10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

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

For the quarterly period ended September 30, 2020

-OR-

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

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.)

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

(510) 450-0761

(Address and telephone number of principal executive offices)

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	The Nasdaq Stock Market, LLC

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  x    No  o

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  x    No  o

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 the 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 x

Shares outstanding of the Registrant's common stock:

Class	Outstanding as of November 4, 2020
Common Stock, $0.0001 par value per share	239,211,413

AMYRIS, INC.

TABLE OF CONTENTS

		Page
	PART I
Item 1.	Financial Statements (unaudited)	3
	Condensed Consolidated Balance Sheets as of September 30, 2020 and December 31, 2019	3
	Condensed Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2020 and 2019	4
	Condensed Consolidated Statements of Comprehensive Loss for the Three and Nine Months Ended September 30, 2020 and 2019	5
	Condensed Consolidated Statements of Stockholders’ Deficit and Mezzanine Equity for the Three-month Periods Ended March 31, June 30, and September 30, 2020 and 2019	6
	Condensed Consolidated Statements of Cash Flows for the Nine Months Ended September 30, 2020 and 2019	8
	Notes to Condensed Consolidated Financial Statements	10
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	42
Item 4.	Controls and Procedures	51
	PART II
Item 1.	Legal Proceedings	52
Item 1A.	Risk Factors	52
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	54
Item 3.	Defaults Upon Senior Securities	54
Item 5.	Other Information	54
Item 6.	Exhibits	55
SIGNATURES

2

PART I

ITEM 1. FINANCIAL STATEMENTS (UNAUDITED)

AMYRIS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(Unaudited)

(In thousands, except shares and per share amounts)	September 30, 2020		December 31, 2019
Assets
Current assets:
Cash and cash equivalents	$	38,280	$	270
Restricted cash	329		469
Accounts receivable, net of allowance of $102 and $45, respectively	27,365		16,322
Accounts receivable - related party, net of allowance of $0 and $0, respectively	419		3,868
Contract assets	2,082		8,485
Contract assets - related party	1,203		—
Inventories	37,212		27,770
Deferred cost of products sold - related party	9,454		3,677
Prepaid expenses and other current assets	14,894		12,750
Total current assets	131,238		73,611
Property, plant and equipment, net	29,791		28,930
Contract assets, noncurrent - related party	—		1,203
Deferred cost of products sold, noncurrent - related party	11,858		12,815
Restricted cash, noncurrent	960		960
Recoverable taxes from Brazilian government entities	5,127		7,676
Right-of-use assets under financing leases, net (Note 2)	10,702		12,863
Right-of-use assets under operating leases (Note 2)	10,904		13,203
Other assets	5,359		9,705
Total assets	$	205,939	$	160,966
Liabilities, Mezzanine Equity and Stockholders' Deficit
Current liabilities:
Accounts payable	$	30,357	$	51,234
Accrued and other current liabilities	28,430		36,655
Financing lease liabilities (Note 2)	3,882		3,465
Operating lease liabilities (Note 2)	5,051		4,625
Contract liabilities	4,430		1,353
Debt, current portion (includes instrument measured at fair value of $25,349 and $24,392, respectively)	31,431		45,313
Related party debt, current portion	—		18,492
Total current liabilities	103,581		161,137
Long-term debt, net of current portion (includes instrument measured at fair value of $0 and $26,232, respectively)	26,176		48,452
Related party debt, net of current portion (includes instrument measured at fair value of $58,466 and $0, respectively)	116,799		149,515
Financing lease liabilities, net of current portion (Note 2)	1,171		4,166
Operating lease liabilities, net of current portion (Note 2)	11,109		15,037
Derivative liabilities	3,834		9,803
Other noncurrent liabilities	21,996		23,024
Total liabilities	284,666		411,134
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 September 30, 2020 and December 31, 2019; 8,280 shares issued and outstanding as of September 30, 2020 and December 31, 2019	—		—
Common stock - $0.0001 par value, 350,000,000 and 250,000,000 shares authorized as of September 30, 2020 and December 31, 2019, respectively; 239,185,985 and 117,742,677 shares issued and outstanding as of September 30, 2020 and December 31, 2019, respectively	24		12
Additional paid-in capital	1,938,411		1,543,668
Accumulated other comprehensive loss	(49,505)		(43,804)
Accumulated deficit	(1,977,075)		(1,755,653)
Total Amyris, Inc. stockholders’ deficit	(88,145)		(255,777)
Noncontrolling interest	4,418		609
Total stockholders' deficit	(83,727)		(255,168)
Total liabilities, mezzanine equity and stockholders' deficit	$	205,939	$	160,966

See the accompanying notes to the unaudited condensed consolidated financial statements.

3

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(Unaudited)

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Revenue:
Renewable products (includes related party revenue of $88, $0, $193 and $2, respectively)	$	27,577	$	17,363	$	70,619	$	41,367
Licenses and royalties (includes related party revenue of $0, $0, $3,750 and $40,302, respectively)	3,563		2,305		9,714		43,387
Grants and collaborations (includes related party revenue of $750, $844, $5,019 and $3,886, respectively)	3,118		15,285		13,060		27,267
Total revenue (includes related party revenue of $838, $844, $8,962 and $44,190, respectively)	34,258		34,953		93,393		112,021
Cost and operating expenses:
Cost of products sold	25,822		20,654		60,710		53,482
Research and development	18,197		19,032		52,288		56,093
Sales, general and administrative	38,321		33,341		100,838		92,456
Total cost and operating expenses	82,340		73,027		213,836		202,031
Loss from operations	(48,082)		(38,074)		(120,443)		(90,010)
Other income (expense):
Interest expense	(6,627)		(16,857)		(41,747)		(44,608)
Gain (loss) from change in fair value of derivative instruments	1,999		(398)		(6,498)		(2,437)
Gain (loss) from change in fair value of debt	34,360		(2,055)		2,908		(18,629)
Loss upon extinguishment of debt	(2,606)		(2,721)		(51,954)		(8,596)
Other income (expense), net	(49)		1,076		1,452		920
Total other expense, net	27,077		(20,955)		(95,839)		(73,350)
Loss before income taxes and loss from investment in affiliate	(21,005)		(59,029)		(216,282)		(163,360)
Provision for income taxes	(83)		(533)		(273)		(533)
Loss from investment in affiliate	(366)		—		(1,058)		—
Net loss	(21,454)		(59,562)		(217,613)		(163,893)
Less: income attributable to noncontrolling interest in Aprinnova	(1,702)		—		(3,809)		—
Net loss attributable to Amyris, Inc.	(23,156)		(59,562)		(221,422)		(163,893)
Less: deemed dividend to preferred stockholder on issuance and modification of common stock warrants	—		—		—		(34,964)
Less: deemed dividend to preferred stockholders upon conversion of Series E preferred stock	(67,151)		—		(67,151)		—
Add: losses allocated to participating securities	6,832		1,655		15,369		6,233
Net loss attributable to Amyris, Inc. common stockholders, basic	$	(83,475)	$	(57,907)	$	(273,204)	$	(192,624)
Loss per share attributable to common stockholders, basic	$	(0.37)	$	(0.56)	$	(1.44)	$	(2.11)
Weighted-average shares of common stock outstanding used in computing loss per share of common stock, basic	227,267,553		103,449,612		189,192,973		91,344,150
Loss per share attributable to common stockholders, diluted	$	(0.41)	$	(0.56)	$	(1.46)	$	(2.11)
Weighted-average shares of common stock outstanding used in computing loss per share of common stock, diluted	242,732,234		103,449,612		191,506,499		91,344,150

See the accompanying notes to the unaudited condensed consolidated financial statements.

4

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(Unaudited)

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Comprehensive loss:
Net loss	$	(21,454)	$	(59,562)	$	(217,613)	$	(163,893)
Foreign currency translation adjustment	(797)		(1,066)		(5,701)		(1,202)
Total comprehensive loss	(22,251)		(60,628)		(223,314)		(165,095)
Income attributable to noncontrolling interest	(1,702)		—		(3,809)		—
Comprehensive loss attributable to Amyris, Inc.	$	(23,953)	$	(60,628)	$	(227,123)	$	(165,095)

See the accompanying notes to the unaudited condensed consolidated financial statements.

5

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' DEFICIT AND MEZZANINE EQUITY

(Unaudited)

	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
Balances at December 31, 2019	8,280	$	—	117,742,677	$	12	1,543,668		$	(43,804)	$	(1,755,653)	$	609	$	(255,168)	$	5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	—	—		6,337,594	1		21,259		—		—		—		21,260		—
Issuance of common stock in private placement	—	—		3,484,321	—		10,000		—		—		—		10,000		—
Issuance of common stock in private placement - related party	—	—		10,505,652	1		27,188		—		—		—		27,189		—
Issuance of common stock upon exercise of warrants	—	—		1,160,929	—		3,332		—		—		—		3,332		—
Issuance of common stock upon exercise of warrants - related party	—	—		24,165,166	2		68,763		—		—		—		68,765		—
Exercise of common stock rights warrant - related party	—	—		—	—		15,000		—		—		—		15,000		—
Issuance of common stock right warrant - related party	—	—		—	—		8,904		—		—		—		8,904		—
Modification of previously issued common stock warrants	—	—		—	—		1,286		—		—		—		1,286		—
Derecognition of liability warrants to equity	—	—		—	—		5,200		—		—		—		5,200		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		495,581	—		(8)		—		—		—		(8)		—
Stock-based compensation	—	—		—	—		3,504		—		—		—		3,504		—
Foreign currency translation adjustment	—	—		—	—		—		(2,549)		—		—		(2,549)		—
Net loss attributable to Amyris, Inc.	—	—		—	—		—		—		(87,844)		—		(87,844)		—
Balances at March 31, 2020	8,280	$	—	163,891,920	$	16	$	1,708,096	$	(46,353)	$	(1,843,497)	$	609	$	(181,129)	$	5,000
Issuance of preferred and common stock in private placement, net of issuance costs	72,156			32,614,573	3		160,014								160,017		—
Issuance of preferred stock in private placement - related party, net of issuance costs	30,000			—	—		30,000								30,000		—
Issuance of common stock upon exercise of warrants				132,746	—		—								—		—
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party				5,226,481	1		(1)								—		—
Fair value of pre-delivery shares released to holder in connection with debt amendment				—	—		10,478								10,478		—
Derecognition of liability warrants to equity				—	—		6,550								6,550		—
Fair value of modification to previously issued common stock warrants				—	—		1,067								1,067		—
Return of pre-delivery shares previously issued in connection with debt agreement				(1,363,636)	—		—								—		—
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity				3,246,489	—		15,778								15,778		—
Stock-based compensation				—	—		2,931								2,931		—
Issuance of common stock upon ESPP purchase				144,523	—		421								421		—
Issuance of common stock upon exercise of stock options				5,227	—		16								16		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				720,100	—		(98)								(98)		—
Foreign currency translation adjustment				—	—		—		(2,355)						(2,355)		—
Net loss attributable to Amyris, Inc.				—	—		—				(110,422)		2,107		(108,315)		—
Balances at June 30, 2020	110,436	$	—	204,618,423	$	20	$	1,935,252	$	(48,708)	$	(1,953,919)	$	2,716	$	(64,639)	$	5,000
Adjustment to costs incurred in connection with June 2020 issuance of preferred and common stock in private placement							20								20		—
Issuance of common stock upon automatic conversion of Series E preferred stock	(102,156)	—		34,052,084	4		(4)								—		—
Beneficial conversion feature related to issuance of Series E preferred stock							67,151								67,151		—
Deemed dividend upon conversion of Series E preferred stock into common stock							(67,151)								(67,151)		—
Stock-based compensation					—		3,438								3,438		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				515,478	—		(295)								(295)		—
Foreign currency translation adjustment					—				(797)						(797)		—
Net loss attributable to Amyris, Inc.					—						(23,156)		1,702		(21,454)		—
Balances at September 30, 2020	8,280	$	—	239,185,985	$	24	$	1,938,411	$	(49,505)	$	(1,977,075)	$	4,418	$	(83,727)	$	5,000

