpaid interest thereon, for 1.1 million shares of common stock and a warrant to purchase up to 0.4 million shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from issuance, in a private exchange. On August 28, 2019, the Company and Foris agreed to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share in connection with the “August 2019 Foris Credit Agreements” below. Also, see Note 6, “Stockholders’ Deficit” for additional information and Note 15, “Subsequent Events” for information regarding the amendment and exercise of the warrants on January 31, 2020.

On May 15, 2019, the Company exchanged $10.0 million aggregate principal amount of 2014 Rule 144A Convertible Notes held by Maxwell (Mauritius) Pte Ltd for 2.5 million shares of common stock in a private exchange.

The Company evaluated the May 2019 note conversions into common stock discussed above and concluded that the transactions resulted in a debt extinguishment. The Company recorded a $5.9 million loss on debt extinguishment of the 2014 144A Convertible Notes in the three months ended June 30, 2019. The loss represented the difference between the $30.8 million fair value of 7.1 million common shares issued upon exchange, $3.8 million fair value of warrants issued to purchase 1.7 million shares of common stock and $0.4 million of fees incurred, less the $29.1 million carrying value of the debt that was extinguished. See Note 6. "Stockholders’ Deficit" for further information regarding the fair value measurement of the common stock and warrants issued in connection with the May 2019 note conversions discussed above.

Total Note Exchange and Extensions

On May 15, 2019, the Company exchanged $9.7 million aggregate principal amount of 2014 Rule 144A Convertible Notes due May 15, 2019 held by Total Raffinage Chimie (Total) for a new senior convertible note (the New Note) with an equal principal amount and with substantially identical terms, except that the New Note had a maturity date of June 14, 2019.

Effective June 14, 2019, the Company and Total agreed to extend the maturity date of the New Note from June 14, 2019 to July 18, 2019. Effective July 18, 2019, the Company and Total agreed to (i) further extend the maturity date of the New Note from July 18, 2019 to August 28, 2019 and (ii) increase the interest rate on the New Note to 10.5% per annum, beginning July 18, 2019. Effective August 28, 2019, the Company and Total agreed to (i) further extend the maturity date of the New Note from August 28, 2019 to October 28, 2019 and (ii) increase the interest rate on the New Note to 12% per annum, beginning August 28, 2019. On October 31, 2019, the Company and Total agreed, effective as of October 28, 2019, to (i) extend the maturity date of the New Note from October 28, 2019 to December 16, 2019 and (ii) capitalize all interest accruing under the New Note from May 15, 2019 through and including November 14, 2019, in the amount of $0.5 million, which interest would be added to the principal of the New Note, which would begin accruing interest on such new principal amount on November 15, 2019. Effective December 16, 2019, the Company and Total agreed to extend the maturity date of the New Note from December 16, 2019 to January 31, 2020. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to repay the $10.2 million New Note by January 31, 2020.

The Company accounted for the note exchange and series of extensions with Total as a debt modification; however, no additional fees were paid in connection with the exchange and extensions, and consequently there was no impact on the carrying value of the debt as of December 31, 2019.

Foris Debt Transactions—Related Party

The Company has loans payable to Foris Ventures, LLC (Foris) with a total principal balance of $115.4 million at December 31, 2019. Foris is an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than five percent of the Company’s outstanding common stock. The notes payable to Foris are comprised of the following (amounts in thousands):

Description	Date Issued	Original Loan Amount		Balance at December 31, 2019		Interest Rate per Annum	Maturity Date
Foris $19 Million Note	August 28, 2019	$	19,000	$	19,000	12.0%	January 1, 2023
Foris LSA	April 15, 2019	36,000		96,351		12.5%	For $81.0 million borrowed prior to November 27, 2019, the maturity date is July 1, 2022; for $10.0 million borrowed November 27, 2019, the maturity date is March 31, 2023.
		$	55,000	$	115,351

Foris Credit Agreements

On April 8, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $8.0 million (the April Foris Credit Agreement), which the Company borrowed in full on April 8, 2019 and issued to Foris a promissory note in the principal amount of $8.0 million (the April Foris Note). The April Foris Note has a maturity date of October 14, 2019, which has no stated interest rate. The Company agreed to pay Foris a fee of $1.0 million, payable on or prior to the maturity date; provided, that the fee will be reduced to $0.5 million if the Company repays the April Foris Note in full by July 15, 2019. The Company accrues this fee as interest expense over the six-month term of the note.

On June 11, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $8.5 million, which the Company borrowed in full on June 11, 2019 and issued to Foris a promissory note in the principal amount of $8.5 million (the June Foris Note). The June Foris Note (i) accrues interest at a rate of 12.5% per annum and is payable on the maturity date or the earlier repayment or other satisfaction of the June Foris Note, and (ii) matured on August 28, 2019.

On July 10, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $16.0 million (the July Foris Credit Agreement), of which the Company borrowed $8.0 million on July 10, 2019 and $8.0 million on July 26, 2019 and issued to Foris promissory notes, each in the principal amount of $8.0 million, on such dates (the July Foris Notes). The July Foris Notes (i) accrue interest at a rate of 12.5% per annum, which is payable on the maturity date or the earlier repayment or other satisfaction of the applicable July Foris Note, and (ii) mature on December 31, 2019.

In connection with the entry into the July Foris Credit Agreement, the Company and Foris amended the warrant issued to Foris on August 17, 2018 to reduce the exercise price of such warrant from $7.52 per share to $2.87 per share. The warrant modification resulted in $4.0 million of incremental value which was accounted for as a debt discount to the $16 million July

Foris Notes. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of the modified warrant.

On August 14, 2019, the April Foris Note, the June Foris Note and the July Foris Notes were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral granted to Foris under the LSA, and such notes were cancelled in connection therewith. See "LSA Assignment, Amendments and Waiver" below for further information.

Foris LSA Assignment, Amendments and Waivers

On April 4, 2019, the Company and GACP Finance Co., LLC (GACP) amended the Loan and Security Agreement, dated June 29, 2018 (as amended, the LSA), to remove, add and modify certain restrictions, covenants and other provisions and to waive breaches of certain covenants under the LSA occurring prior to, as of and after December 31, 2018 through April 8, 2019. In connection with such waiver, the Company agreed to pay GACP fees of $0.8 million, which the Company paid in April 2019. This waiver fee was recorded as interest expense in the statement of operations in the nine months ended September 30, 2019.

On April 15, 2019, the Company, GACP and Foris Ventures, LLC (Foris), an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than 5% of the Company’s outstanding common stock) entered into a Loan Purchase Agreement, pursuant to which Foris agreed to purchase and assume from GACP, the outstanding principal balance under the LSA, which totaled $36.0 million and all documents and assets related thereto. In connection with such purchase and assignment, the Company agreed to repay Foris $2.5 million of the purchase price and accrued interest paid by Foris to GACP (the LSA Obligation). The closing of the loan purchase and assignment occurred on April 16, 2019.

On August 14, 2019, the Company and Foris entered into an Amendment No. 5 and Waiver to the LSA (the LSA Amendment and Waiver), pursuant to which (i) the maturity date of the loans under the LSA was extended from July 1, 2021 to July 1, 2022, (ii) the interest rate for the loans under the LSA was modified to the greater of (A) 12% or (B) the rate of interest payable with respect to any indebtedness of the Company, including, but not limited to, the rate of interest charged pursuant to the Naxyris Loan Agreement, provided, that for such purpose, the rate of interest charged pursuant to the Naxyris Loan Agreement shall be the rate of interest payable by the Borrower pursuant to the Naxyris Loan Agreement, minus 25 basis points (iii) the amortization of the loans under the LSA was delayed until December 16, 2019, (iv) certain accrued and future interest and agency fee payments under the LSA were delayed until December 16, 2019, (v) certain covenants under the LSA, including related definitions, were amended to provide the Company with greater operational and financial flexibility, including, without limitation, to permit the incurrence of the indebtedness under the August 2019 Naxyris Loan (as described below) and the granting of liens with respect thereto, subject to the terms of an intercreditor agreement between Foris and Naxyris S.A. (Naxyris) governing the respective rights of the parties with respect to, among other things, the assets securing the Naxyris Loan Agreement (as defined below) and the LSA (the Intercreditor Agreement), (vi) certain outstanding unsecured promissory notes issued by the Company to Foris on April 8, 2019, June 11, 2019, July 10, 2019 and July 26, 2019 (as described in the “Foris Credit Agreements” section above), in an aggregate principal amount of $32.5 million, as well as the $2.5 million LSA Obligation, were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral granted to Foris under the LSA, and such promissory notes and contractual obligation were canceled in connection therewith, and (vii) Foris agreed to waive certain existing defaults under the LSA, including with respect to covenants related to cross-defaults, minimum liquidity and minimum asset coverage requirements. After giving effect to the LSA Amendment and Waiver, there was $71.0 million aggregate principal amount of loans outstanding under the LSA.

The Company also issued to Foris a warrant (the LSA Warrant) on August 14, 2019 to purchase up to 1.4 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The warrant had a fair value of $2.9 million, which was measured using the Black-Scholes-Merton option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant.

Due to multiple changes in key provisions of the LSA from April 15, 2019 through August 14, 2019, the Company analyzed the before and after cash flows from the prior twelve months of modifications resulting from the increased principal balance, decreased interest rate, extended maturity date, waiver of default interest and the fair value of the new LSA Warrant provided to Foris in order to determine if these changes result in a modification or extinguishment of the original LSA. Based on the combined before and after cash flows of the five separate note balances making up the new principal balance of the LSA and the fair value of the LSA warrant, the change in cash flows was not significantly different. Consequently, the LSA Amendment and Waiver was accounting for as a debt modification with the $2.9 million fair value of the LSA Warrant

recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA.

Foris LSA Amendments, Additional Loan and Warrant Issuance

On October 10, 2019, the Company and Foris entered into Amendment No. 6 to the LSA (the October 2019 LSA Amendment), pursuant to which the maximum loan commitment of Foris under the LSA was increased by $10.0 million. On October 11, 2019, the Company borrowed an additional $10.0 million from Foris under the LSA (the October 2019 LSA Loan), which is subject to the terms and provisions of the LSA, including the lien on substantially all the assets of the Company. After giving effect to the LSA Loan, there was $81.0 million aggregate principal amount of loans outstanding under the LSA. Also, in connection with the October 2019 LSA Amendment, the Company issued a warrant (the October 2019 Foris LSA Warrant) to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The warrant had a fair value of $4.1 million which was measured using the Black-Scholes-Merton option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant.

On October 28, 2019, the Company and Foris entered into an amended and restated LSA (the A&R LSA), pursuant to which, among other things, certain covenants and related definitions were amended to permit the incurrence of the indebtedness under the October 2019 Naxyris Loan (as defined below), subject to the terms of an amended and restated intercreditor agreement, dated October 28, 2019, between Foris and Naxyris governing the respective rights of the parties with respect to, among other things, the assets securing the A&R Naxyris LSA (as defined below) and the A&R LSA, and additional covenants were added relating to, among other things, maintenance of intellectual property, compliance with laws, delivery of reports and repayment of indebtedness.

On November 27, 2019, the Company borrowed an additional $10.0 million from Foris under the A&R LSA dated October 28, 2019. The new loan has identical terms to the previous loans under the LSA except that the maturity date is March 31, 2023 (as opposed to July 1, 2022 for the other loans under the LSA). In connection with the new loan, the Company issued a warrant to purchase up to 1,000,000 shares of common stock at an exercise price of $3.87 per share, exercisable for a period of two years from issuance (the November 2019 Foris Warrant). The warrant had a fair value of $2.1 million which was measured using the Black-Scholes-Merton option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant. After giving effect to the LSA Loan, there was $91.0 million aggregate principal amount of loans outstanding under the A&R LSA.

Due to multiple changes in key provisions of the LSA through November 27, 2019, the Company analyzed the before and after cash flows from the prior twelve months of modifications resulting from the increased principal balance, decreased interest rate, extended maturity date, waiver of default interest and the fair value of the new LSA Warrant, the October 2019 Foris Warrant and the November 2019 Foris Warrant provided to Foris in order to determine if these changes result in a modification or extinguishment of the original LSA. Based on the combined before and after cash flows of the various note balances making up the new principal balance of the LSA and the fair value of the three warrants, the Company determined that the change in cash flows through and including the October 2019 LSA Amendment were significantly different. Consequently, the October 2019 LSA Amendment was accounting for as a debt extinguishment and a new debt issuance. The Company recorded a $12.8 million loss on extinguishment comprised of (i) $8.7 million unamortized debt discount and (ii) the $4.1 million fair value of the October 2019 Foris LSA Warrant (a non-cash fee paid to the lender).

However, the change in cash flows from the October 2019 LSA Amendment to the November 27, 2019 borrowing under the A&R LSA were not significantly different. As a result, the A&R LSA was accounting for as a debt modification. The Company recorded a new $3.5 million debt discount, comprised of (i) $2.1 million fair value of the November 2019 Warrant, recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the A&R LSA, and (ii) $1.4 million fair value of a bifurcated embedded mandatory redemption feature, recorded as a derivative liability and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the A&R LSA. See Note 3, “Fair Value Measurement” for further information on the valuation and subsequent fair value accounting for the bifurcated embedded derivative.

August 2019 Foris Credit Agreements

On August 28, 2019, the Company and Foris entered into a credit agreement for an unsecured credit facility in an aggregate principal amount of $19.0 million (the August 2019 Foris Credit Agreement), which the Company borrowed in full on August 28, 2019 (the Foris $19 Million Note). The Foris $19 Million Note (i) accrues interest at a rate of 12% per annum, which is payable quarterly in arrears on each March 31, June 30, September 30 and December 31, beginning December 31,

2019, and (ii) matures on January 1, 2023. The Company may at its option repay the amounts outstanding under the Foris $19 Million Note before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment.

The Foris $19 Million Note also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.5 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Foris $19 Million Note. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

In connection with the entry into the August 2019 Foris Credit Agreement, the Company issued to Foris a warrant (the August 2019 Foris Warrant) to purchase up to 4.9 million shares of Common Stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant. The warrant had a $8.7 million fair value and a $5.2 million relative fair value after allocating the Foris $19 Million Note proceeds to the $0.5 million fair value of the embedded mandatory redemption feature contained in the Foris $19 Million Note, and allocating on a residual basis, to the relative fair values of the Foris $19 Million Note and the August 2019 Foris Warrant. The $5.2 million relative fair value of the August 2019 Foris Warrant was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the term of the Foris $19 Million Note.

Also, on August 28, 2019 in connection with the entry into the August 2019 Foris Credit Agreement, the Company and Foris amended the warrant to purchase up to 3.9 million shares of common stock issued to Foris on April 26, 2019 to reduce the exercise price from $5.12 per share to $3.90 per share, and amended the warrant to purchase up to 0.4 million shares of common stock issued to Foris on May 14, 2019 to reduce the exercise price from $4.56 per share to $3.90 per share. The warrant modifications resulted in $1.1 million of incremental value that was recorded as an increase to additional paid in capital and a debt discount to be amortized to interest expense under the effective interest method over the term of the Foris $19 Million Note. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of these warrant modifications.

In addition to the $5.2 million relative fair value of the August 2019 Foris Warrant, the $0.5 million fair value of the embedded mandatory redemption feature, and $1.1 million incremental value related to the warrant modifications, the Company incurred $0.1 million of legal fees in connection the issuing the Foris $19 Million Note. These amounts totaled $6.8 million and were recorded as a debt discount to be amortized as interest expense under the effective interest method over the term of the Foris $19 Million Note. This note was repaid in full in January 2020; see "Warrant Exercise, Common Stock Purchase and Debt Equitization by Foris – Related Party" in Note 15, "Subsequent Events" for additional information.

Naxyris LSA

On August 14, 2019, the Company, certain of the Company’s subsidiaries (the Subsidiary Guarantors) and, as lender, Naxyris, an existing stockholder of the Company and an investment vehicle owned by Naxos Capital Partners SCA Sicar, which is affiliated with NAXOS S.A.R.L. (Switzerland), for which director Carole Piwnica serves as director, entered into a Loan and Security Agreement (the Naxyris Loan Agreement) to make available to the Company a secured term loan facility in an aggregate principal amount of up to $10.4 million (the August 2019 Naxyris Loan), which the Company borrowed in full on August 14, 2019. In connection with the funding of the August 2019 Naxyris Loan, the Company paid Naxyris an upfront fee of $0.4 million.

Loans under the August 2019 Naxyris Loan have a maturity date of July 1, 2022 and accrue interest at a rate per annum equal to the greater of (i) 12% or (ii) the rate of interest payable with respect to any indebtedness of the Company plus 25 basis points, which interest will be payable monthly in arrears, provided that all interest accruing from and after August 14, 2019 through December 1, 2019 shall be due and payable on December 15, 2019.

The obligations of the Company under the Naxyris Loan Agreement are (i) guaranteed by the Subsidiary Guarantors and (ii) secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors (the Collateral), junior in payment priority to Foris subject to certain limitations and exceptions, as well as the terms of the Intercreditor Agreement.

Mandatory prepayments of the outstanding amounts under the August 2019 Naxyris Loan will be required upon the occurrence of certain events, including asset sales, a change in control, and the incurrence of additional indebtedness, subject

to certain exceptions and reinvestment rights. Outstanding amounts under the August 2019 Naxyris Loan must also be prepaid to the extent that the borrowing base exceeds the outstanding principal amount of the loans under the August 2019 Naxyris Loan. In addition, the Company may at its option prepay the outstanding principal amount of the loans under the August 2019 Naxyris Loan in full before the maturity date. Any prepayment of the loans under the August 2019 Naxyris Loan prior to the maturity date, whether pursuant to a mandatory or optional prepayment, is subject to a prepayment charge equal to one year’s interest at the then-current interest rate for the August 2019 Naxyris Loan. Upon any repayment of the loans under the August 2019 Naxyris Loan, whether on the maturity date or earlier pursuant to an optional or mandatory prepayment, the Company will pay Naxyris an end of term fee based on a percentage of the aggregate amount borrowed. In addition, (i) the Company will be required to pay a fee equal to 6% of any amount the Company fails to pay within three business days of its due date and (ii) any interest that is not paid when due will be added to principal and will accrue compound interest at the applicable rate.

The August 2019 Naxyris Loan contains customary affirmative and negative covenants and financial covenants, including covenants related to minimum revenue, minimum liquidity and minimum asset coverage requirements.

The August 2019 Naxyris Loan also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.3 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the August 2019 Naxyris Loan. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

In connection with the entry into the August 2019 Naxyris Loan, on August 14, 2019 the Company issued to Naxyris a warrant (the Naxyris LSA Warrant) to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant. The warrant had a $4.0 million fair value and a $3.0 million relative fair value after allocating the August 2019 Naxyris Loan proceeds to the $0.3 million fair value of the embedded mandatory redemption feature contained in the August 2019 Naxyris Loan, and allocating on a residual basis, to the relative fair values of the August 2019 Naxyris Loan and the Naxyris LSA Warrant. The $3.0 million relative fair value of the Naxyris LSA Warrant was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the term of the August 2019 Naxyris Loan.

In addition to the $3.0 million relative fair value of the Naxyris LSA Warrant and the $0.3 million fair value of the embedded mandatory redemption feature, the August 2019 Naxyris Loan contained $0.4 million original issue discount, $0.5 million mandatory end of term fee and $0.3 million of issuances costs, all totaling $4.5 million. All such amounts were recorded as a debt discount to be amortized to interest expense over the term of the August 2019 Naxyris Loan.

Naxyris LSA Amendment

On October 28, 2019, the Company, the Subsidiary Guarantors and Naxyris amended and restated the Naxyris Loan Agreement (the A&R Naxyris LSA), pursuant to which the maximum loan commitment of Naxyris under the Naxyris Loan Agreement was increased by $10.4 million. On October 29, 2019, the Company borrowed an additional $10.4 million (the October 2019 Naxyris Loan) from Naxyris under the A&R Naxyris LSA, which is subject to the terms and provisions of the A&R Naxyris LSA, including the lien on substantially all of the assets of the Company and the Subsidiary Guarantors. Also, under the terms of A&R Naxyris LSA, the Company owes a 5% end of term fee on the October 2019 Naxyris Loan amount and a $2.0 million term loan fee, both of which are due at July 1, 2022 maturity or upon full repayment of the amounts borrowed under the A&R Naxyris LSA. Also, the Company paid Naxyris an upfront fee of $0.4 million at the funding date of the October 2019 Naxyris Loan. After giving effect to the October 2019 Naxyris Loan amount, there is $24.4 million aggregate principal amount of loans outstanding under the A&R Naxyris LSA.

Also, in connection with the entry into the A&R Naxyris LSA, on October 28, 2019 the Company issued to Naxyris a warrant to purchase up to 2.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance (the October 2019 Naxyris Warrant). The warrant had a $3.6 million fair value and a $2.8 million relative fair value after allocating the October 2019 Naxyris Loan proceeds to the $0.5 million fair value of the embedded mandatory redemption feature contained in the October 2019 Naxyris Loan, and allocating on a residual basis, to the relative fair values of the October 2019 Naxyris Loan and the October 2019 Naxyris Warrant. The $2.8 million relative fair value of the October 2019 Naxyris Warrant was recorded as an increase to additional paid in capital and as a loss on debt extinguishment (as discussed below).

Due to changes in key terms of the Naxyris Loan Agreement through the addition of the October 2019 Naxyris Loan, the Company analyzed the before and after cash flows under the August 2019 Naxyris Loan and October 2019 Naxyris Loan in order to determine if these changes result in a modification or extinguishment of the original Naxyris Loan Agreement. Based on the combined before and after cash flows related to the increased principal balance, increased end of term fees and the fair value of new warrants provided to Naxyris, the Company determined that the change in cash flows were significantly different. Consequently, the October 2019 Naxyris Loan was accounting for as a debt extinguishment and new debt issuance. The Company recorded a $9.7 million loss on extinguishment comprised of (i) $4.0 million of unamortized debt discount, net of the $0.3 million fair value of the bifurcated embedded mandatory redemption feature, (ii) $2.9 million of original issue discount and end of term fees and (iii) the $2.8 million fair value of the October 2019 Naxyris Warrant (a non-cash fee paid to the lender).

The October 2019 Naxyris Loan contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.5 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the new debt issuance. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature. The Company also capitalized $0.4 million of legal fees related to the October 2019 Naxyris Loan as a debt discount.

Schottenfeld September 2019 Credit Agreements

On September 10, 2019, the Company entered into separate credit agreements (the Investor Credit Agreements) with each of Schottenfeld Opportunities Fund II, L.P., Phase Five Partners, LP and Koyote Trading, LLC (the Investors or Schottenfeld Holdings Group LLC) to make available to the Company unsecured credit facilities in an aggregate principal amount of $12.5 million, which the Company borrowed in full on September 10, 2019 and issued to the Investors separate promissory notes in the aggregate principal amount of $12.5 million (the Investor Notes). Each Investor Note (i) accrues interest at a rate of 12% per annum, which is payable quarterly in arrears on each March 31, June 30, September 30 and December 31, beginning December 31, 2019, and (ii) matures on January 1, 2023. The Company may at its option repay the amounts outstanding under the Investor Notes before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment.

The Investor Notes also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.3 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Investor Notes. See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

In connection with the September 10, 2019 Investor Credit Agreements, the Company issued to the Investors warrants (the September 2019 Investor Warrants) to purchase up to an aggregate of 3.2 million shares of common stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance. The September 2019 Investor Warrants had a $7.9 million fair value which was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Investor Notes. See Note 3, “Fair Value Measures” for information regarding the fair value measurement and accounting of these liability warrants.

Schottenfeld November 2019 Credit and Security Agreement

On November 14, 2019, the Company entered into a credit and security agreement (the Schottenfeld CSA) with Schottenfeld Opportunities Fund II, L.P. and Phase Five Partners, LP (two investors affiliated with Schottenfeld Group Holdings LLC) to borrow an additional $7.9 million, resulting in net proceeds to the Company of $7.5 million after deduction of a 5% original issue discount, and to grant the Investor Notes a security interest in the collateral granted to the Investors under the Schottenfeld CSA (as described below). The loans accrue interest at 12% per annum, mature on the earlier to occur of (i) the closing of a $50 million or greater financing and (ii) January 15, 2020, and are secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors, junior in payment priority to Foris and Naxyris subject to the Subordination Agreement among Foris, Naxyris and the Investors. In connection therewith, the Company issued to such investors warrants to purchase an aggregate of 2.0 million shares of common stock at an exercise price of $3.87 per share, with an exercise term of 2 years from issuance (the November 2019 Schottenfeld CSA Warrants). In connection with the warrant issuance, the Company will be required to pay the November 2019 Schottenfeld CSA Warrants holders and the September 2019 Investor Warrants holders a fee if the Company issues equity securities in connection with the $50 million or greater financing provision that have an issue, conversion or exercise price of less than $3.90 or $3.87 per share, respectively. In such case, the fee will be the difference between the exercise price of such warrants (i.e., $3.90 or

$3.87) and the issue, conversion or exercise price of the equity securities issued in the $50 million or greater financing, times the total number of warrants issued to such investors in November 2019 and September 2019. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to repay the $7.9 million loan by January 15, 2020.

The November 2019 Schottenfeld CSA Warrants had a $4.0 million fair value which was recorded as a derivative liability and a loss on debt extinguishment (as discussed below). See Note 3, “Fair Value Measures” for information regarding the fair value measurement and accounting of these liability warrants. Also, the Schottenfeld CSA also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.2 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Schottenfeld CSA (as discussed below). See Note 3, “Fair Value Measurement” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature.

Due to multiple changes in key provisions of Investor Credit Agreements and the Schottenfeld CSA, the Company analyzed the before and after cash flows resulting from the increased principal balance and the fair value of the new November 2019 Schottenfeld CSA Warrants to determine whether these changes result in a modification or extinguishment of the original Schottenfeld and Phase Five notes. Based on the combined before and after cash flows of each note, the change in cash flows was significantly different. Consequently, the Schottenfeld CSA was accounted for as a debt extinguishment and a new debt issuance. The Company recorded an $11.2 million loss upon extinguishment of debt, which was comprised of $6.8 million of unaccreted discount and the balance of the derivative liability recorded in connection with the previous debt instrument, the $4.0 million fair value of the November 2019 Schottenfeld CSA Warrant (as a non-cash fee paid to the lender), and a $0.4 million original issue discount that was netted against the Schottenfeld CSA loan proceeds.