6

	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
Balances at 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	—	—		—	—		32,512		—		8,531		—		41,043		—
Issuance of common stock upon exercise of warrants	—	—		450,568	—		1		—		—		—		1		—
Issuance of common stock upon exercise of stock options	—	—		3,612	—		13		—		—		—		13		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		191,672	—		(9)		—		—		—		(9)		—
Stock-based compensation	—	—		—	—		3,452		—		—		—		3,452		—
Fair value of bifurcated embedded conversion feature in connection with debt modification	—	—		—	—		398		—		—		—		398		—
Foreign currency translation adjustment	—	—		—	—		—		964		—		—		964		—
Net loss	—	—		—	—		—		—		(66,243)		—		(66,243)		—
Balances at March 31, 2019	14,656	—		77,210,681	8		1,383,363		(42,379)		(1,579,129)		937		(237,200)		5,000
Issuance of common stock in private placement	—	—		3,610,944	1		14,221		—		—		—		14,222		—
Issuance of common stock in private placement - related party	—	—		10,478,338	—		39,499		—		—		—		39,499		—
Issuance of common stock upon conversion of debt	—	—		7,101,468	1		34,650		—		—		—		34,651		—
Issuance of common stock upon ESPP purchase		—		131,460	—		464		—		—		—		464		—
Issuance of common stock upon exercise of warrants	—	—		2,064,606	—		—		—		—		—		—		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		589,241	—		(347)		—		—		—		(347)		—
Issuance of warrants in connection with debt accounted for at fair value	—	—		—	—		4,428		—		—		—		4,428		—
Stock-based compensation	—	—		—	—		3,375		—		—		—		3,375		—
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock	—	—		—	—		34,964		—		—		—		34,964		—
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock	—	—		—	—		(34,964)		—		—		—		(34,964)		—
Other	—	—		—	—		(238)		—		—		—		(238)		—
Foreign currency translation adjustment	—	—		—	—		—		(1,100)		—		—		(1,100)		—
Net loss	—	—		—	—		—		—		(38,088)		—		(38,088)		—
Balances at June 30, 2019	14,656	$	—	101,186,738	$	10	1,479,415		$	(43,479)	$	(1,617,217)	$	937	$	(180,334)	$	5,000
Issuance of common stock and warrants upon conversion of debt	—	—		1,767,632	—		7,829		—		—		—		7,829		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		445,837	—		(271)		—		—		—		(271)		—
Issuance of warrants in connection with related party debt issuance	—	—		—	—		13,279		—		—		—		13,279		—
Issuance of warrants in connection with related party debt modification	—	—		—	—		2,882		—		—		—		2,882		—
Issuance of warrants in connection with debt accounted for at fair value	—	—		—	—		930		—		—		—		930		—
Stock-based compensation	—	—		—	—		3,234		—		—		—		3,234		—
Foreign currency translation adjustment	—	—		—	—		—		(1,066)		—		—		(1,066)		—
Net loss	—	—		—	—		—		—		(59,562)		—		(59,562)		—
Balances at September 30, 2019	14,656	$	—	103,400,207	$	10	$	1,507,298	$	(44,545)	$	(1,676,779)	$	937	$	(213,079)	$	5,000

See the accompanying notes to the unaudited condensed consolidated financial statements.

7

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)

	Nine Months Ended September 30,
(In thousands)	2020		2019
Operating activities
Net loss	$	(217,613)	$	(163,893)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss upon extinguishment of debt	51,954		8,596
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	10,478		—
Stock-based compensation	9,873		10,061
Contract asset credit loss reserve	8,342		—
Depreciation and amortization	6,740		2,691
Loss from change in fair value of derivative instruments	6,498		2,437
Accretion of debt discount	3,119		9,701
Amortization of right-of-use assets under operating leases	2,103		10,237
Non-cash interest expense in connection with modification of warrants	1,066		—
Loss in equity-method investee	1,058		—
Non-cash interest expense added to debt principal	100		—
Impairment of property, plant and equipment	13		1,263
Loss (gain) on disposal of property, plant and equipment	42		122
Expense for warrants issued for debt covenant waivers	—		5,358
Gain on foreign currency exchange rates	(583)		(361)
(Gain) loss from change in fair value of debt	(2,908)		18,629
Changes in assets and liabilities:
Accounts receivable	(7,736)		(3,482)
Contract assets	(1,939)		(2,567)
Accounts receivable, unbilled - related party	—		8,021
Inventories	(10,561)		(6,609)
Deferred cost of products sold - related party	(4,820)		(13,545)
Prepaid expenses and other assets	696		(4,445)
Accounts payable	(20,201)		(2,050)
Accrued and other liabilities	(1,259)		22,310
Lease liabilities	(3,352)		(12,453)
Contract liabilities	3,077		(3,488)
Net cash used in operating activities	(165,813)		(113,467)
Investing activities
Purchases of property, plant and equipment	(9,619)		(9,013)
Net cash used in investing activities	(9,619)		(9,013)
Financing activities
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs	170,037		14,221
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs - related party	45,000		39,500
Proceeds from issuance of debt, net of issuance costs	15,279		89,217
Proceeds from exercise of common stock rights warrant - related party	15,000		—
Proceeds from exercises of warrants - related party	13,998		—
Proceeds from exercises of warrants	3,332		1
Proceeds from issuance of common stock upon ESPP purchase	421		464
Proceeds from exercises of common stock options	16		13
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(401)		(627)
Principal payments on financing leases	(2,578)		(372)
Principal payments on debt	(46,766)		(63,675)
Net cash provided by financing activities	213,338		78,742
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(36)		(248)
Net increase (decrease) in cash, cash equivalents and restricted cash	37,870		(43,986)
Cash, cash equivalents and restricted cash at beginning of period	1,699		47,054
Cash, cash equivalents and restricted cash at end of the period	$	39,569	$	3,068
Reconciliation of cash, cash equivalents and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$	38,280	$	1,632
Restricted cash, current	329		476
Restricted cash, noncurrent	960		960
Total cash, cash equivalents and restricted cash	$	39,569	$	3,068

See the accompanying notes to the unaudited condensed consolidated financial statements.

8

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS, Continued

(Unaudited)

	Nine Months Ended September 30,
(In thousands)	2020		2019
Supplemental disclosures of cash flow information:
Cash paid for interest	$	13,858	$	10,390
Supplemental disclosures of non-cash investing and financing activities:
Accrued interest added to debt principal	$	2,056	$	986
Unpaid property, plant and equipment balances in accounts payable and accrued liabilities at end of period	$	2,100	$	134
Acquisition of right-of-use assets under operating leases	$	—	$	2,361
Cumulative effect of change in accounting principle for ASU 2017-11	$	—	$	41,043
Derecognition of derivative liabilities to equity upon extinguishment of debt	$	6,461	$	—
Derecognition of derivative liabilities upon authorization of shares	$	6,550	$	—
Derecognition of derivative liabilities upon exercise of warrants	$	5,200	$	—
Exercise of common stock warrants in exchange for debt principal and accrued interest reduction	$	69,918	$	—
Fair value of embedded features in connection with private placement	$	2,962	$	—
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances	$	188	$	8,965
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances - related party	$	747	$	16,155
Fair value of warrants recorded as debt discount in connection with debt modification	$	—	$	398
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$	27,650	$	42,479
Lease liabilities recorded upon adoption of ASC 842	$	—	$	33,552
Right-of-use assets under operating leases recorded upon adoption of ASC 842	$	—	$	29,713

See the accompanying notes to the unaudited condensed consolidated financial statements.

9

AMYRIS, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Basis of Presentation and Summary of Significant Accounting Policies

Amyris, Inc. (Amyris or the Company) is a leading synthetic biotechnology company in Clean Health and Beauty markets through its consumer brands, and is a supplier of sustainable and natural ingredients. Amyris applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Clean Health & Beauty, and Flavor & Fragrance markets. The Company's technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume ingredients. This platform, combined with our proprietary fermentation process, replaces existing complex and oftentimes expensive manufacturing processes, resulting in our successful development and production of many distinct molecules at commercial volumes.

The accompanying unaudited condensed consolidated financial statements of Amyris, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2019 (the 2019 Form 10-K), from which the condensed consolidated balance sheet as of December 31, 2019 is derived. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the accompanying interim condensed consolidated financial statements do not include all the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Raizen Joint Venture Agreement

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into a joint venture agreement for 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 for 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. Due to the COVID-19 pandemic, the parties have agreed to extend the previous July 2020 deadline to conduct the relevant analysis of the sweetener production data in order to determine potential next steps for the joint venture. In addition, notwithstanding the satisfaction of 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. The Company will conclude its evaluation of the accounting treatment for its future interest in the joint venture under ASC 810, Consolidations and ASC 323, Equity Method and Joint Ventures when the economic participation structure and related corporate governance is finalized and the formation of the joint venture is consummated.

Potential Impact of COVID-19 on the Company's Business

With the global spread of the COVID-19 pandemic beginning in the first quarter of 2020 and anticipated continuation throughout 2020, and the resulting shelter-in-place orders covering the Company’s corporate headquarters, primary research and development laboratories, and employees, the Company has implemented policies and procedures to conduct its operations in compliance with local county guidelines. The extent to which the COVID-19 pandemic impacts the Company’s business, financial condition or results of operations will depend on future developments, which are highly uncertain and cannot be accurately predicted. New information may emerge concerning the severity of the COVID-19 pandemic and the actions to contain the pandemic or treat COVID-19, such as the ultimate geographic spread of the disease, the duration of the pandemic, continued travel restrictions, social distancing, business closures or disruptions, and the effectiveness of actions taken to contain or treat COVID-19 in the United States and in other countries. As the COVID-19 pandemic continues to evolve, to the extent it adversely affects our business and financial results, it may also impact other risks to which the Company is subject as set forth in the “Risk Factors” section (Part I, Item 1A) of the 2019 Form 10-K.

10

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 over the course of at least the next 12 months following the issuance of these condensed consolidated financial statements. As of September 30, 2020, the Company had working capital of $27.7 million (compared to negative working capital of $87.5 million as of December 31, 2019), and an accumulated deficit of $2.0 billion.