In recording the new debt issuance, the Company also capitalized $0.2 million of legal fees related to the Schottenfeld CSA and the initial fair value of the mandatory redemption feature of $0.2 million was as a debt discount to be amortized to interest expense under the effective interest method over the term of the new debt issuance.

DSM Credit Agreements—Related Party

DSM $25 Million Note

In December 2017, the Company and DSM entered into a credit agreement (the DSM Credit Agreement) to make available to the Company an unsecured credit facility of $25.0 million. On December 28, 2017, the Company borrowed $25.0 million under the DSM Credit Agreement, representing the entire amount available thereunder, and issued a promissory note to DSM in an equal principal amount (the DSM Note). The Company used the proceeds of the amounts borrowed under the DSM Credit Agreement to repay all outstanding principal under a promissory note in the principal amount of $25.0 million issued to Guanfu Holding Co., Ltd. in December 2016 (the Guanfu Note). Given multiple elements in the arrangements with DSM, the Company fair valued the DSM Note to determine the arrangement consideration that should be allocated to the DSM Note. The fair value of the DSM Note was discounted using a Company specific weighted average cost of capital rate that resulted in a debt discount of $8.0 million. The debt discount is being amortized over the loan term using the effective interest method.

The DSM Note (i) is an unsecured obligation of the Company, (ii) matures on December 31, 2021 and (iii) accrues interest from and including December 28, 2017 at 10% per annum, payable quarterly. The DSM Note may be prepaid in full or in part at any time without penalty or premium. The DSM Credit Agreement and the DSM Note contain customary terms, covenants and restrictions, including certain events of default after which the DSM Note may become due and payable immediately.

DSM $8 Million Note

On September 17, 2019, the Company and DSM entered into a credit agreement (the 2019 DSM Credit Agreement) to make available to the Company a secured credit facility in an aggregate principal amount of $8.0 million, to be issued in separate installments of $3.0 million, $3.0 million and $2.0 million, respectively, with each installment being subject to certain closing conditions, including the payment of certain existing obligations of the Company to DSM. On September 17, 2019, the Company borrowed the first installment of $3.0 million under the 2019 DSM Credit Agreement, all of which proceeds were used to pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of $3.0 million. On September 19, 2019, the Company borrowed the second installment of $3.0 million under the 2019 DSM Credit Agreement, all of which proceeds were used to pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of $3.0 million. On September 23, 2019, the Company borrowed the final

installment of $2.0 million under the 2019 DSM Credit Agreement, $1.5 million of which proceeds were used to pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of $2.0 million. The promissory notes issued under the 2019 DSM Credit Agreement (i) mature on August 7, 2022, (ii) accrue interest at a rate of 12.5% per annum from and including the applicable date of issuance, which interest is payable quarterly in arrears on each January 1, April 1, July 1 and October 1, beginning January 1, 2020, and (iii) are secured by a first-priority lien on certain Company intellectual property licensed to DSM. The Company may at its option repay the amounts outstanding under the 2019 DSM Credit Agreement before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment. In addition, the Company is required to repay the amounts outstanding under the 2019 DSM Credit Agreement (i) in an amount equal to the gross cash proceeds, if any, received by the Company upon the exercise by DSM of any of the common stock purchase warrants issued by the Company to DSM on May 11, 2017 or August 7, 2017 (see Note 6, “Stockholders’ Deficit”) and (ii) in full upon the request of DSM at any time following the receipt by the Company of at least $50.0 million of gross cash proceeds from one or more sales of equity securities of the Company on or prior to June 30, 2020. In connection with issuance of the 2019 DSM Credit Agreement, the Company incurred $0.3 million of legal fees which were recorded as a debt discount to be amortized as interest expense under the effective interest method over the term of the 2019 DSM Credit Agreement.

Ginkgo Note, Partnership Agreement and Note Amendment

In November 2017, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a partnership agreement (Ginkgo Partnership Agreement) to replace and supersede the 2016 Ginkgo Collaboration Agreement. Under the Ginkgo Partnership Agreement, the Company and Ginkgo agreed:

•to issue the $12 million November 2017 Ginkgo Note (as defined below), which effectively guarantees Ginkgo $12 million minimum future royalties under the profit margin sharing provisions noted below;

•to pay Ginkgo quarterly fees of $0.8 million (Partnership Payments) for a total of $12.7 million, beginning on December 31, 2018 and ending on September 30, 2022;

•to share profit margins from sales of a certain product to be developed under the Ginkgo Partnership Agreement on a 50/50 basis, subject to certain conditions, provided that net profits will be payable to Ginkgo for any quarterly period to the extent that such net profits exceed the sum of (a) quarterly interest payments due under the November 2017 Ginkgo Note and (b) Partnership Payments due in such quarter;

•to continue to collaborate on limited research and development; and

•to provide each other licenses (with royalties) to specified intellectual property for limited purposes.

The Ginkgo Partnership Agreement provides for an initial term of two years and will automatically renew for successive one-year terms thereafter unless otherwise terminated. The Company does not expect to recognize any future revenue under this arrangement.

The Company recorded the $6.1 million present value of the $12.7 million partnership payments in other liabilities (see Note 2, "Balance Sheet Details"), with the remaining $6.6 million recorded as a debt discount to be recognized as interest expense under the effective interest method over the five-year payment term. The Company also concluded the partnership payment obligation under the Ginkgo Partnership Agreement represents consideration payable to a former customer; and consequently, the present value of the partnership payments should be recorded as a reduction of cumulative revenue recognized to date from Ginkgo in the period the partnership agreement was executed. The Company reached a similar conclusion regarding the $12.0 million Ginkgo Note described below. In total, the Company recorded a $13.1 million reduction in licenses and royalties revenue and $13.1 million in notes payable and other liabilities as of and for the year ended December 31, 2017 upon execution of the Ginkgo Partnership Agreement.

In November 2017, the Company issued an unsecured promissory note in the principal amount of $12.0 million to Ginkgo (the November 2017 Ginkgo Note) in connection with the termination of the Ginkgo Collaboration Agreement and the execution of the Ginkgo Partnership Agreement. The November 2017 Ginkgo Note accrues interest at 10.5% per annum, payable monthly, and has a maturity date of October 19, 2022. The November 2017 Ginkgo Note may be prepaid in full without penalty or premium at any time, provided that certain payments have been made under the Company’s partnership agreement with Ginkgo. The November 2017 Ginkgo Note also contains customary terms, covenants and restrictions, including certain events of default after which the note may become due and payable immediately. The Company recorded the $7.0 million present value of the November 2017 Ginkgo Note as a note payable liability, and the remaining $5.0 million was recorded as a debt discount which is being accreted to interest expense over the loan term using the effective interest method.

On September 29, 2019, in connection with Ginkgo granting certain waivers under the November 2017 Ginkgo Note and the Ginkgo Partnership Agreement, (i) the Company and Ginkgo amended the November 2017 Ginkgo Note to increase the

interest rate from 10.5% per annum to 12% per annum, beginning October 1, 2019, (ii) Ginkgo agreed to waive default interest, defer past due interest and partnership payments under the November 2017 Ginkgo Note and Ginkgo Partnership Agreement until December 15 and (iii) the Company agreed to pay a cash waiver fee of $1.3 million, payable in installments of $0.5 million on December 15, 2019 and $0.8 million on March 31, 2020. The Company accounted for this amendment as a modification and accrued the $1.3 million waiver fee in other current liabilities and a charge to interest expense during the year ended December 31, 2019. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to pay the $5.2 million past due interest, default interest on past due amounts, partnership payments and the $0.5 million waiver fee installment on December 15, 2019.

6% Convertible Notes Due 2021

In December 2018, the Company issued $60.0 million in aggregate principal amount of senior convertible notes (the 6% Convertible Notes Due 2021) for $56.2 million of net proceeds, after deducting offering expenses and placement agent and advisory fees.

The Company elected to account for the 6% Convertible Notes Due 2021 at fair value as of the issuance date. Management believes that the fair value option better reflects the underlying economics of the 6% Convertible Notes Due 2021, which contain multiple embedded derivatives. Under the fair value election, changes in fair value are reported in the consolidated statements of operations as "(Loss) gain from change in fair value of debt" in each reporting period subsequent to the issuance of the 6% Convertible Notes Due 2021.

In May, June and July 2019, the Company exchanged the 6% Convertible Notes Due 2021 for new senior convertible notes and warrants to purchase common stock. Since the Company elected the fair value accounting option for the 6% Convertible Notes and records all changes in fair value through (Loss) gain from change in fair value of debt in the consolidated statement of operations, this series of exchanges was not required to be evaluated for modification or extinguishment accounting treatment. However, the Company considered the issuance of the warrant in connection with these exchanges as compensation to the noteholders for waiving certain covenant violations during the period, and recorded a $5.3 million increase to additional paid in capital and a charge to interest expense for the fair value of the equity-classified May 15, 2019, June 24, 2019 and July 24, 2019 warrants. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant.

On November 8, 2019, the Company entered into a Securities Exchange Agreement with certain private investors (the Investors), pursuant to which the Investors purchased the 6% Convertible Notes Due 2021 from the original holder and subsequently exchanged the 6% Convertible Notes Due 2021 with the Company for new 5% Senior Convertible Notes (the Senior Convertible Notes Due 2022) having an aggregate principal amount of $66.0 million. See the Senior Convertible Notes Due 2022 section below for further information on the exchange.

The Company evaluated the Investor’s purchase of the 6% Convertible Notes Due 2021 from the original holder and subsequent exchange with the Company for the Senior Convertible Notes Due 2022 and determined the purchase and exchange met the criteria for extinguishment accounting. The Company recorded a $1.9 million loss of debt extinguishment as of December 31, 2019, determined as follows:

In thousands
Fair value at December 31, 2018	$	57,918
Less: principal paid in cash during 2019	(13,395)
Less: principal converted to common stock during 2019	(15,000)
Loss on change in fair value during 2019	18,303
Accrued interest	3,168
Carrying value of registration rights liability	5,757
Net carrying value at extinguishment	56,751
Total reacquisition price	58,640
Loss on debt extinguishment	$	1,889

Senior Convertible Notes Due 2022

As discussed above under the 6% Convertible Notes Due 2021 section, on November 8, 2019, the Company entered into a securities exchange agreement with certain private investors (the Investors). The Investors completed the purchase of the Second Exchange Note from the current holder, and on November 15, 2019 the Company exchanged the 6% Convertible Notes Due 2021 held by the Investors for the Senior Convertible Notes Due 2022.

The Senior Convertible Notes Due 2022 are general unsecured obligations of the Company and will mature on September 30, 2022 unless earlier converted or redeemed.

The Senior Convertible Notes Due 2022 are payable in fixed monthly installments of $3.0 million from February 1, 2020 through July 1, 2020 and then $3.4 million monthly thereafter in either cash or, at the Company’s option, subject to the satisfaction of certain equity conditions, in shares of common stock at a discount to the then-current market price, subject to a price floor. The holders have the right, upon notice to the Company, to defer all or any portion of any installment amount to a future installment date. Each installment payment will reduce the principal amount under the Senior Convertible Notes Due 2022 by 90% of the amount of such installment payment.

The Senior Convertible Notes Due 2022 accrue interest at a rate of 5% per annum, and is payable on each installment date. Interest on the Senior Convertible Notes Due 2022 may be paid in either cash or, at the Company’s option, subject to the satisfaction of the equity conditions, shares of common stock at the installment conversion price. Upon the occurrence and during the continuation of an event of default, interest on the Senior Convertible Notes Due 2022 will accrue at a rate of 15% per annum.

The Company may at its option redeem the Senior Convertible Notes Due 2022, in full, at a price equal to 115% of the greater of (A) the principal amount of the Senior Convertible Notes Due 2022 being redeemed and (B) the intrinsic value of the shares of common stock underlying the principal amount of the Senior Convertible Notes Due 2022 being redeemed. In addition, the Company is required to (i) redeem the Senior Convertible Notes Due 2022 in an aggregate amount of $10.0 million following the receipt by the Company of at least $75.0 million of aggregate net cash proceeds from one or more financing transactions, at a price equal to 110% of the amount being redeemed and (ii) redeem the Senior Convertible Notes Due 2022 in an aggregate amount of $10.0 million on December 31, 2019, at a price equal to 110% of the amount being redeemed, in each case unless such redemption is deferred by the holder, and (iii) raise aggregate net cash proceeds of $30 million by December 31, 2019 and an additional $75 million by March 15, 2020 from one or more financing transactions by January 31, 2020. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to redeem $10 million of the Senior Convertible Notes Due 2022 and raise aggregate cash proceeds of $30 million on or by December 31, 2019 and a description of an amendment to certain other redemption provisions in the Senior Convertible Notes Due 2022.

The Senior Convertible Notes Due 2022 are convertible from time to time, at the election of the holders, into shares of common stock at an initial conversion price of $5.00 per share. The conversion price is subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

The Senior Convertible Notes Due 2022 contain customary terms and covenants, including (i) a restriction on the Company’s ability to incur additional indebtedness, (ii) covenants related to minimum revenue, minimum liquidity, financing activity and the conversion or exchange of existing indebtedness into equity, (iii) certain events of default, after which the holders may (A) require the Company to redeem all or any portion of their Senior Convertible Notes Due 2022 in cash at a price equal to 115% of the amount being redeemed and (B) convert all or any portion of their Senior Convertible Notes Due 2022 at a discount to the Installment conversion price and (iv) certain other events, after which the holders may convert all or any portion of their Senior Convertible Notes Due 2022 at a discount to the conversion price. See Note 15, “Subsequent Events” for further information regarding the amendment to certain conversion provisions in the Senior Convertible Notes Due 2022.