As of September 30, 2020, the Company's outstanding debt principal (including related party debt) totaled $175.3 million, of which $36.2 million is classified as current. 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, including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. Further, at March 31, 2020, the Company failed to meet certain covenants and provisions under several credit arrangements, including those associated with cross-default provisions. In March 2020 and again in May 2020, most of these lenders provided waivers to the Company for breaches of all past covenant violations and cross-default payment failures, under the respective credit agreements through the earlier of the closing of a significant equity offering or May 31, 2020. The Company cured these defaults with the closing of the $200 million equity offering described below and the repayment of these past due amounts. As of September 30, 2020, the Company failed to achieve the minimum revenue thresholds under the Foris LSA, Naxyris LSA and Senior Convertible Notes Due 2022, which are described in more detail in Note 4, “Debt”, and obtained a waiver from each of these lenders to cure the September 30, 2020 minimum revenue covenant violations. The minimum revenue threshold test is based on 4-quarters trailing revenue and has been significantly impacted by the elimination of a $37.5 million royalty from the measurement period that was recorded in April 2020 related to the DSM Value Sharing Agreement. See Note 9, “Revenue” for more information.

Beginning in May 2020 and continuing through June 2020, the Company executed a series of financial transactions to minimize cash outflows related to debt service payments and to increase operating cash. On May 1, 2020, the Company amended the Senior Convertible Notes Due 2022 to eliminate the monthly amortization payments and change the interest payment frequency from monthly to quarterly. On May 7, 2020, the Company received a $10 million Paycheck Protection Plan loan (PPP Loan). On June 1, 2020, the Company amended the Foris LSA to eliminate the quarterly principal payments and defer all interest payments until maturity on July 1, 2022, and to provide for the conversion of all outstanding indebtedness under the LSA at a $3.00 per share conversion price, which conversion was approved by the Company’s stockholders on August 14, 2020. Further, on June 1, 2020 and June 4, 2020, the Company entered into securities purchase agreements with investors for the private placement of an aggregate of $200 million of common and preferred stock, resulting in the Company receiving approximately $190 million of net proceeds. A portion of the proceeds from the offering was used to pay down approximately $37.1 million of debt principal (which included $10 million to repay the PPP Loan) and $6.1 million of accrued interest. Also, on June 2, 2020, Total Raffinage Chimie (Total) converted approximately $9.3 million of debt principal and accrued interest into common stock under the terms of the 2014 Rule 144A Convertible Note, further reducing the Company’s outstanding indebtedness. On August 10, 2020, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Second Amendment to Promissory Note and Partnership Agreement to reduce the frequency of partnership payments from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022. See Note 4, “Debt.” for more information. As a result of closing the equity offering, making past due payments, converting the $9.1 million 2014 Rule 144A Convertible Note principal into equity, and executing amendments to the Foris LSA, the Senior Convertible Notes Due 2022, and the Ginkgo Note, the Company cured all payment defaults and other events of default, including cross-defaults under the Company’s various debt instruments as of June 30, 2020. Although the Company has been able to obtain waivers in the past for substantially all its prior defaults to date and was able to cure the existing minimum revenue covenant default, it may not be able to cure or obtain a waiver for any defaults in the future.

Further, the Company's cash and cash equivalents of $38.3 million as of September 30, 2020 will not be sufficient to fund expected cash flows requirements from operations and cash debt service obligations through November 2021. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date these condensed consolidated financial statements are issued. The condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to eliminate or minimize the anticipated negative cash flows from operations during the 12 months from the date of this filing and to either raise additional cash proceeds through financings or refinance the debt maturities occurring in December 2020 and June 2021, all of which are uncertain and outside the control of the Company. Further, the Company's operating plan for the remainder of 2020 contemplates (i) revenue growth from sales of existing and

11

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, (iv) continued cash inflows from collaborations and grants, and (v) the monetization of certain contractual assets. If the Company is unable to complete these actions, it may be unable to meet its operating cash flow needs and its obligations under its existing debt facilities over the next 12 months. 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 condensed consolidated financial statements.

Significant Accounting Policies

Note 1, "Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the 2019 Form 10-K includes a discussion of the significant accounting policies and estimates used in the preparation of the Company’s consolidated financial statements. There have been no material changes to the Company's significant accounting policies and estimates during the nine months ended September 30, 2020.

Accounting Standards or Updates Recently Adopted

In the nine months ended September 30, 2020, the Company adopted these accounting standards or updates:

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. ASU 2018-13 became effective in the first quarter of fiscal 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements.

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. ASU 2018-18 became effective in the first quarter of fiscal year 2020 retrospectively. The adoption of this standard did not have any impact on the Company’s condensed consolidated financial statements.

Accounting Standards or Updates Not Yet Adopted

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 is effective for the Company in the first quarter of 2023. The Company is currently evaluating the impact this standard will have on its condensed consolidated financial statements.

Accounting for Income Taxes In December 2019, the FASB issued ASU 2019-12, “Simplifying the Accounting for Income Taxes” (“ASU 2019-12”). The amendments in ASU 2019-12 simplify the accounting for income taxes by removing certain exceptions to the general principles in ASC Topic 740, Income Taxes. The amendments also improve consistent application of and simplify U.S. GAAP for other areas of ASC Topic 740 by clarifying and amending existing guidance. ASU 2019-12 will be effective for the Company commencing in the first quarter of fiscal year 2021. The transition requirements are dependent upon each amendment within this update and will be applied either prospectively or retrospectively. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Convertible Debt, and Derivatives and Hedging On August 5, 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, to improve financial reporting associated with accounting for convertible instruments and contracts in an entity’s own equity. ASU 2020-06 is effective for the

12

Company in the first quarter of 2022. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

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 condensed consolidated 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 condensed consolidated financial statements.

2. Balance Sheet Details

Allowance for Doubtful Accounts

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Period
Nine months ended September 30, 2020	$	45	$	57	$	—	$	102
Year ended December 31, 2019	$	642	$	110	$	(707)	$	45

Inventories

(In thousands)	September 30, 2020		December 31, 2019
Raw materials	$	7,136	$	3,255
Work-in-process	12,083		7,204
Finished goods	17,993		17,311
Inventories	$	37,212	$	27,770

Deferred cost of products sold - related party

(In thousands)	September 30, 2020		December 31, 2019
Deferred cost of products sold - related party	$	9,454	$	3,677
Deferred cost of products sold, noncurrent - related party	11,858		12,815
Total	$	21,312	$	16,492

In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for sweetener production through December 2022. See Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K for information regarding the November 2018 Supply Agreement Amendment. As part of the amendment, the Company made a series of manufacturing capacity fee payments from November 2018 to March 31, 2020. Of these payments $17.4 million was recorded as deferred cost of products sold. In June 2020, the Company paid an additional $6.9 million manufacturing capacity fee, which represents the final payment under the amendment. The capitalized 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 produced and sold over the five-year term of the supply agreement. Each quarter, the Company evaluates its estimated future production volumes through the end of the agreement and adjusts the unit cost to be expensed over the remaining estimated production volume. During the three and nine months ended September 30, 2020, the Company expensed $0.7 million and $2.0 million, respectively, of the deferred cost of products sold asset to cost of products sold. Inception-to-date amortization through September 30, 2020 totaled $3.0 million.

13

Prepaid expenses and other current assets

(In thousands)	September 30, 2020		December 31, 2019
Prepayments, advances and deposits	$	6,117	$	4,726
Non-inventory production supplies	3,746		5,376
Recoverable taxes from Brazilian government entities	1,978		—
Other	3,053		2,648
Total prepaid expenses and other current assets	$	14,894	$	12,750

Property, Plant and Equipment, Net

(In thousands)	September 30, 2020		December 31, 2019
Machinery and equipment	$	48,893	$	48,041
Leasehold improvements	43,198		41,478
Computers and software	10,589		9,822
Furniture and office equipment, vehicles and land	3,485		3,510
Construction in progress	7,369		9,752
	113,534		112,603
Less: accumulated depreciation and amortization	(83,743)		(83,673)
Property, plant and equipment, net	$	29,791	$	28,930

During the three and nine months ended September 30, 2020 and 2019, depreciation and amortization expense was as follows:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Depreciation and amortization expense	$	1,905	$	969	$	5,300	$	2,691

Leases

Operating Leases

The Company has operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 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 ROU assets under operating leases on the Company's condensed consolidated balance sheets 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 "Lease liabilities" and "Lease liabilities, net of current portion" on the Company's condensed consolidated balance sheets. Operating lease right-of-use assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. The Company had $10.9 million and $13.2 million of right-of-use assets as of September 30, 2020 and December 31, 2019, respectively. Operating lease liabilities were $16.2 million and $19.7 million as of September 30, 2020 and December 31, 2019, respectively. During the three and nine months ended September 30, 2020 and 2019, respectively, the Company recorded $1.5 million, $4.6 million, $5.9 million and $14.1 million of operating lease amortization that was charged to expense, of which $0, $0, $0.9 million and $5.2 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:

14

	Nine Months Ended September 30,
	2020	2019
Cash paid for operating lease liabilities, in thousands	$5,759	$15,908
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$—	$32,074
Weighted-average remaining lease term	2.7	2.6
Weighted-average discount rate	18.0%	17.5%

(1) 2019 amount includes $29.7 million for operating leases existing on January 1, 2019 and $2.4 million for operating leases that commenced during the nine months ended September 30, 2019.

Financing Leases

The Company has 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 condensed 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. Accumulated amortization of assets under financing leases totaled $3.9 million and $1.7 million as of September 30, 2020 and December 31, 2019, respectively.

Maturities of Financing and Operating Leases

Maturities of lease liabilities as of September 30, 2020 were as follows:

Years ending December 31: (In thousands)	Financing Leases		Operating Leases		Total Leases
2020 (remaining three months)	$	1,086	$	1,960	$	3,046
2021	4,568		7,480		12,048
2022	—		7,657		7,657
2023	—		3,322		3,322
2024	—		151		151
Total lease payments	5,654		20,570		26,224
Less: amount representing interest	(601)		(4,410)		(5,011)
Total lease liability	$	5,053	$	16,160	$	21,213
Current lease liability	$	3,882	$	5,051	$	8,933
Noncurrent lease liability	1,171		11,109		12,280
Total lease liability	$	5,053	$	16,160	$	21,213

Other Assets

(In thousands)	September 30, 2020		December 31, 2019
Equity-method investment	$	4,054	$	4,734
Deposits	126		295
Contingent consideration	—		3,303
Other	1,179		1,373
Total other assets	$	5,359	$	9,705

In connection with the December 2017 sale of its subsidiary Amyris Brasil Ltda. (Amyris Brasil), the Company recorded a long-term receivable related to certain contingent consideration to be received from DSM upon DSM’s realization of certain Brazilian value-added tax benefits it acquired with its purchase of Amyris Brasil. In the three months ended June 30, 2020, the Company received the $3.3 million remaining balance of contingent consideration due to the Company under the 2017 asset purchase agreement.