Notwithstanding the foregoing, the holders do not have the right to convert any portion of a New Note, and the Company does not have the option to pay any amount under the Senior Convertible Notes Due 2022 in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding immediately after giving effect to such conversion or payment, as applicable (the Ownership Limitation) or (b) the aggregate number of shares issued with respect to the Senior Convertible Notes Due 2022 (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed the limitation imposed by Nasdaq Listing Standard Rule 5635(d) (the Exchange Cap), unless Stockholder Approval (as defined below) has been obtained. In the event that (i) the Company is prohibited from issuing any shares of common stock under the Senior Convertible Notes Due 2022 as a result of the Ownership Limitation (other than in connection with a conversion of Senior Convertible Notes Due 2022), the related principal amount of the Senior Convertible Notes Due 2022 shall be deferred to a future installment date as determined by the holder, and (ii) after January 31, 2020, the Company is prohibited from issuing

any shares of common stock under the Senior Convertible Notes Due 2022 as a result of the Exchange Cap, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Exchange Cap.

Pursuant to the Senior Convertible Notes Due 2022, the Company agreed to use commercially reasonable efforts to obtain from the Company’s stockholders the approval contemplated by Nasdaq Listing Standard Rule 5635(d) with respect to the issuance of shares of common stock upon conversion of, or otherwise pursuant to, the Senior Convertible Notes Due 2022 in excess of the limitation imposed by such rule, including without limitation the issuance of shares of common stock upon conversion of, or otherwise pursuant to, the Senior Convertible Notes Due 2022 in excess of the Exchange Cap (the Stockholder Approval), at an annual or special meeting of stockholders to be held on or prior to January 31, 2020. Pursuant to the Senior Convertible Notes Due 2022, if the Company does not obtain the Stockholder Approval by January 31, 2020, the Company will use best efforts to obtain the Stockholder Approval thereafter. See Note 15, “Subsequent Events” for further information regarding the amendment, forbearance and waiver to certain provisions in the Senior Convertible Notes Due 2022, including the deadline for the Company to seek the Stockholder Approval.

The Company has elected to account for the Senior Convertible Notes Due 2022 at fair value, as of the issuance date. Management believes that the fair value option better reflects the underlying economics of the Senior Convertible Notes Due 2022, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the Senior Convertible Notes Due 2022. For the year ended December 31, 2019, the Company recorded a gain of $3.8 million, which is shown as Fair Value Adjustment in the table at the beginning of this Note 4. See Note 3, "Fair Value Measurement" for information about the assumptions that the Company used to measure the fair value of the Senior Convertible Notes Due 2022.

Nikko Loan Agreements and Notes

The loans payable to Nikko Chemicals Co., Ltd. at December 31, 2019 are comprised of the following (amounts in thousands):

Description	Date Issued	Original Loan Amount		Balance at December 31, 2019		Interest Rate per Annum	Maturity Date
Nikko $5.0M Note	July 29, 2019	$	5,000	$	5,000	5.00%	December 18, 2020
Nikko $4.5M Note	December 19, 2019	4,500		4,500		2.75%	January 31, 2020
Nikko $3.9M Note	December 19, 2016	3,900		2,862		5.00%	December 1, 2029
Nikko $1.5M Note B	August 3, 2017	1,500		900		2.75%	August 1, 2020
Nikko $450K Note	December 9, 2019	450		450		2.75%	March 31, 2020
Nikko $350K Note	November 20, 2019	350		350		2.75%	January 31, 2020
Nikko $200K Capex Loan	February 1, 2019	200		171		5.00%	January 1, 2026
Nikko $500K Note	October 31, 2019	500		84		2.75%	January 10, 2020
		$	16,400	$	14,317

Nikko Loan Agreements

On July 29, 2019, the Company and Nikko entered into a loan agreement (the Nikko Loan Agreement) to make available to the Company secured loans in an aggregate principal amount of $5.0 million, to be issued in separate installments of $3.0 million and $2.0 million, respectively. On July 30, 2019, the Company borrowed the first installment of $3.0 million under the Nikko Loan Agreement and received net cash proceeds of $2.8 million, with the remaining $0.2 million being withheld by Nikko as prepayment of the interest payable on such loan through the maturity date. On August 8, 2019, the Company borrowed the remaining $2.0 million available under the Nikko Loan Agreement and received net cash proceeds of $1.9 million, with the remaining $0.1 million being withheld by Nikko as prepayment of the interest payable on such loan through the maturity date. The loans (i) mature on December 18, 2020, (ii) accrue interest at a rate of 5% per annum from and including the applicable loan date through the maturity date, which interest is required to be prepaid in full on the date of the applicable loan, and (iii) are secured by a first-priority lien on 12.8% of the Aprinnova JV interests owned by the Company.

On December 19, 2019, the Company borrowed $4.5 million from Nikko under a second secured loan agreement. The loan (i) matures on January 31, 2020, (ii) accrues interest at a rate of 2.75% per annum, and (iii) is secured by a first-priority lien on 27.2% of the Aprinnova JV interests owned by the Company. See Note 15, “Subsequent Events” for further information regarding the Company’s failure to pay the $4.5 million loan on January 31, 2020.

Nikko Notes

Facility Note: In December 2016, in connection with the Company's formation of its cosmetics joint venture (the Aprinnova JV) with Nikko Chemicals Co., Ltd. (Nikko), Nikko made a loan to the Company in the principal amount of $3.9 million and the Company issued a promissory note (the Nikko Note) to Nikko in an equal principal amount. The proceeds of the Nikko Note were used to satisfy the Company's remaining liabilities related to the Company's purchase of a manufacturing facility in Leland, North Carolina and related assets in December 2016, including liabilities under a promissory note in the principal amount of $3.5 million issued in connection therewith. The Nikko Note (i) accrues interest at 5% per year, (ii) has a term of 13 years, (iii) is payable in equal monthly installments of principal and interest beginning on January 1, 2017 and (iv) is secured by a first-priority lien on 10% of the Aprinnova JV interests owned by the Company. In addition, the Company is required to repay the Nikko Note with any profits distributed to the Company by the Aprinnova JV, beginning with the distributions for the fourth fiscal year of the Aprinnova JV, until the Nikko Note is fully repaid. The Nikko Note may be prepaid in full or in part at any time without penalty or premium. The Nikko Note contains customary terms and provisions, including certain events of default after which the Nikko Note may become due and payable immediately.

Aprinnova JV Working Capital Notes: In February 2017, in connection with the formation of the Aprinnova JV in December 2016, Nikko made a working capital loan to the Aprinnova JV in the principal amount of $1.5 million (the First Aprinnova Note). The First Aprinnova Note was fully repaid in January 2018. In August 2017, Nikko made a second working capital loan to the Aprinnova JV in the principal amount of $1.5 million (the Second Aprinnova Note). The Second Aprinnova Note was payable in full on August 1, 2019, with interest payable quarterly. Both notes accrue interest at 2.75% per annum. Effective July 31, 2019, the Company repaid $500,000 and agreed with Nikko to extend the term of the Second Aprinnova Note to August 1, 2020. Under the terms of the extension, the Company is required to make four quarterly principal payments of $100,000 each beginning November 1, 2019 through May 1, 2020 and a final payment of $700,000 at August 1, 2020 maturity.

Aprinnova JV Palladium Notes: In October, November and December 2019, Nikko advanced Aprinnova JV a total of $1.3 million under three separate promissory notes to purchase a palladium catalyst used in the manufacturing process at the Leland facility. These short-term notes accrue interest at 2.75% per annum and mature between January 10, 2020 and March 31, 2020. As of February 28, 2020, the total $1.3 million of note balances has been fully repaid in cash and are no longer outstanding.

Aprinnova JV CapEx Note: On February 1, 2019, the Aprinnova JV and Nikko agreed to fund Nikko’s $0.2 million share of the joint venture’s 2018 capital expenditures through an unsecured seven-year promissory note (the 2018 CapEx Note). The 2018 CapEx note (i) requires quarterly principal payments of $7,200 beginning April 1, 2019, (ii) accrues 5% simple interest per annum, and (iii) matures on January 1, 2026.

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.0 million of restricted cash, noncurrent in connection with this arrangement as of December 31, 2019 and 2018.

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Commitments and Contingencies

12 Months Ended

Dec. 31, 2019

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

Guarantor Arrangements

The Company has agreements whereby it indemnifies its executive officers and directors for certain events or occurrences while the executive officer or director is serving in his or her official capacity. The indemnification period remains enforceable for the executive officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of December 31, 2019 and 2018.

The Foris LSA debt facility (see Note 4, "Debt") is collateralized by first-priority liens on substantially all of the Company's assets, including Company intellectual property, other than certain Company intellectual property licensed to DSM and the Company's shares of Aprinnova. Certain of the Company’s subsidiaries have guaranteed the Company’s obligations under the Foris LSA.

The obligations of the Company under the Naxyris note (see Note 4, "Debt") are (i) guaranteed by the Subsidiary Guarantors and (ii) secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors (the Collateral), junior in payment priority to Foris subject to certain limitations and exceptions, as well as the terms of the Intercreditor Agreement.

The Nikko debt instruments are collateralized as follows:

•Nikko $3.9 million note: first-priority lien on 10.0% of the Aprinnova JV interests owned by the Company

•Nikko $5.0 million note: first-priority lien on 12.8% of shares of Aprinnova

•Nikko $4.5 million note: first-priority lien on 27.2% of shares of Aprinnova

The promissory notes issued under the 2019 DSM Credit Agreement (see Note 4, "Debt") are secured by a first-priority lien on certain Company intellectual property licensed to DSM.

The obligations of the Company under the Investor Notes and the Schottenfeld CSA (see Note 4, "Debt" and Note 15, “Subsequent Events”) are secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors, junior in payment priority to Foris and Naxyris subject to the Subordination Agreement among Foris, Naxyris and the Investors.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgement. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all persons and entities that purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The complaint, which was amended by the lead plaintiff on September 13, 2019, alleges securities law violations based on statements and omissions made by the Company during such period. On October 25, 2019, the defendants filed a motion to dismiss the securities class action

complaint. The hearing on such motion to dismiss was held on February 18, 2020 and we are awaiting a ruling from the Court. Subsequent to the filing of the securities class action complaint described above, on June 21, 2019 and October 1, 2019, respectively, two separate purported shareholder derivative complaints were filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr, et al., and Carlson v. Doerr, et al.) based on similar allegations to those made in the securities class action complaint described above and named the Company and certain of the Company’s current and former officers and directors as defendants. The derivative lawsuits sought to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and omissions made in connection with the Company’s securities filings. The derivative lawsuits were dismissed on October 18, 2019 (Bonner) and December 10, 2019 (Carlson), without prejudice. We believe the securities class action complaint lacks merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

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Related Party Transactions - Related Party Accounts Payable (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Due to Related Parties, Current, Total	$ 18,492	$ 23,667
Related party debt, net of current portion	149,515	18,689
Accounts Payable, Accrued Liabilities, And Other Current Liabilities | DSM International B.V.
Related Party Transaction [Line Items]
Due to Related Parties, Current, Total	14,000	2,100
Other Noncurrent Liabilities | DSM International B.V.
Related Party Transaction [Line Items]
Related party debt, net of current portion	$ 3,800	$ 3,600

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Basis of Presentation and Summary of Significant Accounting Policies - Concentration of Credit Risk (Details) - Customer Concentration Risk	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Accounts Receivable | Customer A
Concentration risk, percentage	19.00%
Accounts Receivable | Customer B
Concentration risk, percentage	21.00%	24.00%
Accounts Receivable | Customer C
Concentration risk, percentage		19.00%
Accounts Receivable | Customer E
Concentration risk, percentage		11.00%
Accounts Receivable | Customer F
Concentration risk, percentage	10.00%
Revenues | Customer A
Concentration risk, percentage	35.00%	17.00%
Revenues | Customer B
Concentration risk, percentage		18.00%
Revenues | Customer C
Concentration risk, percentage		13.00%
Revenues | Customer D
Concentration risk, percentage		13.00%
Revenues | Customer G
Concentration risk, percentage	12.00%