15

Accrued and Other Current Liabilities

(In thousands)	September 30, 2020		December 31, 2019
Accrued interest	$	8,116	$	8,209
Payroll and related expenses	7,063		7,296
Contract termination fees	4,315		5,347
Asset retirement obligation	2,603		3,184
Professional services	1,804		2,968
Ginkgo partnership payments	951		4,319
Tax-related liabilities	550		1,685
Other	3,028		3,647
Total accrued and other current liabilities	$	28,430	$	36,655

Other noncurrent liabilities

(In thousands)	September 30, 2020		December 31, 2019
Liability for unrecognized tax benefit	$	7,440	$	7,204
Liability in connection with acquisition of equity-method investment	6,354		5,249
Ginkgo partnership payments, net of current portion	7,098		4,492
Contract liabilities, net of current portion	111		1,449
Refund liability(1)	—		3,750
Other	993		880
Total other noncurrent liabilities	$	21,996	$	23,024

(1) In April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" in Part II, Item 8 of the 2019 Form 10-K for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in $12.5 million of prepaid variable consideration to the Company. The $12.5 million was recorded as a refund liability. During the three months ended March 31, 2020, the Company concluded that it would not be required to return any portion of the remaining refund liability to DSM, and recorded $3.8 million of royalty revenue related to this change in estimate and reduction of the refund liability.

Ginkgo Partnership Payments Modification

On August 10, 2020, the Company and Ginkgo entered into a Second Amendment to Promissory Note and Partnership Agreement (Second Amendment) to reduce the partnership payments frequency from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022 (the “End of Term Payment”), provided that, if the Ginkgo Promissory Note is not fully repaid by April 19, 2022, the End of Term Payment shall be of $10.4 million. See Note 4, “Debt.” for more information.

As a result of changes to key provisions in the partnership payments, the Company analyzed the combined before and after cash flows under the Promissory Note and Partnership Agreement that resulted from (i) the reduced interest rate on the Promissory Note, (ii) reduced payment frequency under the Promissory Note and Partnership Agreement, and (iii) changes in the periodic and total payment amounts under the Partnership Agreement, to determine whether these changes resulted in a modification or extinguishment of the obligations under the Second Amendment. Based on the combined before and after cash flows of the Promissory Note and Partnership Agreement, the change was significantly different. Consequently, the modifications resulting from the Second Amendment were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $0.1 million loss upon extinguishment of the partnership payment obligation, related to the write-off of the unamortized debt discount. Further, since the partnership payment obligation does not contain an explicit interest rate, the Company recorded the $11.9 million of total payments at its net present value of $8.1 million in other liabilities, with the $3.8 million difference recorded as a discount that is accreted to interest expense over the repayment term using the effective interest method.

16

3. Fair Value Measurement

Liabilities Measured and Recorded at Fair Value on a Recurring Basis

The following tables summarize liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	September 30, 2020								December 31, 2019
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Foris Convertible Note (LSA Amendment)	$	—	$	—	$	58,467	$	58,467	$	—	$	—	$	—	$	—
Senior Convertible Notes	—		—		25,349		25,349		—		—		50,624		50,624
Embedded derivatives bifurcated from debt instruments	—		—		597		597		—		—		2,832		2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		3,237		3,237		—		—		6,971		6,971
Total liabilities measured and recorded at fair value	$	—	$	—	$	87,650	$	87,650	$	—	$	—	$	60,427	$	60,427

The Company did not hold any financial assets to be measured and recorded at fair value on a recurring basis as of September 30, 2020 and December 31, 2019. Also, there were no transfers between the levels during the three months ended September 30, 2020 or the year ended December 31, 2019.

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 embedded derivative liabilities is described subsequently in this note. Market risk associated with embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

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".

Fair Value of Debt — Foris Convertible Note (LSA Amendment)

On June 1, 2020, the Company and 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, entered into an Amendment No. 1 to the Amended and Restated Foris LSA (LSA Amendment), pursuant to which, among other provisions, Foris has the option, in its sole discretion, to convert all or a portion of the secured indebtedness under the LSA Amendment, including accrued interest, into shares of Common Stock at a $3.00 conversion price (Conversion Option), which Conversion Option was approved by the Company’s stockholders on August, 14, 2020. See Note 4, “Debt” for further information regarding the LSA Amendment and related extinguishment accounting treatment. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). The LSA Amendment also contains certain change in control embedded derivatives and a contingent beneficial conversion feature and management believes the fair value option best reflects the underlying economics of new convertible note. 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 LSA Amendment.

At June 30, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $81.6 million. The Company measured the initial fair value of the LSA Amendment using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $4.27 stock price, (ii) 25% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. At September 30, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $58.5 million. The Company remeasured the fair value of the LSA Amendment using the following inputs: (i) $2.92 stock price, (ii) 21% discount yield, (iii) 0.13% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. At both dates, the Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year. The Company recorded

17

gains of $23.1 million and $13.6 million related to change in fair value of the LSA Amendment for the three and nine months ended September 30, 2020, respectively.

Fair Value of Debt — Senior Convertible Notes

On January 14, 2020, the Company exchanged the $66 million Senior Convertible Notes (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), (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 (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). Due to the legal extinguishment and exchange of the Prior Notes and significantly different cash flows contained in the New Notes, the Company accounted for the exchange as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt, which was comprised of the $4.1 million fair value of the Warrants, the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and Rights over the $2.87 per share contractual value. See Note 4, "Debt” for further information regarding the transaction.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported as "Gain (loss) from change in fair value of debt" in the consolidated statements of operations in each reporting period subsequent to the issuance of the New Notes. At January 14, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $51.0 million and the fair value was $35.8 million. The Company measured the fair value at January 14, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $2.90 stock price, (ii) 226% discount yield, (iii) 1.59% risk free interest rate (iv) 45% equity volatility, (v) 25% / 75% probability of principal repayment in cash or stock, respectively and (vi) 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.

At September 30, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $30.0 million and the fair value was $25.3 million. The Company measured the fair value at September 30, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $2.92 stock price, (ii) 233% discount yield, (iii) 0.11% risk free interest rate (iv) 45% equity volatility, and (v) 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.

For the three and nine months ended September 30, 2020, the Company recorded an $11.3 million gain and a $10.7 million loss from change in fair value of debt, respectively, in connection with the fair value remeasurement of the Prior Notes and the New Senior Convertible Notes, as follows:

In thousands
Fair value at December 31, 2019	$	50,624
Less: principal paid	(35,980)
Loss from change in fair value	10,705
Fair value at September 30, 2020	$	25,349

A binomial lattice model was used to determine whether the LSA Amendment and the Senior Convertible Notes (Debt Instruments) 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 Debt Instruments using the "with-and-without method", where the fair value of the Debt Instruments including the embedded and freestanding features is defined as the "with," and the fair value of the Debt Instruments excluding the embedded and freestanding features is defined as the "without." This method estimates the fair value of the Debt Instruments by looking at the difference in the values of the Debt Instruments with the embedded and freestanding derivatives and the fair value of the Debt Instruments without the embedded and freestanding features. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility, estimated credit spread and other instrument-specific assumptions. The

18

Company remeasures the fair value of the Debt Instruments 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.

Derivative Liabilities Recognized in Connection with the Issuance of Debt 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 instruments, either freestanding or embedded, measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Derivative Liability
Balance at December 31, 2019	$	9,803
Fair value of derivative liabilities issued during the period	8,751
Change in fair value of derivative instruments	6,498
Derecognition on settlement or extinguishment	(21,218)
Balance at September 30, 2020	$	3,834

Freestanding Derivative Instruments

In connection with the January 14, 2020 issuance of the New Senior Convertible Notes as discussed above and in Note 4, “Debt” (which was accounted for as an extinguishment of the original $66 million Senior Convertible Notes), the Company issued warrants (the Warrants) to purchase up to an aggregate of 3.0 million shares of common stock (the Warrant Shares). Due to stock exchange ownership limitations, which if exceeded would require stockholder approval and possibly require cash settlement for failure to deliver shares upon exercise, the Company concluded that a portion of the Warrant Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Warrant Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Warrants had an initial fair value of $4.1 million, which was recorded as: (i) $4.1 million loss upon extinguishment of debt, (ii) $2.4 million additional paid in capital and (iii) $1.7 million derivative liability. The Warrant Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Warrants was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Warrant Shares derivative liability portion was $1.5 million, and the Company recorded a $0.2 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to remove the stock ownership limitations. As a result, the Company is able to physically deliver shares under the Warrants without the potential for cash settlement. In the three months ended June 30, 2020, the Company recorded a $1.3 million final mark-to-market loss on change in derivative liability, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and derecognized the $2.8 million derivative liability balance relate to this portion of the Warrant Shares into additional paid in capital.

In connection with the January 31, 2020 private placement transaction with Foris (an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock discussed in Note 6, “Stockholders’ Deficit”), the Company issued a right (the Right) to purchase up to an aggregate of 5.2 million shares of common stock (the Right Shares). Due to certain contractual provisions in the Right, the Company concluded that a portion of the Right Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Right Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Right had an initial fair value of $5.3 million, of which $2.3 million was recorded as additional paid in capital and $3.0 million was recorded as a derivative liability. The Right Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Right Shares derivative liability portion was $2.0 million, and the Company recorded a $1.0 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to increase its authorized common share count from 250 million to 350 million. As a result, the portion of the Right Shares initially accounting for as a derivative liability was no longer precluded from the derivative scope exception and met the criteria for equity classification. In the three months ended June 30, 2020, the Company recorded a $1.8 million final mark-to-market loss on change in fair value of derivative instruments using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and derecognized the $3.7 million derivative liability balance into additional paid in capital.

19

In connection with the January 31, 2020 Debt Equitization transaction with Foris, which was accounted for as a debt extinguishment as discussed in Note 4, “Debt” and Note 6, “Stockholders’ Deficit”, the Company issued rights (the Right) to purchase up to of 8.8 million shares of common stock at $2.87 per share for twelve months from the issuance date. The Company concluded that the Right met the derivative scope exception and criteria to be accounted for in equity. The Right had a fair value of $8.9 million which was recorded as additional paid in capital and a charge to loss upon extinguishment of debt. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below.

During the second half of 2019, the Company issued five freestanding liability warrants related to the September 2019 and November 2019 Schottenfeld Notes (the Schottenfeld Notes), which the Company recorded at fair value as a derivative liability and debt discount on the respective issuance dates (see Note 4, “Debt” for further information). These freestanding liability warrants had a collective fair value of $7.0 million at December 31, 2019. As a result of the Foris Debt Equitization transaction on January 31, 2020, the variability causing these instruments to be recorded as a derivative liability was eliminated and upon derecognition of this liability into equity, the Company recorded a $1.8 million gain on change in fair value of derivative instruments in the three months ended March 31, 2020, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and reclassified the derivative liability balance of $5.2 million to additional paid in capital.

On February 28, 2020, the Company entered into forbearance agreements with certain affiliates of the Schottenfeld Group LLC (the Lenders) related to certain defaults under the Schottenfeld Notes. The transaction was accounted for as a debt extinguishment. See Note 4, “Debt” for further information. In connection with entering into the forbearance agreements, the Company committed to issuing new warrants (the New Warrants) to the Lenders under certain contingent events for 1.9 million shares of common stock at a $2.87 purchase price and a two-year term. The contingent obligation to issue the New Warrants did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The contingently issuable New Warrants derivative liability had an initial fair value of $3.2 million and was recorded as a derivative liability with a $3.2 million charge to loss upon extinguishment of debt. The New Warrants derivative liability will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the New Warrants derivative liability was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At September 30, 2020, the fair value of the contingently issuable New Warrants derivative liability was $3.2 million, and for the three and nine months ended September 30, 2020, respectively, the Company recorded a $2.0 million gain and a $0.1 million loss on change in fair value of derivative instruments.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price from $56.16 to $2.87 per share. See Note 4, “Debt” for further information. Historically, the embedded conversion option was bifurcated and accounted for as a derivative liability, and at December 31, 2019 and March 31, 2020 had a $0 fair value due to the Note’s short maturity and the significant conversion price differential when compared to the Company’s current stock price. As a result of the conversion price reduction, the Company remeasured the fair value of the conversion option using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and recorded a $6.5 million loss on change in fair value of derivative instruments in the three months ended June 30, 2020. On June 2, 2020, Total elected to convert all the outstanding principal and interest under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $6.5 million liability was derecognized into additional paid in capital, along with the debt principal and interest balance.