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Related Party Transactions - Schedule of Related Party Debt (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Long-term debt, gross	$ 297,462	$ 228,921
Unaccreted Debt (Discount) Premium	(20,314)	(17,142)
Long-term debt	261,772	209,697
Related Party Debt | DSM International B.V. | DSM Note
Related Party Transaction [Line Items]
Long-term debt, gross	33,000	25,000
Unaccreted Debt (Discount) Premium	(4,621)	(6,311)
Long-term debt	28,379	18,689
Related Party Debt | Foris Ventures, LLC
Related Party Transaction [Line Items]
Long-term debt, gross	182,966	49,705
Unaccreted Debt (Discount) Premium	(14,959)	(7,349)
Long-term debt	168,007	42,356
Related Party Debt | Foris Ventures, LLC | Foris Notes
Related Party Transaction [Line Items]
Long-term debt, gross	115,351	0
Unaccreted Debt (Discount) Premium	(9,516)	0
Long-term debt	105,835	0
Related Party Debt | Foris Ventures, LLC | Related Party 2014 144A Convertible Notes
Related Party Transaction [Line Items]
Long-term debt, gross	0	5,000
Unaccreted Debt (Discount) Premium	0	(181)
Long-term debt	0	4,819
Related Party Debt | Foris Ventures, LLC | Foris Debt
Related Party Transaction [Line Items]
Long-term debt, gross	115,351	5,000
Unaccreted Debt (Discount) Premium	(9,516)	(181)
Long-term debt	105,835	4,819
Related Party Debt | Naxyris S.A. | Naxyris Note
Related Party Transaction [Line Items]
Long-term debt, gross	24,437	0
Unaccreted Debt (Discount) Premium	(822)	0
Long-term debt	23,615	0
Related Party Debt | Temasek | Related Party 2014 144A Convertible Notes
Related Party Transaction [Line Items]
Long-term debt, gross	0	10,000
Unaccreted Debt (Discount) Premium	0	(435)
Long-term debt	0	9,565
Related Party Debt | Total | The 2014 144A Notes
Related Party Transaction [Line Items]
Long-term debt, gross	10,178	9,705
Unaccreted Debt (Discount) Premium	0	(422)
Long-term debt	$ 10,178	$ 9,283

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Stock-based Compensation (Tables)

12 Months Ended

Dec. 31, 2019

Compensation Related Costs [Abstract]

Share-based Payment Arrangement, Expensed and Capitalized, Amount

Stock-based compensation expense related to all employee stock compensation plans, including options, restricted stock units and ESPP, was as follows:

Years Ended December 31, (In thousands)	2019		2018
Research and development	$	2,900	$	1,797
Sales, general and administrative	9,654		7,393
Total stock-based compensation expense	$	12,554	$	9,190

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions

The assumptions used to estimate the fair value of this award with performance and market vesting conditions were as follows:

Stock Option Award with Performance and Market Vesting Conditions:
Fair value of the Company’s common stock on grant date	$	5.08
Expected volatility	70		%
Risk-free interest rate	2.75		%
Dividend yield	0.0		%

The fair value of employee stock options and employee stock purchase plan rights was estimated using the following weighted-average assumptions:

Years Ended December 31,	2019	2018
Expected dividend yield	—%	—%
Risk-free interest rate	1.8%	2.8%
Expected term (in years)	6.9	6.9
Expected volatility	84%	80%

Disclosure of Share-based Compensation Arrangements by Share-based Payment Award

Stock option activity is summarized as follows:

Year ended December 31,	2019		2018
Options granted	530,140		4,337,119
Weighted-average grant-date fair value per share	$	3.83	$	5.18
Compensation expense related to stock options (in millions)	$	2.0	$	2.6
Unrecognized compensation costs as of December 31 (in millions)	$	4.5	$	8.5

Share-based Payment Arrangement, Option and Stock Appreciation Rights, Activity

The Company’s stock option activity and related information for the year ended December 31, 2019 was as follows:

	Number of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding - December 31, 2018	5,390,270	$	11.55	8.5	$	29
Options granted	530,140	$	3.83
Options exercised	(7,445)	$	3.60
Options forfeited or expired	(292,546)	$	17.18
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Vested or expected to vest after December 31, 2019	5,037,260	$	10.88	7.7	$	23
Exercisable at December 31, 2019	1,314,113	$	27.46	6.1	$	10

Share-based Payment Arrangement, Restricted Stock and Restricted Stock Unit, Activity

The Company’s RSU and restricted stock activity and related information for the year ended December 31, 2019 was as follows:

	Number of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life (in years)
Outstanding - December 31, 2018	5,294,803	$	5.50	1.4
Awarded	2,996,660	$	3.96
Vested	(1,891,931)	$	5.51
Forfeited	(616,881)	$	4.84
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Vested or expected to vest after December 31, 2019	5,338,558	$	4.78	1.6

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Related Party Transactions - Office Sublease (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Related Party Transactions [Abstract]
Operating leases, rent expense, sublease rentals	$ 0.6	$ 0.6

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Stockholders' Deficit (Tables)

12 Months Ended

Dec. 31, 2019

Stockholders' Equity Note [Abstract]

Schedule of Debt Conversions

In connection with various debt transactions (see Note 4, "Debt"), the Company issued certain convertible notes and preferred shares that are convertible into shares of common stock as follows as of December 31, 2019, at any time at the election of each debtholder:

	Number of Shares Instrument Is Convertible into as of December 31, 2019
Senior convertible notes due 2022	13,200,000
2014 Rule 144A convertible notes	181,238
Series D preferred stock (8,280 shares outstanding at December 31, 2019)	1,943,661
	15,324,899

Schedule of Stockholders' Equity Note, Warrants or Rights

The following table summarizes warrant activity for the year ended December 31, 2019:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2018	Additional Warrants Issued	Exercises	Expiration	Exercise Price per Share of Warrants Exercised		Number Outstanding as of December 31, 2019	Exercise Price per Share as of December 31, 2019
Foris LSA warrants	2019	August 14, 2021	—	3,438,829	—	—	$	—	3,438,829	$2.87
November 2019 Foris warrant	2019	November 27, 2021	—	1,000,000	—	—	$	—	1,000,000	$3.87
August 2019 Foris warrant	2019	August 28, 2021	—	4,871,795	—	—	$	—	4,871,795	$3.90
April 2019 PIPE warrants	2019	April 6, 2021, April 29, 2021 and May 3, 2021	—	8,084,770	—	—	$	—	8,084,770	$3.90/$4.76/$5.02
April 2019 Foris warrant	2019	April 16, 2021	—	5,424,804	—	—	$	—	5,424,804	$2.87
September and November 2019 Investor Credit Agreement warrants	2019	September 10, 2021 and November 14, 2021	—	5,233,551	—	—	$	—	5,233,551	$3.87/$3.90
Naxyris LSA warrants	2019	October 28, 2021	—	2,000,000	—	—	$	—	2,000,000	$2.87
October 2019 Naxyris warrant	2019	October 28, 2021	—	2,000,000	—	—	$	—	2,000,000	$3.87
May-June 2019 6% Note Exchange warrants	2019	May 15, 2021 and June 24, 2021	—	2,181,818	—	—	$	—	2,181,818	$2.87/$5.12
May 2019 6.50% Note Exchange warrants	2019	May 10, 2021 and May 14, 2021	—	1,744,241	—	—	$	—	1,744,241	$3.90/$5.02
July 2019 Wolverine warrant	2019	July 8, 2021	—	1,080,000	—	—	$	—	1,080,000	$2.87
August 2018 warrant exercise agreements	2018	May 17, 2020 and May 20, 2020	12,097,164	—	—	—	$	—	12,097,164	$2.87/$7.52
April 2018 warrant exercise agreements	2018	July 12, 2019	3,616,174	—	—	(3,616,174)	$	—	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,244,820	—	(166,664)	—	$	2.87000	6,078,156	$2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	0.00015	3,968,116	$2.87
May 2017 dilution warrants	2017	July 10, 2022	47,978	4,795,924	(1,758,009)	—	$	0.00015	3,085,893	$0.0015
August 2017 dilution warrants	2017	May 23, 2023	—	3,028,983	—	—	$	—	3,028,983	$0.0001
February 2016 related party private placement	2016	February 12, 2021	171,429	—	—	—	$	—	171,429	$0.15
July 2015 related party debt exchange	2015	July 29, 2020 and July 29, 2025	133,334	—	—	—	$	—	133,334	$0.15
July 2015 private placement	2015	July 29, 2020	81,197	—	(8,547)	—	$	0.15000	72,650	$0.15
July 2015 related party debt exchange	2015	July 29, 2020	58,690	—	—	—	$	—	58,690	$0.15
July 2015 related party debt exchange	2015	July 29, 2020	471,204	245,558	(716,762)	—	$	0.15000	—	$	—
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$160.05
			26,891,512	45,130,273	(2,649,982)	(3,616,174)	$	0.22166	65,755,629

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Fair Value Measurement - Senior Convertible Notes Due 2022 (Details) $ in Thousands	Nov. 15, 2019 USD ($) shares	Dec. 31, 2019 USD ($) shares	Dec. 31, 2018 USD ($) shares
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt		$ 261,772	$ 209,697
Common stock issued (in shares) | shares		117,742,677	76,564,829
Convertible Senior Notes 6.0% due in 2022
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument, face amount	$ 66,000
Common stock issued (in shares) | shares	7,500,000
Subordinated borrowing, interest rate	9.75%
Additional paid in capital	$ 4,200
Debt instrument, term	19 months
Convertible Senior Notes 6.0% due in 2022 | Measurement Input, Discount Rate
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt, measurement input	2.33
Convertible Senior Notes 6.0% due in 2022 | Stock price volatility
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt, measurement input	0.45
Convertible Senior Notes 6.0% due in 2022 | Probability of Principal Repayment in Cash
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt, measurement input	0.25
Convertible Senior Notes 6.0% due in 2022 | Probability of Principal Repayment in Stock
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt, measurement input	0.75
Convertible Senior Notes 6.0% due in 2022 | Probability of Change of Control
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt, measurement input	0.05
Convertible Senior Notes 6.0% due in 2022 | Convertible Debt Securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Long-term debt	$ 50,600

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Fair Value Measurement - Derivative Liabilities Recognized in Connection with the Issuance of Debt and Equity Instruments (Details) $ in Thousands	3 Months Ended	12 Months Ended
	Dec. 31, 2019 USD ($) derivative instrument	Dec. 31, 2019 USD ($) derivative	Dec. 31, 2018 USD ($)	Nov. 14, 2019 USD ($)	Sep. 10, 2019 USD ($)	Jan. 01, 2019 USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative liabilities	$ 41,000	$ 41,000				$ 41,000
Debt instrument, number issued | instrument	4
Long-term and short-term debt	$ 195,800	195,800	$ 151,800	$ 4,000	$ 7,900
Loss upon extinguishment of debt		(44,208)	$ (17,424)
Warrants not settleable in cash, fair value disclosure	$ 6,900	6,900
Fair value adjustment of warrants, loss (gain)		$ (4,800)
Maximum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivative, number Of instruments held | derivative	4	4
Minimum
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivative, number Of instruments held | derivative	2	2
DSM Securities Purchase Agreement
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative liabilities	$ 3,800	$ 3,800
Two Derivative Liabilities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative liabilities	2,500	2,500
Loss upon extinguishment of debt		500
Fair value of embedded derivative liability	700	700
Four Derivative Liabilities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of embedded derivative liability	$ 2,800	$ 2,800

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Fair Value Measurement - Assets and Liabilities Measured and Recorded at Fair Value on a Non-Recurring Basis (Details) $ in Thousands			12 Months Ended
	Mar. 29, 2019 USD ($)	Nov. 19, 2018 USD ($) shares	Dec. 31, 2019 USD ($)	Dec. 31, 2018 USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Issuance of common stock for cash (in shares) | shares		1,643,991
Issuance of common stock in private placement, net of issuance costs of $0			$ 14,221	$ 1,415
DSM Supply Agreement
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Contract with customer after allowance for credit loss		$ 22,700
Issuance of common stock for cash (in shares) | shares		1,643,991,000,000
Issuance of common stock in private placement, net of issuance costs of $0	$ 7,300	$ 6,100
Warrant modification		2,900
Payments for obligation settlements		$ 1,800
DSM Supply Agreement | Measurement Input, Discount Rate
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Supply agreement, measurement input		0.225
DSM Supply Agreement | Discount to Gross Cash Flows
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Supply agreement, measurement input		0

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Debt - Letters of Credit (Details) - USD ($)	Dec. 31, 2019	Dec. 31, 2018	Jun. 30, 2012
Debt Conversion [Line Items]
Letters of credit outstanding			$ 1,000,000.0
Restricted cash, noncurrent	$ 960,000	$ 960,000
Letter of Credit
Debt Conversion [Line Items]
Restricted cash, noncurrent	$ 1,000,000.0

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Debt - Schottenfeld November 2019 Credit and Security Agreement (Details) $ / shares in Units, shares in Millions		12 Months Ended
	Nov. 14, 2019 USD ($) investors $ / shares shares	Dec. 31, 2019 USD ($)	Dec. 31, 2018 USD ($)
Debt Conversion [Line Items]
Fair value adjustments of warrants		$ (4,800,000)
Loss upon extinguishment of debt		$ (44,208,000)	$ (17,424,000)
Schottenfeld November 2019 Credit and Security Agreement
Debt Conversion [Line Items]
Number of Investors | investors	2
Debt instrument, additional face amount	$ 7,900,000
Proceeds from debt	$ 7,500,000
Basis spread on variable rate	5.00%
Interest rate per annum	12.00%
Extinguishment of debt	$ 50,000,000
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	2.0
Exercise price of warrants or rights (in dollars per share) | $ / shares	$ 3.87
Debt instrument, term	2 years
Debt conversion, converted instrument, amount	$ 50,000,000
Fair value adjustments of warrants	4,000,000.0
Fair value of embedded derivative liability	200,000
Loss upon extinguishment of debt	11,200,000
Debt instrument, unamortized discount	6,800,000
Debt conversion, original debt	400,000
Debt instrument, fee	$ 200,000
Schottenfeld November 2019 Credit and Security Agreement | Maximum
Debt Conversion [Line Items]
Exercise price of warrants or rights (in dollars per share) | $ / shares	$ 3.90