Bifurcated Embedded Features in Debt Instruments

During the second half of 2019, the Company issued four debt instruments with embedded mandatory redemption features which were bifurcated from the debt host instruments and recorded at fair value as a derivative liability and debt discount. The collective fair value of the four bifurcated derivatives totaled $2.8 million at December 31, 2019. In January and February 2020, the Company again modified certain key terms in three of the four underlying debt instruments, resulting in a debt extinguishment of the three modified debt instruments. Consequently, in the three months ended March 31, 2020, the collective fair value of the three extinguished bifurcated derivatives totaling $2.3 million was recorded as a loss upon extinguishment of debt and the $0.9 million collective fair value of the new bifurcated embedded mandatory redemption features was recorded as a derivative liability and new debt discount at the modification date. The fair value of the bifurcated derivative liability was determined using a probability weighted discounted cash flow analysis which is discussed in the valuation methodology and approach section below. At September 30, 2020, the fair value of the bifurcated embedded mandatory redemption features totaled $0.6 million, and the Company recorded a $0.1 million gain on change in fair value derivative instruments during the nine months ended September 30, 2020. Also, one of the bifurcated features was embedded in the Foris LSA, which was modified and accounted for as an extinguishment in the three months ended June 30, 2020. As a result, the $0.7 million

20

derivative liability balance was derecognized and recorded into the initial fair value of the new Foris Convertible Note (see “Fair Value of Debt – Foris Convertible Note (LSA Amendment)” above).

Valuation Methodology and Approach to Measuring the Derivative Liabilities

The liabilities associated with the Company’s freestanding and embedded derivatives outstanding at September 30, 2020 and December 31, 2019 represent the fair value of freestanding equity instruments and mandatory redemption features embedded in certain debt 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 instruments or embedded derivatives using the Black-Scholes-Merton option pricing model or a probability weighted discounted cash flow analysis measuring the fair value of the debt instrument both with and without the embedded feature, both of which are discussed in more detail below.

The Company used the Black-Scholes-Merton option pricing model to determine the fair value of its liability classified warrants as of September 30, 2020 and December 31, 2019. Input assumptions for these freestanding instruments are as follows:

	Range for the Period
Input assumptions for liability classified warrants:	September 30, 2020		December 31, 2019
Fair value of common stock on issue date	$2.56 – $4.27		$3.09 – $4.76
Exercise price of warrants	$2.87 – $2.87		$3.87 – $3.90
Expected volatility	117% – 117%		94% – 105%
Risk-free interest rate	0.13% – 0.17%		1.58% – 1.67%
Expected term in years	1.75 – 2.26		1.51 – 2.00
Dividend yield	0.0	%	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 debt instruments. 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 market-based assumptions and estimates used in valuing the embedded derivative liabilities include amounts in the following ranges/amounts:

	September 30, 2020	December 31, 2019
Risk-free interest rate	0.09% - 0.17%	1.6% - 1.7%
Risk-adjusted discount yield	25.0% - 26.0%	20.0% - 27.0%
Probability of change in control	5.0%	5.0%
Credit spread	24.7% - 36.8%	18.4% - 25.4%
Estimated conversion dates	Not applicable	2022 - 2023

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, generally, an increase in the Company’s stock price, change of control probability, risk-adjusted yields term to maturity/conversion or stock price volatility increases the value of the derivative liability.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

21

The carrying amounts 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. 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 September 30, 2020 and at December 31, 2019, excluding the debt instruments recorded at fair value, was $90.6 million and $195.8 million, respectively. The fair value of such debt at September 30, 2020 and at December 31, 2019 was $76.1 million and $194.8 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.

4. Debt

Net carrying amounts of debt are as follows:

	September 30, 2020								December 31, 2019
(In thousands)	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Convertible notes payable
Senior convertible notes	$	30,020	$	—	$	(4,671)	$	25,349	$	66,000	$	—	$	(15,376)	$	50,624
	30,020		—		(4,671)		25,349		66,000		—		(15,376)		50,624
Related party convertible notes payable
Foris convertible note	50,041		—		8,426		58,467		—		—		—		—
2014 Rule 144A convertible notes	—		—		—		—		10,178		—		—		10,178
	50,041		—		8,426		58,467		10,178		—		—		10,178
Loans payable and credit facilities
Schottenfeld notes	12,500		(269)		—		12,231		20,350		(1,315)		—		19,035
Nikko notes	7,868		(794)		—		7,074		14,318		(901)		—		13,417
Ginkgo note	12,000		—		—		12,000		12,000		(3,139)		—		8,861
Other loans payable	953		—		—		953		1,828		—		—		1,828
	33,321		(1,063)		—		32,258		48,496		(5,355)		—		43,141
Related party loans payable
Foris notes	5,000		—		—		5,000		115,351		(9,516)		—		105,835
DSM notes	33,000		(3,007)		—		29,993		33,000		(4,621)		—		28,379
Naxyris note	23,914		(575)		—		23,339		24,437		(822)		—		23,615
	61,914		(3,582)		—		58,332		172,788		(14,959)		—		157,829
Total debt	$	175,296	$	(4,645)	$	3,755	174,406		$	297,462	$	(20,314)	$	(15,376)	261,772
Less: current portion							(31,431)								(63,805)
Long-term debt, net of current portion							$	142,975							$	197,967

Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (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 (the Rights Shares), (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 (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 Exchange Shares and Warrants were issued on January 14, 2020. The unpaid interest and cash fees were paid in accordance with the Exchange Agreements. The Rights were exercised by the Holder and common stock shares issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020.

The New Notes have substantially similar terms as the Prior Notes, except under the New Notes (i) the requirement to redeem an aggregate principal amount of $10 million on December 31, 2019 was eliminated, (ii) the Company would 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

22

redeemed, (iii) the financing activity requirement was reduced such that the Company would 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 stockholder approval for the Holders to exceed a 19.99% stock exchange ownership limitation (the Stockholder Approval) would be extended from January 31, 2020 to March 15, 2020.

Due to multiple changes in key provisions of the Prior Notes, the Company analyzed the before and after cash flows between the (i) fair value of the New Notes and (ii) reacquisition price of the Prior Notes resulting from the (A) decreased principal from $66 million to $51 million, (B) fair value of the Exchange Shares, (C) fair value of the Rights, (D) fair value of the Warrants and (E) cash fees to be paid prior to January 31, 2020 to determine whether these changes resulted in a modification or extinguishment of the Prior Notes. Based on the before and after cash flows of each note, the change was significantly different. Consequently, the Exchange Agreements were accounted for as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt in the three months ended March 31, 2020, which was comprised of the $4.1 million fair value of the Warrants (considered a non-cash fee paid to the lender), the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and the Rights Shares over the contractual value. See Note 6, “Stockholders’ Deficit” for further information on the accounting treatment of the Exchange Shares and the Rights Shares upon issuance of the New Notes. Also, see Note 3, “Fair Value Measurement” for more information regarding the valuation methodology used to determine the fair value of the Warrants.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, 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 New Notes. For the three months ended March 31, 2020, the Company recorded a loss of $1.1 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.

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 the $20.4 million of indebtedness outstanding under the Schottenfeld Credit Agreements (discussed under the Schottenfeld Forbearance Agreement below) 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 would be in the aggregate amount of $10.0 million (the Amortization Payment), split proportionally among the Holders, and that the Company would elect to pay such amortization payment in shares of Common Stock in accordance with the terms of the New Notes, provided however, that: (A) the Amortization Stock Payment Price (as defined in the New Notes) would be $3.00, (B) the Amortization Share Payment Period (as defined in the New Notes) with respect to the Amortization Payment would end on April 30, 2020 rather than March 31, 2020; and (C) in the event that Holder did not elect to receive the full Amortization Share Amount (as defined in the New Notes) during such Amortization Share Payment Period, then the Amortization Payment would be automatically reduced by the portion of such Amortization Payment not received by the Holder, (ii) there would be no amortization payment due on April 1, 2020, and (iii) the amortization payment due on May 1, 2020 would be in the aggregate amount of $8.9 million split proportionally among the Holders. The W&F Agreements were accounted for as a debt modification, as the before and after cash flows were not significantly different.

Amendment to Senior Convertible Notes Due 2022

On May 1, 2020, the Company and the holders of the New Senior Convertible Notes Due 2022 entered into separate amendments to the New Notes and the W&F Agreements (Note Amendment), pursuant to which the Company and the Holders agreed: (i) to amend the maturity date of the New Notes from September 30, 2022 to June 1, 2021 (Maturity Date); (ii) to remove from the New Notes all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances other than events of default; (iii) that the Company would no longer be required to

23

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; (iv) that interest payments would be due quarterly (as opposed to monthly), starting on August 1, 2020; (v) that an aggregate amortization payment of approximately $16.4 million (split proportionally among the Holders) would be due on or before the earlier of May 31, 2020 and the date on which the Company receives at least $50 million of aggregate net proceeds in an offering of securities (Amended May Amortization), an amortization payment of $5 million (to the largest Holder) would be due on December 1, 2020 unless the Company receives at least $50 million of aggregate net cash proceeds from one or more financing transactions after May 1, 2020, and no other amortization payment would be due prior to the Maturity Date; (vi) to reduce the conversion price of the New Notes from $5.00 to $3.50; (vii) to reduce the redemption price with respect to optional redemptions by the Company prior to October 1, 2020 to 100%, prior to December 31, 2020 to 105% and to 110% thereafter (as opposed to 115%), of the amount being redeemed; and (viii) that an aggregate of 2,836,364 shares of Common Stock held by the Holders would not be considered as Pre-Delivery Shares (issued in connection with the November 15, 2019 Senior Convertible Notes Due 2022 and as defined in the New Notes) and would be subject to certain selling restrictions until June 15, 2020, and that an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders would be promptly returned to the Company. These Pre-Delivery Shares were returned to the Company on May 5, 2020 and May 6, 2020. The Company paid $16.4 million on June 1, 2020 to satisfy the required amortization payment and is no longer required to make the $5.0 million amortization payment on December 1, 2020. On June 4, 2020, the Company released an additional 700,000 Pre-Delivery Shares to the largest Holder in connection with the Second Amendment to New Notes and the W&F Agreements. The Company recorded $10.5 million of additional interest expense, representing the fair value of the 3,536,364 Pre-Delivery Shares released to the Holders.

Further, in connection with the Note Amendment, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share, from $3.25, with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s Common Stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share, from $5.02, and the exercise term of such warrant was extended to January 31, 2022, from May 10, 2021; and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s Common Stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022, from January 31, 2021. See Note 6, “Stockholders’ Deficit” for more information regarding the accounting treatment of these warrant modifications.

Debt Equitization – Foris, Related Party

As of December 31, 2019, the Company had two loans payable to Foris with a total principal balance of $110.0 million, excluding capitalized interest of $5.3 million. 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 first loan (Foris $19 million Note) was a $19 million unsecured borrowing that accrued interest at 12% per annum and matures on January 1, 2023. The second loan (Foris LSA) is a $91.0 million secured borrowing that accrues interest at 12.5% per annum and matured on March 1, 2023. The Foris LSA required quarterly principal payments and monthly interest payments. See Amendment No. 1 to Amended and Restated LSA — Foris, Related Party below for more information on the maturity date and payment terms of the Foris LSA.

On January 31, 2020, the Company completed a series of equity transactions with Foris that resulted in the Company (i) reducing its aggregate debt principal with Foris by $60.0 million and accrued interest and fees due to Foris by $9.9 million (including $5.4 million of capitalized interest), (ii) issuing an aggregate of 19,287,780 shares of common stock as a result of the exercise of outstanding warrants at a weighted average exercise price of approximately $2.84 per share for an aggregate of $54.8 million, (iii) issuing an aggregate of 5,279,171 shares of common stock at $2.87 per share for an aggregate of $15.1 million in a private placement, and (iv) issuing rights (the Rights) to purchase an aggregate of 8,778,230 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months. The exercise price of the outstanding warrants and the purchase price of the private placement common stock was paid through the cancellation of principal and accrued interest and fees totaling $69.9 million. See Note 6, “Stockholders’ Deficit” for information on the accounting treatment of the various equity related instruments.

As a result of the transaction described above, on January 31, 2020, the principal balance of the Foris $19 million Note and accrued but unpaid interest was fully settled through the exercise price of certain of outstanding warrants. Upon settlement of the Foris $19 million Note, the Company recorded a $5.7 million loss upon extinguishment debt, which was comprised of $6.1 million of unaccreted discount, less the $0.4 million fair value of the extinguished bifurcated derivative liability.

In addition, this series of equity transactions directly impacted the cash flows of the Foris LSA and, as a result, the Company analyzed the before and after cash flows resulting from the significant decrease in principal, the warrant exercise price modifications and the issuance rights to purchase additional shares of common stock at $2.87, to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was

24

significantly different. Consequently, the accelerated paydown of the Foris LSA loan balance through the exercise price of the remaining outstanding warrants and the purchase price of the private placement common stock was accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $10.4 million loss upon extinguishment of debt, which was comprised of $8.9 million fair value of the Rights and $3.1 million of unaccreted discount, less the $1.6 million fair value of the extinguished bifurcated derivative liability. See Note 6, “Stockholders’ Deficit” for further information on the valuation methodology and related accounting treatment of the Rights. In recording the new debt issuance, the Company capitalized $0.7 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

Amendment No. 1 to Foris LSA — Foris, Related Party

On June 1, 2020, the Company and Foris entered into Amendment No. 1 to the Foris LSA (LSA Amendment), pursuant to which: (i) the interest rate applicable to the then outstanding secured indebtedness (Secured Indebtedness) was amended from and after June 1, 2020 to a per annum rate of interest equal to 6.00% (previously 12.5%), (ii) the Company shall not be required to make any interest payments outstanding as of May 31, 2020 or accruing thereafter prior to July 1, 2022 (previously due monthly), (iii) the quarterly principal amortization payments were eliminated and all outstanding principal under the LSA Amendment became due on July 1, 2022, and (iv) Foris shall have the option, in its sole discretion, to convert all or portion of the Secured Indebtedness, including accrued interest, into shares of common stock at a $3.00 conversion price (Conversion Option), subject to the Company’s stockholder approval to issue shares of common stock upon exercise of the Conversion Option in accordance with applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d); for which stockholder approval was obtained on August 14, 2020.

The Company analyzed the before and after cash flows resulting from the LSA Amendment to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was significant. Consequently, the LSA Amendment was accounted for as a debt extinguishment and a new debt issuance. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). Management believes the fair value option best reflects the underlying economics of the LSA Amendment, which contains embedded derivatives, a conversion option requiring bifurcation and a beneficial conversion feature. 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 LSA Amendment. The Company also recorded gains of $23.1 million and $13.6 million for the three and nine months ended September 30, 2020 related to the change in fair value of the LSA Amendment after the June 1, 2020 issuance date, 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 LSA Amendment.

Schottenfeld Forbearance Agreement

The Company, Schottenfeld Group LLC (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 Schottenfeld Warrants) to purchase shares (the Warrant Shares) of the Company’s common stock. See Note 6, “Stockholders’ Deficit” for further information. Indebtedness under the September Notes totals $12.5 million, accrues interest at 12% per annum and matures on January 1, 2023. Indebtedness under the November Notes total $7.9 million, accrued interest at 12% per annum and originally matured on January 15, 2020. The Company failed to repay the $7.9 million November Notes by January 15, 2020.

On February 28, 2020, the Company entered into a forbearance agreement with the Lenders (Forbearance Agreement), 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 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

25

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) issue new warrants upon the occurrence of certain contingent events and (v) amend 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.

Due to multiple changes in key provisions of Schottenfeld Credit Agreements, the Company analyzed the before and after cash flows resulting from the warrant modification and forbearance fee 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 was significantly different. Consequently, the modifications resulting from the Forbearance Agreement were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $5.6 million loss upon extinguishment of debt, which was comprised of the $3.2 million fair value of contingent warrant issuance obligation, the $1.3 million incremental fair value of the modified warrants, $1.1 million of unaccreted discount and the forbearance fee, less the balance of the extinguished bifurcated derivative liability. In recording the new debt issuance, the Company capitalized $0.2 million of legal fees and $0.2 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

On April 19, 2020, the Company failed to pay the amounts due under the Forbearance Agreement, including the past due interest on the September Notes, and was unable to obtain a waiver or extension for the past due amounts. As a result, $20.4 million of principal outstanding under the Schottenfeld Notes was classified as a current liability on the condensed consolidated balance sheet as of March 31, 2020. On June 5, 2020, the Company repaid the past due November 2019 Notes totaling $7.9 million. Consequently, the September 2019 Notes due January 1, 2023 totaling $12.5 million were reclassified to a non-current liability as of September 30, 2020.

2014 Rule 144A Note Exchange and Extensions – Total, Related Party

On March 11, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement (the Extension Agreement) due to the Company’s failure to pay the $10.2 million principal amount due under the December 20, 2019 reissued 2014 Rule 144A Convertible Notes that matured on January 31, 2020. The Extension Agreement resulted in the reissuance and extension of the December 20, 2019 promissory note to March 31, 2020. Under the terms of the 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: (i) had a maturity date of March 31, 2020, (ii) had a $9.1 million principal amount due, (iii) accrued interest at a rate of 12.0% per annum, and (iv) had terms substantially identical to the December 20, 2019 promissory note. The Extension Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note to $2.87 per share. Effective April 30, 2020, the Company and Total entered into a subsequent Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The 2014 Rule 144A Convertible Note was reissued as a result of such extensions with terms substantially identical to the previously issued promissory notes. On June 2, 2020, Total elected to convert all the outstanding principal and interest due under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the fair value of the conversion option was derecognized into additional paid in capital. See Note 3, “Fair Value Measurement” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

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, pursuant to which Ginkgo agreed to (a) waive the Company’s failure to pay past due interest and partnership payments, including interest thereon of $6.7 million by December 15, 2019, and to comply with a reporting covenant prior to March 31, 2020, (b) to make a prior waiver fee payment of $0.5 million on

26

December 15, 2019, (c) waive any cross defaults due to events of default under other debt obligations by the Company, (d) 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, and (e) to defer all past due payments totaling $7.2 million until April 30, 2020. The Ginkgo Waiver was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On May 6, 2020, the Company entered into a waiver agreement under which the maturity date for all past due amounts to Ginkgo was extended to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The Company paid all past-due amounts to Ginkgo.

On August 10, 2020, the Company and Ginkgo entered into a Second Amendment to Promissory Note and Partnership Agreement (Second Amendment) to, among other things, (i) with respect to the Promissory Note, amend the interest payment frequency from monthly to quarterly beginning September 30, 2020 and reduce the interest rate from 12% to 9% beginning January 1, 2021, conditioned to the timely payment of interest on September 30, 2020 and December 31, 2020; and (ii) with respect to the Partnership Agreement, reduce the partnership payments frequency from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022 (the “End of Term Payment”), provided that, if the Promissory Note is not fully repaid by April 19, 2022, the End of Term Payment shall be of $10.4 million.

As a result of changes to key provisions of both the Promissory Note and Partnership Agreement, the Company analyzed the before and after cash flows resulting from (i) a reduced interest rate of the Promissory Note, (ii) reduced payment frequency for the Promissory Note interest and Partnership Agreement payments and (iii) changes in the periodic and total payment amounts under the Partnership Agreement, in order to determine whether these changes result in a modification or extinguishment of the obligations under the Second Amendment. Based on the combined before and after cash flows of the Promissory Note and Partnership Agreement, the change was significantly different. Consequently, the modifications resulting from the Second Amendment were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $2.5 million loss upon extinguishment of the Promissory Note and a $0.1 million loss upon extinguishment of the partnership payments, which was primarily related to the unamortized debt discounts. The $12.0 million principal amount due under the Promissory Note was unchanged and reflects the present value of the obligation after the modifications. See Note 2, “Balance Sheet Details”, for more information on the payments due under the Partnership Agreement.

Nikko Secured Loan Agreement Amendment

On March 12, 2020, the Company and Nikko Chemicals Co. Ltd. (Nikko), entered into an amendment to the secured loan agreement (Loan Agreement) under which the Company paid Nikko $0.5 million to reduce the principal balance of the Loan Agreement to $4.0 million, extended the maturity date of the loan from January 31, 2020 to March 31, 2020 and increased the interest rate to 8.0% per annum. The loan (i) matured on March 31, 2020, (ii) accrued interest at a rate of 2.75% per annum, and (iii) was secured by a first-priority lien on 27.2% of the Aprinnova JV interests owned by the Company. The Loan Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 3, 2020, the Company entered into a second amendment to the Loan Agreement under which the maturity date of the loan was extended to April 30, 2020. Subsequently, on May 7, 2020, the Company entered into a third amendment to the Loan Agreement under which the maturity date of the loan was extended to May 31, 2020. The Company fully repaid the $4.0 million loan on June 5, 2020.

Paycheck Protection Plan Loan

On April 7, 2020, the Company applied for a Paycheck Protection Plan loan (PPP Loan) established by the Coronavirus Aid, Relief, and Economic Security Act (CARES Act). On May 7, 2020, the Company received a $10 million loan pursuant to a promissory note issued by the Company. The PPP Loan accrued interest at an annual fixed rate of 1% and had a term of 2 years with no payments due in the first six months of such term; however, interest still accrued during this six-month period. Upon receipt of the PPP Loan, the Company applied the funds to payroll and building rent expenses. Following the completion of the private placement of its securities in early June 2020, the Company repaid the PPP Loan in full, including applicable interest, on June 12, 2020.

Foris $5 Million Note – Foris, Related Party

On April 29, 2020, the Company borrowed $5.0 million from Foris, an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock. The note is unsecured and accrues interest at 12% per annum. Principal and interest will be payable at maturity, on December 31, 2022.