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Debt - August 2019 Foris Credit Agreements (Details) - USD ($) $ / shares in Units, $ in Millions		12 Months Ended
	Aug. 28, 2019	Dec. 31, 2019	May 14, 2019	Apr. 26, 2019
Debt Conversion [Line Items]
Warrants and rights outstanding	$ 8.7
Fair value adjustments of warrants		$ (4.8)
Foris Ventures, LLC | Private Placement, April 26, 2019
Debt Conversion [Line Items]
Exercise price of warrants or rights (in dollars per share)	$ 3.90			$ 5.12
Foris Ventures, LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Debt Conversion [Line Items]
Exercise price of warrants or rights (in dollars per share)	$ 3.90		$ 4.56
August Foris Credit Agreement
Debt Conversion [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	4,900,000		400,000	3,900,000
Exercise price of warrants or rights (in dollars per share)	$ 3.90
Warrants and rights outstanding	$ 5.2
Class of warrant or right, term	2 years
August Foris Credit Agreement | Foris Ventures, LLC
Debt Conversion [Line Items]
Maximum borrowing capacity	$ 19.0
Interest rate per annum	12.00%
Debt instrument, percent of face amount	100.00%
Fair value of embedded derivative liability	$ 0.5
Warrants and rights outstanding	8.7
Warrants and rights outstanding, relative fair value	5.2
Fair value adjustments of warrants	1.1
Debt instrument, fee	0.1
Debt instrument, unamortized discount	$ 6.8
August Foris Credit Agreement | Foris Ventures, LLC | Private Placement, April 26, 2019
Debt Conversion [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,900,000
Exercise price of warrants or rights (in dollars per share)	$ 3.90			$ 5.12
August Foris Credit Agreement | Foris Ventures, LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Debt Conversion [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			400,000
Exercise price of warrants or rights (in dollars per share)	$ 3.90		$ 4.56

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Debt - Senior Convertible Notes Due 2022 (Details) - USD ($)			1 Months Ended	4 Months Ended	12 Months Ended
	Mar. 15, 2020	Mar. 12, 2020	Dec. 31, 2018	Jun. 01, 2020	Dec. 31, 2019	Dec. 31, 2018	Nov. 15, 2019	Nov. 08, 2019	Jul. 24, 2019
Debt Conversion [Line Items]
Loss (gain) from change in fair value of debt					$ (15,376,000)	$ 2,082,000
Subsequent Event
Debt Conversion [Line Items]
Proceeds from debt, net of issuance costs		$ 4,500,000
Convertible Senior Notes, 6 Percent Due in 2021
Debt Conversion [Line Items]
Interest rate per annum			6.00%			6.00%	6.00%	6.00%
Debt instrument, face amount								$ 66,000,000.0
Debt conversion, original debt			$ 60,000,000.0			$ 57,918,000
Proceeds from debt, net of issuance costs			$ 56,200,000
Senior Convertible Notes Due 2022
Debt Conversion [Line Items]
Interest rate per annum					15.00%		5.00%		5.00%
Debt instrument, reduction rate of installment payment							90.00%
Debt conversion, original debt					$ 10,000,000
Proceeds from debt					75,000,000.0
Proceeds from debt, net of issuance costs					$ 30,000,000
Debt instrument, convertible, conversion price (in dollars per share)					$ 5.00
Convertible debt, stock ownership, maximum percentage except under specified conditions					4.99%
Loss (gain) from change in fair value of debt					$ 3,800,000
Senior Convertible Notes Due 2022 | Maximum
Debt Conversion [Line Items]
Debt instrument, percent of face amount					115.00%
Senior Convertible Notes Due 2022 | Minimum
Debt Conversion [Line Items]
Debt instrument, percent of face amount					110.00%
Senior Convertible Notes Due 2022 | Subsequent Event
Debt Conversion [Line Items]
Debt instrument, fixed period payment				$ 3,000,000.0
Debt instrument, periodic payment				$ 3,400,000
Proceeds from debt, net of issuance costs	$ 75,000,000

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Balance Sheet Details - Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Accrued interest	$ 8,209	$ 3,853
Payroll and related expenses	7,296	9,220
Contract termination fees	5,347	4,092
Ginkgo partnership payments obligation	4,319	2,155
Asset retirement obligation	3,184	3,063
Professional services	2,968	1,173
Tax-related liabilities	1,685	2,139
Other	3,647	3,284
Total accrued and other current liabilities	$ 36,655	$ 28,979

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Balance Sheet Details - Property, Plant and Equipment (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2019
Property, Plant and Equipment [Line Items]
Total property, plant and equipment, gross	$ 98,387	$ 112,603
Less: accumulated depreciation and amortization	(78,631)	(83,673)
Total property, plant and equipment, net	19,756	28,930
Machinery and Equipment
Property, Plant and Equipment [Line Items]
Total property, plant and equipment, gross	43,713	48,041
Leasehold Improvements
Property, Plant and Equipment [Line Items]
Total property, plant and equipment, gross	39,922	41,478
Computer Equipment and Software
Property, Plant and Equipment [Line Items]
Total property, plant and equipment, gross	9,987	9,822
Furniture and Office Equipment, Vehicles and Land
Property, Plant and Equipment [Line Items]
Total property, plant and equipment, gross	3,016	3,510
Construction in Progress
Property, Plant and Equipment [Line Items]
Total property, plant and equipment, gross	1,749	$ 9,752
Capital leases
Property, Plant and Equipment [Line Items]
Less: accumulated depreciation and amortization	(2,300)
Total property, plant and equipment, net	5,000
Amortization expense	$ (700)

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Balance Sheet Details - Allowance for Doubtful Accounts (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Off-Balance Sheet, Credit Loss, Liability [Roll Forward]
Balance at Beginning of Year	$ 642	$ 642
Provisions	110	0
Write-offs, Net	(707)	0
Balance at End of Year	$ 45	$ 642

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Commitments and Contingencies (Details) - USD ($)	Dec. 31, 2019	Dec. 19, 2019	Nov. 30, 2019	Oct. 31, 2019	Jul. 29, 2019	Dec. 31, 2018	Feb. 28, 2017	Dec. 31, 2016
Debt Instrument [Line Items]
Liabilities recorded for agreements	$ 0					$ 0
Nikko Loan Agreement
Debt Instrument [Line Items]
Debt instrument, face amount		$ 4,500,000			$ 5,000,000.0
Aprinnova JV | Nikko Notes
Debt Instrument [Line Items]
Debt instrument, face amount	$ 1,300,000		$ 1,300,000	$ 1,300,000	$ 3,900,000		$ 1,500,000
First priority lien on interests owned by the company					10.00%			10.00%
Aprinnova JV | Nikko Loan Agreement
Debt Instrument [Line Items]
First priority lien on interests owned by the company		27.20%			12.80%

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Debt - August 2013 Financing Convertible Note (Details) - USD ($) $ / shares in Units, $ in Thousands		12 Months Ended
	Jul. 08, 2019	Dec. 31, 2019	Dec. 31, 2018	Aug. 28, 2019	Jan. 14, 2019
Obligation with Joint and Several Liability Arrangement [Line Items]
Debt instrument, fair value		$ 194,800	$ 149,300
Warrants and rights outstanding				$ 8,700
Loss upon extinguishment of debt		$ (44,208)	$ (17,424)
Warrants Issued in Exchange for August 2013 Financing Convertible Note
Obligation with Joint and Several Liability Arrangement [Line Items]
Debt conversion, converted instrument (in shares)	1,800,000
Debt instrument, fair value	$ 5,900
Exercise price of warrants or rights (in dollars per share)	$ 3.30
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,100,000
Warrants and rights outstanding	$ 1,900
Loss upon extinguishment of debt	(2,700)
Secured Tranche | Related Party Convertible Notes
Obligation with Joint and Several Liability Arrangement [Line Items]
Debt instrument, cash waiver fee amount payable					$ 600
Debt instrument, face amount	$ 5,100

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Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Net loss attributable to Amyris, Inc.	$ (242,767)	$ (230,235)
Foreign currency translation adjustment	(461)	(1,187)
Comprehensive loss attributable to Amyris, Inc.	$ (243,228)	$ (231,422)

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Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Assets, Current [Abstract]
Cash and cash equivalents	$ 270	$ 45,353
Restricted cash	469	741
Accounts receivable, net of allowance of $45 and $642, respectively	16,322	16,003
Accounts receivable - related party, net of allowance of $0 and $0, respectively	3,868	1,349
Accounts receivable, unbilled - related party	0	8,021
Contract assets	8,485	0
Inventories	27,770	9,693
Deferred cost of products sold - related party	3,677	489
Prepaid expenses and other current assets	12,750	10,566
Total current assets	73,611	92,215
Property, plant and equipment, net	28,930	19,756
Right-of-use assets under financing leases, net (Note 2)	12,863
Contract assets	1,203	1,203
Deferred cost of products sold, noncurrent - related party	12,815	2,828
Restricted cash, noncurrent	960	960
Recoverable taxes from Brazilian government entities	7,676	3,005
Right-of-use asset under operating leases	13,203
Other assets	9,705	7,958
Total assets	160,966	127,925
Liabilities, Current [Abstract]
Accounts payable	51,234	26,844
Accrued and other current liabilities	36,655	28,979
Finance Lease, Liability, Current	3,465
Operating Lease, Liability, Current	4,625
Contract liabilities	1,353	8,236
Debt, current portion (includes instrument measured at fair value of $24,392 and $57,918, respectively)	45,313	124,010
Related party debt, current portion	18,492	23,667
Total current liabilities	161,137	211,736
Long-term debt, net of current portion (includes instrument measured at fair value of $26,232 and $0, respectively)	48,452	43,331
Related party debt, net of current portion	149,515	18,689
Financing lease liabilities, net of current portion (Note 2)	4,166
Operating lease liabilities, net of current portion (Note 2)	15,037
Derivative liabilities	9,803	42,796
Other noncurrent liabilities	23,024	23,192
Total liabilities	411,134	339,744
Commitments and contingencies
Contingently redeemable common stock	5,000	5,000
Stockholders' Equity, Including Portion Attributable to Noncontrolling Interest [Abstract]
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of December 31, 2019 and 2018, and 8,280 and 14,656 shares issued and outstanding as of December 31, 2019 and 2018, respectively	0	0
Common stock - $0.0001 par value, 250,000,000 shares authorized as of December 31, 2019 and 2018, respectively; 117,742,677 and 76,564,829 shares issued and outstanding as of December 31, 2019 and 2018, respectively	12	8
Additional paid-in capital	1,543,668	1,346,996
Accumulated other comprehensive loss	(43,804)	(43,343)
Accumulated deficit	(1,755,653)	(1,521,417)
Total Amyris, Inc. stockholders’ deficit	(255,777)	(217,756)
Noncontrolling interest	609	937
Total stockholders' deficit	(255,168)	(216,819)
Total liabilities, mezzanine equity and stockholders' deficit	$ 160,966	$ 127,925

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Debt - Total Note Exchange and Extensions (Details) - USD ($) $ in Thousands		6 Months Ended	12 Months Ended
	May 15, 2019	Nov. 14, 2019	Dec. 31, 2019	Dec. 31, 2018	Aug. 28, 2019	Jul. 18, 2019
Debt Conversion [Line Items]
Interest expense			$ 58,665	$ 42,703
Total | Rule 144A Convertible Notes
Debt Conversion [Line Items]
Debt conversion, original debt	$ 9,700
Interest rate per annum					12.00%	10.50%
Interest expense		$ 500
Debt instrument, periodic payment, principal			$ 10,200

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Revenue Recognition - Contract Balances (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Accounts receivable, net	$ 16,322	$ 16,003
Accounts receivable - related party, net	3,868	1,349
Accounts receivable, unbilled - related party	0	8,021
Contract assets	8,485	0
Contract assets, noncurrent - related party	1,203	1,203
Contract liabilities	1,353	8,236
Contract liabilities, noncurrent	$ 1,449	$ 1,587

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Divestiture

12 Months Ended

Dec. 31, 2019

Discontinued Operations and Disposal Groups [Abstract]

Divesture

Divestiture

On December 28, 2017, the Company completed the sale of its subsidiary Amyris Brasil Ltda. (Amyris Brasil), which operated the Company’s production facility located in Brotas, Brazil, to DSM and concurrently entered into a series of commercial agreements and a credit agreement with DSM. At closing, the Company received $33.0 million in contractual cash consideration for the capital stock of Amyris Brasil, which was subject to certain post-closing working capital adjustments; and reimbursements contingent upon DSM’s utilization of certain Brazilian tax benefits it acquired with its purchase of Amyris Brasil. The Company used $12.6 million of the cash proceeds received to repay certain indebtedness of Amyris Brasil. The total fair value of the contractual consideration received by the Company for Amyris Brasil was $56.9 million and resulted in a pretax gain of $5.7 million from continuing operations. In November 2018, the Company paid DSM $1.8 million related to the final post-closing working capital adjustment. In connection with the payment, $1.8 million was recorded as a loss on divestiture in the 2018 consolidated statement of operations, in the line captioned "(Loss) gain on divestiture".