27

Future Minimum Payments

Future minimum payments under the Company's debt agreements as of September 30, 2020 are as follows:

(In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020 (remaining three months)	$	375	$	5,945	$	—	$	1,547	$	7,867
2021	33,898		3,902		—		31,823		69,623
2022	—		14,768		59,578		40,939		115,285
2023	—		12,899		—		—		12,899
2024	—		398		—		—		398
Thereafter	—		1,870		—		—		1,870
Total future minimum payments	34,273		39,782		59,578		74,309		207,942
Less: amount representing interest	(4,253)		(6,460)		(9,537)		(12,396)		(32,646)
Present value of minimum debt payments	30,020		33,322		50,041		61,913		175,296
Less: current portion of debt principal	(30,020)		(5,236)		—		—		(35,256)
Noncurrent portion of debt principal	$	—	$	28,086	$	50,041	$	61,913	$	140,040

5. Mezzanine Equity

Mezzanine equity at September 30, 2020 and December 31, 2019 is comprised of proceeds from shares of common stock sold on May 10, 2016 to the Bill & Melinda Gates Foundation (Gates Foundation). In connection with the stock sale, the Company and the Gates Foundation entered into an agreement under which the Company agreed to expend an aggregate amount not less than the proceeds from the stock sale 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. If the Company defaults in its obligation to use the proceeds from the stock sale as set forth above or defaults under certain other commitments in the agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party, the 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 September 30, 2020, the Company's remaining research and development obligation under this arrangement was $0.3 million.

6. Stockholders' Deficit

Foris Warrant Exercises for Cash

On January 13, 2020, 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. The Company received approximately $14.0 million from Foris in connection with the warrant exercise representing 4,877,386 shares of common stock issued and recorded $14.0 million as additional paid-in capital.

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. The Company and Foris agreed to defer the issuance of the shares until such time as stockholder approval has been obtained to increase the Company’s authorized share count. At March 31, 2020, the PIPE Rights exercise proceeds were recorded as additional paid-in capital as there is no contractual obligation to return the consideration if stockholder approval is not obtained. Stockholder approval was obtained on May 29, 2020 and the 5,226,481 shares of common stock were issued to Foris on June 2, 2020.

January 2020 Warrant Amendments and Exercises, Foris Debt Equitization and Private Placement

28

As described below in further detail, on January 31, 2020, the Company completed a series of equity 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 $9.9 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. See Note 4, “Debt,” for more information regarding the accounting treatment of the $60.0 million debt reduction.

Warrant Amendments and Exercises by Certain Holders

On January 31, 2020, the Company entered into separate warrant amendment agreements (the Warrant Amendments) with certain holders (the Warrant Holders) of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of certain warrants (the Amended Warrants) held by the Warrant Holders totaling 1.2 million shares was reduced to $2.87 per share. In connection with the entry into the Warrant Amendments, on January 31, 2020, the Warrant Holders exercised their Amended Warrants, representing an aggregate of 1,160,929 shares of common stock (the Warrant Amendment Shares), and the Company issued the Warrant Amendment Shares to the Holders along with a right 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 recorded the $3.3 million as additional paid in capital. The Company also measured the before and after fair value of the Amended Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Rights warrants met the derivative scope exception and equity classification criteria to be accounted for in equity.

Warrant Amendments and Exercises, Common Stock Purchase and Debt Equitization by Foris – Related Party

On January 31, 2020, the Company and Foris entered into certain warrant amendment agreements (the Foris Warrant Amendments) totaling 10.2 million shares of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of these certain warrants (the Amended Foris Warrants) was reduced to $2.87 per share. In connection with the Foris Warrant Amendments, on January 31, 2020 (i) Foris exercised all its then-outstanding common stock purchase warrants, including the Amended Foris Warrants, totaling 19,287,780 shares of common stock, at a weighted average exercise price of approximately $2.84 per share for an aggregate exercise price of $54.8 million (the Exercise Price), and purchased 5,279,171 shares of common stock (the Foris Shares) at $2.87 per share for a total purchase price of $15.1 million (Purchase Price), (ii) Foris paid the Exercise Price and the Purchase Price through the cancellation of $60 million of principal and $9.9 million of accrued interest and fees owed by the Company to Foris under the Foris $19 million Note and the Foris LSA (which was treated as a debt extinguishment as discussed in Note 4, "Debt") and (iii) the Company issued to Foris the Foris Shares and an additional right (the 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 execution of the warrant exercise agreement.

Upon exercise of the Amended Foris Warrants and issuance of the Foris Shares, the Company recorded a $69.9 million increase to additional paid-in capital. The Company also measured the before and after fair value of the Amended Foris Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Company concluded the Additional Rights met the derivative scope exception and criteria to be accounted for in equity and recorded the $8.9 million fair value of the Additional Rights to additional paid-in capital and loss upon extinguishment of debt. The fair value was determined using a Black-Scholes-Merton option pricing model based on the following input assumptions: (i) $2.56 stock price, (ii) 112% volatility, (iii) 1.45% risk free rate and (iv) 0% dividend.

January 2020 Private Placement

On January 31, 2020, the Company entered into separate Security Purchase Agreements with certain accredited investors and Foris, for the issuance and sale of an aggregate of 8,710,802 shares of common stock and rights to purchase an aggregate of 8,710,802 shares of common stock (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. The $25 million in proceeds was recorded as additional paid-in capital. See Note 3, “Fair Value Measurement,” for information regarding the valuation methodology used to determine fair value and the related accounting treatment of the PIPE rights.

Principal Conversion into Common Stock and New Warrants Issued in Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior

29

Convertible Notes), (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 (the Rights Shares), and (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, The New Notes, Exchange Shares, Rights and Warrants were issued on January 14, 2020. The Rights were exercised by the Holder and the Rights Shares were issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020. The contractual value of the Exchange Shares and the Rights Shares was $2.87 per share. Upon issuance of the New Notes, Exchange Shares and Rights, the $15.0 million of debt principal was extinguished and the $15.2 million fair value of the Exchange Shares and the Rights Shares was recorded as additional paid in capital. See Note 3, “Fair Value Measurement,” for more information regarding the valuation methodology used to determine the fair value and the related accounting treatment of the Warrants, and see Note 4, “Debt,” for further information on the accounting treatment and the terms of the note exchange.

Release of Pre-Delivery Shares and Amendment to Warrants Issued to Holders of Senior Convertible Notes Due 2022

Under the terms of the November 15, 2019 Senior Convertible Notes Due 2022 and the January 14, 2020 New Senior Convertible Notes, the Company was required to pre-deliver 7.5 million shares of common stock (the Pre-Delivery Shares) to the Holders, which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the 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 Holders 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 accounted for the fair value of the Pre-Delivery Shares within equity.

On May 1, 2020, in connection with the amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”, the Company and the Holders of the New Senior Convertible Notes Due 2022 agreed, among other provisions described in Note 4, “Debt”: (i) to remove all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances; (ii) to reduce the conversion price of the New Notes from $5.00 to $3.50; (iii) to release to the Holders an aggregate of 2,836,364 shares of common stock originally required to be returned under the Pre-Delivery Share arrangement, and (iv) return an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders to the Company. Further, on June 4, 2020, the Company agreed to release an additional 700,000 Pre-Delivery Shares to one of the Holders, in connection with the second amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”. After the release and return of the Pre-Delivery Shares on May 1, 2020 and June 4, 2020, the total number of Pre-Delivery Shares subject to the arrangement is 2,600,000 and must be returned to the Company following full redemption or repayment of the New Senior Convertible Notes Due 2022. As a result of releasing the 3,536,364 Pre-Delivery Shares to the Holders, the Company recorded $10.5 million of additional interest expense, representing the fair value of the released share.

Further, in connection with the May 1, 2020 amendment to the Senior Convertible Notes Due 2022, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share (from $3.25) with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s common stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share (from $5.02), and the exercise term of such warrant was extended to January 31, 2022 (from May 10, 2021); and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s common stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022 (from January 31, 2021). Each of these warrant instruments were previously accounted for in equity. As a result of the warrant amendments, the Company performed a before and after remeasurement of the warrants using the Black-Scholes-Merton option pricing model and recorded $1.1 million of incremental interest expense and a corresponding increase to additional paid in capital.

Increase in Authorized Common Stock

On May 29, 2020, through a proxy vote at the Company’s Annual Stockholder meeting, the Company’s stockholders approved an increase in the Company’s authorized common stock share count from 250 million to 350 million.

Total Conversion Price Reduction and Subsequent Conversion into Common Stock

30

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note from $56.16 to $2.87 per share. See Note 4, “Debt” for further information related to this debt instrument. On June 2, 2020, Total elected to convert all the outstanding principal and interest totaling $9.3 million due under the 2014 Rule 144A Convertible Note into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the conversion option was derecognized into additional paid-in capital. See Note 3, “Fair Value Measurement,” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

June 2020 PIPE

On June 1, 2020 and June 4, 2020, the Company entered into separate security purchase agreements (Purchase Agreements) with certain accredited investors (Investors), including Foris and Vivo Capital LLC, stockholders that beneficially own more than 5% of the Company’s outstanding common stock and are, respectively, owned by or affiliated with individuals serving on the Company’s Board of Directors, for the issuance and sale of an aggregate of 32,614,573 shares of the Company’s common stock, $0.0001 par value per share and 102,156 shares of the Company’s Series E Convertible Preferred Stock, $0.0001 par value per share, convertible into 34,052,070 shares of common stock, at a price of $3.00 per common share and $1,000 per preferred share, resulting in an aggregate purchase price of $200 million (Offering). The transaction closed on June 5, 2020, following the satisfaction of customary closing conditions. Upon closing, the Company received aggregate net proceeds of approximately $190 million after payment of the Offering expenses and placement agent fees. The Company used the proceeds from the Offering for the repayment of certain outstanding indebtedness and the remainder for general corporate purposes.

The Purchase Agreements included customary representations, warranties and covenants of the parties. In addition, the Company executed a letter agreement pursuant to which, subject to certain exceptions, the Company, the members of the Company’s Board of Directors, and the Company’s named executive officers agreed not to issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for common stock until September 2, 2020. The securities issued pursuant to the Purchase Agreements were sold in private placements pursuant to an exemption from registration under Section 4(a)(2) of the Securities Act of 1933, as amended (Securities Act) and Rule 506(b) of Regulation D promulgated under the Securities Act, without general solicitation, made only to and with accredited investors as defined in Regulation D.

Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws

On June 5, 2020, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series E Convertible Preferred Stock (Preferred Stock) with the Secretary of State of Delaware. Each share of Series E Preferred Stock issued in the June 2020 PIPE had a stated value of $1,000 and was convertible into 333.33 shares of common stock. All preferred shares automatically converted into common stock without any action by the holders on the first trading day after the Company obtains stockholder approval (as described below). Unless and until converted into common stock in accordance with its terms, the Preferred Stock had no voting rights, other than as required by law or with respect to matters specifically affecting the Preferred Stock.