Concurrent with the sale of Amyris Brasil, the Company and DSM entered into a series of commercial agreements including (i) a license agreement to DSM of its farnesene product for DSM to use in the Vitamin E and lubricant markets; (ii) a royalty agreement, pursuant to which DSM agreed to pay the Company specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene sold under the Nenter Supply Agreement assigned to DSM; (iii) a performance agreement for the Company to perform research and development to optimize farnesene for production and sale of farnesene products; and (iv) a transition services agreement for the Company to provide finance, legal, logistics, and human resource services to support the Brotas facility under DSM ownership for a six-month period with a DSM option to extend for six additional months (see Note 9, “Revenue Recognition” for additional information). At closing, DSM paid the Company a $27.5 million nonrefundable license fee and a $15.0 million nonrefundable royalty payment, and agreed to pay two additional future nonrefundable minimum annual royalty payments totaling $18.1 million for 2019 and 2020 royalties. These future payments were determined to be fixed and determinable with a fair value of $17.8 million and were included as part of the total consideration subject to allocation in the December 2017 multiple-element divestiture transaction with DSM. In June 2018, the Company received the 2019 non-refundable minimum royalty payment of $9.3 million (net of a $0.7 million early payment discount) and in March 2019, the Company received the 2020 payment of $7.4 million (net of a $0.7 million early payment discount). See Note 9, “Revenue Recognition” and Note 10, "Related Party Transactions" for a full listing and details of agreements entered into with DSM. Additionally, the Company and DSM entered into a $25.0 million credit agreement that the Company used to repay all outstanding amounts under the Guanfu Note; see Note 4, “Debt” for additional information.

The Company accounted for the sale of Amyris Brasil as a sale of a business for proceeds of $54.8 million. The agreements entered into concurrently with the sale of Amyris Brasil including the license agreement, royalty agreement, performance agreement, transition services agreement, and credit agreement contain various elements and, as such, are deemed to be an arrangement with multiple deliverables as defined under U.S. GAAP. The Company performed an analysis to determine the fair value for all elements in the agreements with DSM and separated the elements between the non-revenue and revenue elements. After allocating the total fair value of the non-revenue elements from the fixed and determinable consideration received, the Company allocated the remaining fixed and determinable consideration to the revenue elements based on relative fair value. As such, the Company recognized $54.7 million of license revenue and $2.1 million of deferred revenue related to the performance option and transition services agreements with DSM as of December 31, 2017.

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Income Taxes - Effective Tax Rate Reconciliation (Details)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Income Tax Disclosure [Abstract]
Statutory tax rate	(21.00%)	(21.00%)
Federal R&D credit	(0.70%)	(0.60%)
Derivative liability	4.70%	4.30%
Nondeductible interest	1.00%	1.00%
Other	2.40%	(0.10%)
Foreign losses	0.90%	0.90%
Change in valuation allowance	13.00%	15.50%
Effective income tax rate	0.30%	0.00%

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Basis of Presentation and Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Consolidation

Basis of Consolidation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States (U.S. GAAP). The consolidated financial statements include the accounts of Amyris, Inc. and its wholly-owned and partially-owned subsidiaries in which the Company has a controlling interest after elimination of all significant intercompany accounts and transactions.

Investments and joint venture arrangements are assessed to determine whether the terms provide economic or other control over the entity requiring consolidation of the entity. Entities controlled by means other than a majority voting interest are referred to as variable-interest entities (VIEs) and are consolidated when Amyris has both the power to direct the activities of the VIE that most significantly impact its economic performance and the obligation to absorb losses or the right to receive benefits that could potentially be significant to the entity. For any investment or joint venture in which (i) the Company does not have a majority ownership interest, (ii) the Company possesses the ability to exert significant influence and (iii) the entity is not a VIE for which the Company is considered the primary beneficiary, the Company accounts for the investment or joint venture using the equity method. Equity investments in which the Company does not exert significant influence and that do not have readily determinable fair values are measured at cost, adjusted for changes from observable market transactions, less impairment (“adjusted cost basis”). The Company evaluates its investments for impairment by considering a variety of factors, including the earnings capacity of the related investments. Fair value measurements for the Company’s equity investments are classified within Level 3 of the fair value hierarchy based on the nature of the fair value inputs. Realized and unrealized gains or losses are recognized in other income or expense.

Use of Estimates and Judgements

Use of Estimates and JudgementsThe preparation of financial statements in conformity with U.S. GAAP requires management to make estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates, and such differences may be material to the consolidated financial statements. Significant estimates and judgements used in these consolidated financial statements are discussed in the relevant accounting policies below or specifically discussed in the Notes to Consolidated Financial Statements where such transactions are disclosed.

Cash and Cash Equivalents

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with an original or remaining maturity of three months or less at the date of purchase to be cash equivalents. Cash and cash equivalents are maintained with various financial institutions.

Inventories

Inventories

Inventories, which consist of farnesene-derived products, flavors and fragrances ingredients and clean beauty products, are stated at the lower of actual cost or net realizable value and are categorized as finished goods, work in process or raw material inventories. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds their estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or net realizable value approach that is used to value inventory. Cost for farnesene-derived products and flavors and fragrances ingredients are computed on a weighted-average basis. Cost for clean beauty products are computed on a standard cost basis.

Property, Plant and Equipment, Net

Property, Plant and Equipment, Net

Property, plant and equipment are recorded at cost. Depreciation and amortization are computed straight-line based on the estimated useful lives of the related assets, ranging from 3 to 15 years for machinery, equipment and fixtures, and 15 years for buildings. Leasehold improvements are amortized over their estimated useful lives or the period of the related lease, whichever is shorter.

The Company expenses costs for maintenance and repairs and capitalizes major replacements, renewals and betterments. For assets retired or otherwise disposed, both cost and accumulated depreciation are eliminated from the asset and accumulated depreciation accounts, and gains or losses related to the disposal are recorded in the statement of operations for the period.

Impairment

Impairment

Long-lived assets that are held and used by the Company are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. Determination of recoverability of long-lived assets is based on an estimate of the undiscounted future cash flows resulting from the use of the asset and its eventual disposition. Measurement of an impairment loss for long-lived assets that management expects to hold and use is based on the difference between the fair value of the asset and its carrying value. Long-lived assets to be disposed of are reported at the lower of carrying amount or fair value less costs to sell.

Recoverable Taxes from Brazilian Government Entities

Recoverable Taxes from Brazilian Government Entities

Recoverable taxes from Brazilian government entities represent value-added taxes paid on purchases in Brazil, which are reclaimable from the Brazilian tax authorities, net of reserves for amounts estimated not to be recoverable.

Fair Value Measurements

Fair Value Measurements

The carrying amounts of certain financial instruments, such as cash equivalents, short-term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities.

The Company measures the following financial assets and liabilities at fair value:

•Freestanding and bifurcated derivatives in connection with certain debt and equity financings; and

•Senior Convertible Notes Due 2022 and 6% Convertible Notes Due 2021 (see Note 3, "Fair Value Measurement" and Note 4, "Debt", for which the Company elected fair value accounting.

Fair value is based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation techniques are applied. These valuation techniques involve some level of management estimation and judgement, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

Changes to the inputs used in these valuation models can have a significant impact on the estimated fair value of the Senior Convertible Notes Due 2022, 6% Convertible Notes Due 2021 and the Company's embedded and freestanding derivatives. For example, a decrease (increase) in the estimated credit spread for the Company results in an increase (decrease) in estimated fair value. Conversely, a decrease (increase) in the stock price results in a decrease (increase) in estimated fair value.

The changes during 2019 and 2018 in the fair values of the bifurcated compound embedded derivatives are primarily related to the change in price of the Company's common stock and are reflected in the consolidated statements of operations as “Gain (loss) from change in fair value of derivative instruments”.

For debt instruments for which the Company has not elected fair value accounting, fair value is based on the present value of expected future cash flows and assumptions about the then-current market interest rates as of the reporting period and the creditworthiness of the Company. Most of the Company's debt is carried on the consolidated balance sheet on a historical cost basis net of unamortized discounts and premiums, because the Company has not elected the fair value option of accounting. However, for the Senior Convertible Notes Due 2022 and the 6% Notes Due 2021, the Company elected fair value accounting, so that balances reported for those debt instruments represent fair value as of the applicable balance sheet date; see Note 3, "Fair Value Measurement", for additional information. Changes in fair value of the Senior Convertible Notes Due 2022 and the 6% Convertible Notes Due 2021 are reflected in the consolidated statements of operations as “Gain (loss) from change in fair value of debt”.

For all debt instruments, including any for which the Company has elected fair value accounting, the Company classifies interest that has been accrued during each period as Interest expense on the consolidated statements of operations.

Derivatives

Derivatives

Embedded derivatives that are required to be bifurcated from the underlying debt instrument (i.e., host) are accounted for and valued as separate financial instruments. The Company has evaluated the terms and features of its convertible notes payable and convertible preferred stock and identified compound embedded derivatives requiring bifurcation and accounting at fair value, using the valuation techniques mentioned in the Fair Value Measurements section of this Note, because the economic and contractual characteristics of the embedded derivatives met the criteria for bifurcation and separate accounting due to the instruments containing conversion options, certain “make-whole interest” provisions, down-round conversion price adjustment provisions and/or conversion rate adjustments, and mandatory redemption features that are not clearly and closely related to the debt host instrument.

Prior to the adoption of ASU 2017-11, certain previously issued warrants with a fair value of $41 million issued in conjunction with the convertible debt and equity financings were freestanding financial instruments and classified as derivative liabilities as of December 31, 2019. Upon adoption of ASU 2017-11 on January 1, 2019, these freestanding instruments met the criteria to be accounted for within equity and the $41 million derivative liability balance was reclassified to stockholders’ equity.

During the third and fourth quarter of 2019, the Company issued warrants in connection with a debt financing that met the criteria of a freestanding instrument but did not qualify for equity accounting treatment. As a result, these warrants are accounting for at fair value until settled and are classified as derivative liabilities at December 31, 2019. See Note 6 “Stockholders’ Deficit” for further information.

Noncontrolling Interest

Noncontrolling Interest

Noncontrolling interests represent the portion of net income (loss), net assets and comprehensive income (loss) that is not allocable to the Company, in situations where the Company consolidates its equity investment in a joint venture for which there are other owners. The amount of noncontrolling interest is comprised of the amount of such interests at the date of the Company's original acquisition of an equity interest in a joint venture, plus the other shareholders' share of changes in equity since the date the Company made an investment in the joint venture.

Concentration of Credit Risk

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents, short-term investments and accounts receivable. The Company places its cash equivalents and investments (primarily certificates of deposits) with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Revenue Recognition

Revenue Recognition

The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer, and transaction price is allocated utilizing stand-alone selling price. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does not incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators, among others, when determining if it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does not meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in Note 9, "Revenue Recognition".

The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to receive payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. For most of the Company's renewable products customers, supply agreements between the Company and each customer indicate when transfer of title occurs.

In some cases, the Company may make a payment to a customer. When that occurs, the Company evaluates whether the payment is for a distinct good or service receivable from the customer. If the fair value of the goods or services receivable is greater than or equal to the amount paid to the customer, then the entire payment is treated as a purchase. If, on the other hand, the fair value of goods or services is less than the amount paid, then the difference is treated as a reduction in transaction price of the Company's sales to the customer or a reduction of cumulative to-date revenue recognized from the customer in the period the payment is made or goods or services are received from the customer.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts may contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis.

The following is a description of the principal goods and services from which the Company generates revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does not have the ability to direct the product to a different customer. It is at this point that the Company has the right to receive payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do not include rights of return, except for direct-to-consumer products, for which the Company estimates sales returns subsequent to sale and reduces revenue accordingly. For renewable products other than direct-to-consumer, returns are accepted only if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception which requires the Company to estimate the revenue that is recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts, using the best evidence available at the time, derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends. Estimates are adjusted to actual or as new information becomes available.

When the Company’s intellectual property license is not the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts.

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services: The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to

scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaboration partners with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include one or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement, and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Generally, revenue is recognized using an input-based measure of progress towards the satisfaction of the performance obligations which can be labor hours expended or time-based in proportion to the estimated total project effort or total projected time to complete. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Certain performance obligations are associated with milestones agreed between the Company and its customer. Revenue generated from the performance of services in accordance with these milestones is recognized upon confirmation from the customer that the milestone has been achieved. In these cases, amounts recognized are constrained to the amount of consideration received upon achievement of the milestone.

The Company generally invoices its collaboration partners on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Contract liabilities arise from amounts received in advance of performing the research and development activities and are recognized as revenue in future periods as the performance obligations are satisfied.

Grants: The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect grant revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

The Company receives certain consideration from AICEP Portugal Global (AICEP), and entity funded by government of Portugal, under the Consortium Internal Regulatory Agreement and an AICEP Investment Contract (the “Agreements”) entered

into by Amyris (the “Company”) with Universidade Católica Portuguesa (UCP) Porto Campus. The Company considered this arrangement to be a government grant and accounts for the arrangement under International Accounting Standard 20 “Accounting for Government Grants and Disclosure of Government Assistance”. Grant revenue is recognized when there is reasonable assurance that monies will be received and that conditions attached to the grant have been met.

Cost of Products Sold

Cost of Products Sold

Cost of products sold includes the production costs of renewable products, which include the cost of raw materials, in-house manufacturing labor and overhead, amounts paid to contract manufacturers, including amortization of tolling fees, and period costs including inventory write-downs resulting from applying lower of cost or net realizable value inventory adjustments. Cost of products sold also includes certain costs related to the scale-up of production. Shipping and handling costs charged to customers are recorded as revenues. Outbound shipping costs incurred are included in cost of products sold. Such charges were not material for any of the periods presented.

The Company recognizes deferred cost of products sold as an asset on the balance sheet when a cost is incurred in connection with a revenue performance obligation that will not be fulfilled until a future period. The Company also recorded a deferred cost of products asset in 2018 and 2019 for the fair value of amounts paid to DSM under a supply agreement for manufacturing capacity to produce its sweetener product at the Brotas facility in Brazil. The deferred cost of products sold asset is expensed to cost of products sold on a units of production basis over the five-year term of the supply agreement. On a quarterly basis, the Company evaluates its future production volumes for its sweetener product and adjusts the unit cost to be expensed over the remaining estimated production volume. The Company also periodically evaluates the asset for recoverability based on changes business strategy and product demand trends over the term of the supply agreement.

Research and Development

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants, including internal research. Research and development costs consist of direct and indirect internal costs related to specific projects, as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Debt Extinguishment

Debt Extinguishment

The Company accounts for the income or loss from extinguishment of debt in accordance with ASC 470, Debt, which indicates that for all extinguishments of debt, including instances where the terms of a debt instrument are modified in a manner that significantly changes the underlying cash flows, the difference between the reacquisition consideration and the net carrying amount of the debt being extinguished should be recognized as gain or loss when the debt is extinguished. Losses from debt extinguishment are shown in the consolidated statements of operations under "Other income (expense)" as "Loss upon extinguishment of debt".

Stock-based Compensation

Stock-based Compensation

The Company accounts for stock-based employee compensation plans under the fair value recognition and measurement provisions of U.S. GAAP. Those provisions require all stock-based payments to employees, including grants of stock options and restricted stock units (RSUs), to be measured using the grant-date fair value of each award. The Company recognizes stock-based compensation expense net of expected forfeitures over each award's requisite service period, which is generally the vesting term. Expected forfeiture rates are estimated based on the Company's historical experience. Stock-based compensation plans are described more fully in Note 11, "Stock-based Compensation".

Income Taxes

Income Taxes

The Company is subject to income taxes in the United States and foreign jurisdictions and uses estimates to determine its provisions for income taxes. The Company uses the asset and liability method of accounting for income taxes, whereby deferred tax asset or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. The Company recognizes a valuation allowance against its net deferred tax assets unless it is more likely than not that such deferred tax assets will be realized. This assessment requires judgement as to the likelihood and amounts of future taxable income by tax jurisdiction.

The Company applies the provisions of Financial Accounting Standards Board (FASB) guidance on accounting for uncertainty in income taxes. The Company assesses all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position’s sustainability, and the tax benefit to be recognized is measured at the largest amount of benefit that is greater than 50 percent likely of being realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and the Company will determine whether (i) the factors underlying the sustainability assertion have changed and (ii) the amount of the recognized tax benefit is still appropriate. The recognition and measurement of tax benefits requires significant judgement, and such judgements may change as new information becomes available.

Foreign Currency Translation

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into U.S. dollars at the rates in effect at each balance sheet date, and revenue and expense amounts are translated at average rates during each period, with resulting foreign currency translation adjustments recorded in other comprehensive loss, net of tax, in the consolidated statements of stockholders’ deficit. As of December 31, 2019 and 2018, cumulative translation adjustment, net of tax, were $43.8 million and $43.3 million, respectively.

Where the U.S. dollar is the functional currency, remeasurement adjustments are recorded in other income (expense), net in the accompanying consolidated statements of operations. Net losses resulting from foreign exchange transactions were $0.2 million and $1.6 million for the years ended December 31, 2019 and 2018, respectively and are recorded in other income (expense), net in the consolidated statements of operations.

New Accounting Standards or Updates Recently Adopted and Recent Accounting Standards or Updates Not Yet Effective

New Accounting Standards or Updates Recently Adopted

During the year ended December 31, 2019 the Company adopted the following Accounting Standards Updates (ASUs):

Leases In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) (ASU 2016-02). The standard requires the recognition of lease liabilities and right-of-use (ROU) assets on the balance sheet arising from lease transactions at the lease commencement date and the disclosure of key information about leasing arrangements. In July 2018, the FASB issued ASU 2018-11, Leases (Topic 842): Targeted Improvements, which provided entities the option to use the effective date as the date of initial application on transition to the new guidance. The Company elected this transition method, and as a result, the Company did not adjust comparative information for prior periods. The Company elected certain additional practical expedients permitted by the new guidance allowing the Company to carry forward historical accounting related to lease identification and classification for existing leases upon adoption.

The Company adopted this standard on January 1, 2019 using the modified retrospective approach and elected the package of practical expedients permitted under transition guidance, which allowed the Company to carry forward its historical assessments of: (1) whether contracts are or contain leases, (2) lease classification and (3) initial direct costs, where applicable. The Company did not elect the practical expedient allowing the use-of-hindsight which would require the Company to reassess the lease term of its leases based on all facts and circumstances through the effective date and did not elect the practical expedient pertaining to land easements as this is not applicable to the Company’s current contracts. The Company elected the post-transition practical expedient to not separate lease components from non-lease components for all leases of manufacturing equipment. The Company also elected a policy of not recording leases on its condensed consolidated balance sheets when the leases have a term of 12 months or less and the Company is not reasonably certain to elect an option to purchase the leased asset.

The Company's adoption of this standard had the effect of increasing assets and liabilities by $25.7 million, after considering prepaid and other current and noncurrent assets previously recorded on the condensed consolidated balance sheet but did not have a material impact on the condensed consolidated statements of operations or cash flows. The most significant impact relates to (1) the recognition of new ROU assets and lease liabilities on the balance sheet for the Company's operating leases; and (2) providing significant new disclosures about the Company's leasing activities.

Upon adoption, the Company recognized operating lease liabilities of $33.6 million, based on the present value of the remaining minimum rental payments under current leasing standards for existing operating leases. The Company also recognized ROU assets of $29.7 million, which represents the operating lease liability, adjusted for prepaid expenses and deferred rent. The difference between the operating lease ROU assets and lease liabilities reflects the net of advanced rent payments and deferred rent balances that were derecognized at the time of adoption.

Financial Instruments with "Down Round" Features In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features. The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update became effective in the first quarter of fiscal year 2019, and the Company adopted the standard using a modified retrospective approach. Since the adoption of ASU 2017-11 would have classified the warrants effected as equity at inception, the cumulative-effect adjustment should (i) record the issuance date value of the warrants as if they had been equity classified at the issuance date, (ii) reverse the effects of changes in the fair value of the warrants that had been recorded in the statement of operations of each period, and (iii) eliminate the derivative liabilities from the balance sheet. Upon adoption, the Company (i) recorded an increase of $32.5 million to additional paid-in capital, (ii) recorded a decrease to accumulated deficit of $8.5 million and (iii) decreased the warrant liability by $41.0 million.

Recent Accounting Standards or Updates Not Yet Effective

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement, which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for fair value measurements by removing, modifying or adding certain disclosures. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative arrangement is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. The ASU provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020 retroactively. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments—Credit Losses (Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to measure all expected credit losses for most financial assets held at the reporting date based on an expected loss model which includes historical experience, current conditions, and reasonable and supportable forecasts. Entities will now use forward-looking information to better form their credit loss estimates. ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand significant estimates and judgments used in estimating credit losses, as well as the credit quality and underwriting standards of an entity's portfolio. ASU 2016-13 will become effective for the Company beginning in the first quarter of fiscal year 2020. The Company does not believe that the impact of the new standard on its consolidated financial statements will be material.

In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments- Credit Losses. This ASU clarifies and addresses certain items related to amendments in ASU 2016-13. This new guidance is effective for the Company beginning on January 1, 2020. This new guidance is not expected to have a material impact on the Company’s consolidated financial statements.

Income Taxes In December 2019, the FASB issued ASU 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes, which simplifies the accounting for income taxes. This guidance will become effective for the Company in the first quarter of fiscal year 2021 on a prospective basis. The Company is currently evaluating the impact of the new guidance on its consolidated financial statements.

In January 2020, the FASB issued ASU 2020-01, Investments-Equity Securities (Topic 321), Investments-Equity Method and Joint Ventures (Topic 323), and Derivatives and Hedging (Topic 815)-Clarifying the Interactions between Topic 321, Topic 323, and Topic 815. The guidance provides clarification of the interaction of rules for equity securities, the equity method of accounting and forward contracts and purchase options on certain types of securities. This new guidance is effective for the

Company beginning on January 1, 2021. While the Company is currently assessing the impact of the new guidance, it is not expected to have a material impact on the Company’s consolidated financial statements.

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Stock-based Compensation - Share-based Payment Award, Stock Options with Performance, Valuation Assumptions (Details) - Performance-based Stock Options	12 Months Ended
	Dec. 31, 2019 $ / shares
Compensating Balances [Line Items]
Fair value of the Company’s common stock on grant date (in dollars per share)	$ 5.08
Expected volatility	70.00%
Risk-free interest rate	2.75%
Dividend yield	0.00%

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Debt (Tables)

12 Months Ended

Dec. 31, 2019

Debt Disclosure [Abstract]

Schedule of Long-term Debt Instruments

Future minimum payments under the debt agreements as of December 31, 2019 are as follows:

Years ending December 31 (In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020	$	43,384	$	26,324	$	10,437	$	33,730	$	113,875
2021	40,177		3,342		—		53,566		97,085
2022	—		15,177		—		113,818		128,995
2023	—		13,011		—		24,323		37,334
2024	—		398		—		—		398
Thereafter	—		1,870		—		—		1,870
Total future minimum payments	83,561		60,122		10,437		225,437		379,557
Less: amount representing interest(1)	(17,561)		(11,626)		(259)		(52,649)		(82,095)
Less: future conversion of accrued interest to principal	—		—		—		—		—
Present value of minimum debt payments	66,000		48,496		10,178		172,788		297,462
Less: current portion of debt principal	(31,800)		(21,193)		(10,178)		(11,380)		(74,551)
Noncurrent portion of debt principal	$	34,200	$	27,303	$	—	$	161,408	$	222,911

______________

⁽¹⁾ Excluding net debt discount of $20.3 million that will be amortized to interest expense over the term of the debt.

Schedule of Extinguishment of Debt

The Company recorded a $1.9 million loss of debt extinguishment as of December 31, 2019, determined as follows:

In thousands
Fair value at December 31, 2018	$	57,918
Less: principal paid in cash during 2019	(13,395)
Less: principal converted to common stock during 2019	(15,000)
Loss on change in fair value during 2019	18,303
Accrued interest	3,168
Carrying value of registration rights liability	5,757
Net carrying value at extinguishment	56,751
Total reacquisition price	58,640
Loss on debt extinguishment	$	1,889

Schedule of Related Party Transactions

The notes payable to Foris are comprised of the following (amounts in thousands):

Description	Date Issued	Original Loan Amount		Balance at December 31, 2019		Interest Rate per Annum	Maturity Date
Foris $19 Million Note	August 28, 2019	$	19,000	$	19,000	12.0%	January 1, 2023
Foris LSA	April 15, 2019	36,000		96,351		12.5%	For $81.0 million borrowed prior to November 27, 2019, the maturity date is July 1, 2022; for $10.0 million borrowed November 27, 2019, the maturity date is March 31, 2023.
		$	55,000	$	115,351

Schedule of Debt

The loans payable to Nikko Chemicals Co., Ltd. at December 31, 2019 are comprised of the following (amounts in thousands):

Description	Date Issued	Original Loan Amount		Balance at December 31, 2019		Interest Rate per Annum	Maturity Date
Nikko $5.0M Note	July 29, 2019	$	5,000	$	5,000	5.00%	December 18, 2020
Nikko $4.5M Note	December 19, 2019	4,500		4,500		2.75%	January 31, 2020
Nikko $3.9M Note	December 19, 2016	3,900		2,862		5.00%	December 1, 2029
Nikko $1.5M Note B	August 3, 2017	1,500		900		2.75%	August 1, 2020
Nikko $450K Note	December 9, 2019	450		450		2.75%	March 31, 2020
Nikko $350K Note	November 20, 2019	350		350		2.75%	January 31, 2020
Nikko $200K Capex Loan	February 1, 2019	200		171		5.00%	January 1, 2026
Nikko $500K Note	October 31, 2019	500		84		2.75%	January 10, 2020
		$	16,400	$	14,317

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Stock-based Compensation - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity (Details) - Period-end restricted stock units - $ / shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Number of Restricted Stock Units
Outstanding, RSUs (in shares)	5,294,803
Grants in period (in shares)	2,996,660	5,452,664
Vested (in shares)	(1,891,931)
Forfeited (in shares)	(616,881)
Outstanding, RSUs (in shares)	5,782,651	5,294,803
Vested or expected to vest (in shares)	5,338,558
Weighted- average Exercise Price
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 5.50
Weighted average grant date fair value, grants in period (in dollars per share)	3.96	$ 5.36
Weighted average grant date fair value, vested in period (in dollars per share)	5.51
Weighted average grant date fair value, forfeitures (in dollars per share)	4.84
Outstanding, weighted average grant-date fair value (in dollars per share)	4.77	$ 5.50
Vested or expected to vest, weighted average grant-date fair value (in dollars per share)	$ 4.78
Outstanding, weighted average remaining contractual life (Year)	1 year 8 months 12 days	1 year 4 months 24 days
Vested or expected to vest, weighted average remaining contractual life (Year)	1 year 7 months 6 days