The Company agreed to obtain stockholder approval for the issuance of common stock upon conversion of the Preferred Stock as is required by the applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d), and including the issuance of common stock upon conversion of the Preferred Shares in excess of 19.99% of the issued and outstanding common stock on the date of the Purchase Agreements. Pursuant to the Purchase Agreements, the Company was required to hold a special meeting of stockholders within 75 calendar days of the date of the Purchase Agreements for the purpose of obtaining stockholder approval. This special meeting of stockholders was held on August 14, 2020, at which the Company’s stockholders approved the conversion of the Series E Preferred Stock and as a result, 34,052,084 shares of common stock were issued on August 17, 2020 in exchange for the 102,156 shares of the Company’s Series E Convertible Preferred Stock.

The Company analyzed the automatic conversion provision related to the Series E Preferred Stock at the original commitment dates and determined the holders received a contingent beneficial conversion feature (BCF) equal to $67.2 million. This amount represents the difference between the Company’s closing stock price at the June 1, 2020 and June 4, 2020 commitment dates ($5.35 and $4.88, respectively) and the $3.00 conversion price. As the automatic conversion provision was contingent on stockholder approval on August 14, 2020, the BCF would be recognized when the contingency was resolved. Upon obtaining stockholder approval, the $67.2 million BCF was recognized in additional paid-in capital and reflected as a deemed dividend to the preferred stockholders in the September 30, 2020 condensed consolidated statement of operations, increasing the net loss attributable to common stockholders and increasing basic net loss per share.

31

Warrants and Rights Activity Summary

In connection with various debt and equity transactions (see Note 4, “Debt” above and Note 4, "Debt" and Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 2019 Form 10-K), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrants activity for the nine months ended September 30, 2020:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2019	Additional Warrants Issued	Exercises	Expired	Exercise Price per Share of Warrants Exercised		Number Outstanding as of September 30, 2020	Exercise Price per Share as of September 30, 2020
High Trail/Silverback warrants	2020	January 14, 2022	—	3,000,000	—	—	$	—	3,000,000	$2.87/$3.25
2020 PIPE right shares	2020	February 4, 2021	—	8,710,802	(5,226,481)	—	$	2.87	3,484,321	$	2.87
January 2020 warrant exercise right shares	2020	January 31, 2021 and January 31, 2022	—	9,939,159	—	—	$	—	9,939,159	$	2.87
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)	—	$	2.87	—	$	—
August 2019 Foris warrant	2019	August 28, 2021	4,871,795	—	(4,871,795)	—	$	2.87	—	$	—
April 2019 PIPE warrants	2019	April 26, 2021, April 29, 2021 and May 3, 2021	8,084,770	—	(4,712,781)	—	$	2.87	3,371,989	$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	$	2.87
Naxyris LSA warrants	2019	August 14, 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 14, 2021 and January 31, 2022	1,744,241	—	(784,016)	—	$	2.87	960,225	$	2.87
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	—	(4,877,386)	(7,219,778)	$	2.87	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,078,156	—	—	—	$	—	6,078,156	$	2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	—	3,968,116	$	2.87
May 2017 dilution warrants	2017	July 10, 2022	3,085,893	—	—	—	$	—	3,085,893	$	—
August 2017 dilution warrants	2017	May 23, 2023	3,028,983	—	—	—	$	—	3,028,983	$	—
February 2016 related party private placement	2016	February 12, 2021	171,429	—	(152,381)	—	$	0.15	19,048	$	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	72,650	—	(72,650)	—	$	0.15	—	$	—
July 2015 related party debt exchange	2015	July 29, 2025	58,690	—	—	—	$	—	58,690	$	0.15
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$	160.05
			65,755,629	21,649,961	(30,694,457)	(7,219,778)			49,491,355

7. Loss per Share

For the three and nine months ended September 30, 2019, basic loss per share was the same as diluted loss per share, because the inclusion of all potentially dilutive securities outstanding was antidilutive.

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.

32

The following table presents the calculation of basic and diluted loss per share:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Numerator:
Net loss attributable to Amyris, Inc.	$	(23,156)	$	(59,562)	$	(221,422)	$	(163,893)
Less: deemed dividend to preferred stockholder on issuance and modification of common stock warrants	—		—		—		(34,964)
Less: deemed dividend to preferred stockholders upon conversion of Series E preferred stock	(67,151)		—		(67,151)		—
Add: losses allocated to participating securities	6,832		1,655		15,369		6,233
Net loss attributable to Amyris, Inc. common stockholders, basic	$	(83,475)	$	(57,907)	$	(273,204)	$	(192,624)
Adjustment to earnings allocated to participating securities	744		—		120		—
Interest on convertible debt	1,081		—		317		—
Gain from change in fair value of debt	(17,221)		—		(5,945)		—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(98,871)	$	(57,907)	$	(278,712)	$	(192,624)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	227,267,553		103,449,612		189,192,973		91,344,150
Basic loss per share	$	(0.37)	$	(0.56)	$	(1.44)	$	(2.11)
Weighted-average shares of common stock outstanding	227,267,553		103,449,612		189,192,973		91,344,150
Effect of dilutive convertible debt	15,464,681		—		2,313,526		—
Weighted-average shares of common stock equivalents used in computing loss per share of common stock, diluted	242,732,234		103,449,612		191,506,499		91,344,150
Diluted loss per share	$	(0.41)	$	(0.56)	$	(1.46)	$	(2.11)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted loss per share of common stock because including them would have been antidilutive:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2020	2019	2020	2019
Period-end common stock warrants	43,298,741	52,612,330	43,298,741	52,612,330
Convertible promissory notes(1)	—	14,259,214	8,574,399	14,259,214
Period-end stock options to purchase common stock	6,571,703	5,398,834	6,571,703	5,398,834
Period-end restricted stock units	7,722,630	4,543,190	7,722,630	4,543,190
Period-end preferred stock	1,943,661	2,955,732	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted loss per share	59,536,735	79,769,300	68,111,134	79,769,300

______________

(1)    The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. 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.

8. Commitments and Contingencies

Contingencies

The Company has levied indirect taxes on sugarcane-based biodiesel sales that took place several years ago by Amyris Brasil Ltda. (see Note 12, “Divestiture” in Part II, Item 8 of the 2019 Form 10-K) to customers in Brazil, based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate the Company levied.

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

33

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, which was denied by the court on October 5, 2020. The Company filed its answer to the securities class action complaint on October 26, 2020. 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 naming 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.

On July 24, 2020, a securities class action complaint was filed against Amyris and the members of our Board in the Court of Chancery of the State of Delaware (Flatischler v. Melo, et. al.). The complaint alleged a breach of fiduciary obligation to disclose material information to stockholders in the proxy statement filed with the Securities and Exchange Commission on July 6, 2020 (Proxy), with respect to the Company’s special stockholders’ meeting held on August 14, 2020 (Special Meeting), at which stockholders were to vote to approve the conversion of all outstanding indebtedness under the Foris Convertible Note and of our Series E Preferred Stock issued in the June 2020 PIPE into shares of common stock, in accordance with Nasdaq Listing Standard Rule 5635(d). See Note 4, “Debt,” “Amendment No. 1 to Foris LSA — Foris, Related Party,” and Note 6, “Stockholders’ Deficit,” “June 2020 PIPE,” and “Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws” in Part I, Item 1 of this Quarterly Report on Form 10-Q for more information. The plaintiffs sought to enjoin the Special Meeting. On August 6, 2020, the plaintiffs withdrew their complaint as moot following the Company’s filing of a supplement to the Proxy on August 5, 2020. The Proxy supplement provided additional information regarding the approval process of the LSA Amendment and the June 2020 PIPE, and the relationships between the Company and its financial advisors to the June 2020 PIPE. The plaintiffs currently seek an amount for their attorney’s fees and certain legal expenses related to filing the complaint, which the parties are negotiating. Three substantially similar complaints were filed: one on July 28, 2020, in the United States District Court of Delaware (Sabatini v. Amyris, Inc.); one on July 31, 2020, in the Northern District of California (Nair v. Amyris); and another on August 4, 2020, in the Southern District of New York (Chamorro v. Amyris). Amyris answered the Chamorro case on October 19, 2020. The Sabatini and Nair cases were voluntarily dismissed by the plaintiffs on October 8 and October 22, 2020, respectively. For this matter, as of September 30, 2020, the Company has accrued a liability for the plaintiffs’ legal fees and expenses, which are not material.

On September 10, 2020, LAVVAN, Inc. (Lavvan) filed a suit against the Company in the United States District Court for the Southern District of New York alleging breach of contract, patent infringement, and trade secret misappropriation in connection with that certain Research, Collaboration and License Agreement between Lavvan and Amyris, dated March 18, 2019, as amended (Cannabinoid Agreement). Amyris filed motions to compel arbitration or to dismiss on October 2, 2020. On October 30, Lavvan filed its opposition to the Company’s motions. The Company believes that the suit lacks merit and intends to continue to defend itself vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result therefrom.

In addition, 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 that are not predictable with reasonable assurance, and therefore, an estimate of all the reasonably possible losses cannot be determined at this time. 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.

34

Other Matters

Certain conditions may exist as of the date the condensed consolidated 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.

9. Revenue Recognition and Contract Assets and Liabilities

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	20,759	$	—	$	263	$	21,022	$	9,927	$	—	$	9,114	$	19,041
Europe	3,752		3,563		919		8,234		2,609		2,305		1,354		6,268
Asia	1,542		—		1,936		3,478		2,398		—		4,789		7,187
Brazil	1,298		—		—		1,298		2,272		—		28		2,300
Other	226		—		—		226		157		—		—		157
	$	27,577	$	3,563	$	3,118	$	34,258	$	17,363	$	2,305	$	15,285	$	34,953
	Nine Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	49,568	$	—	$	263	$	49,831	$	22,806	$	—	$	16,015	$	38,821
Europe	10,100		9,714		6,073		25,887		7,565		43,387		6,180		57,132
Asia	7,901		—		6,724		14,625		8,015		—		5,038		13,053
Brazil	2,546		—		—		2,546		2,787		—		34		2,821
Other	504		—		—		504		194		—		—		194
	$	70,619	$	9,714	$	13,060	$	93,393	$	41,367	$	43,387	$	27,267	$	112,021

Significant Revenue Agreements During the Nine Months Ended September 30, 2020

Cannabinoid Agreement

On March 18, 2019, the Company entered into a Research, Collaboration and License Agreement (as amended, the Cannabinoid Agreement) with LAVVAN, Inc., an investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids, subject to certain closing conditions. Under the Cannabinoid Agreement, the Company performs research and development activities, and Lavvan is responsible for manufacturing and commercialization, related to the cannabinoids developed in accordance with the Cannabinoid Agreement. The Cannabinoid Agreement principally funds milestones that include both technical R&D targets and completion of production campaigns, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. Additionally, the Cannabinoid

35

Agreement provides for profit share to the Company on Lavvan's gross profit margin once the cannabinoid products are commercialized. On May 2, 2019, the parties formed 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 Convertible Note (see Note 4, “Debt”). On March 11, 2020, the parties revised the agreement to reflect product specifications and cost assumptions.

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 obligation. The Company concluded the agreement contained a single performance obligation of research and development services. The Company also concluded that the performance obligation is continuously delivered over time and that revenue recognition is based on an input measure of progress of labor hours incurred compared to total estimated labor hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, based on changes in estimated project plan hours, with proportional performance adjustments to quarterly revenue as necessary. Prior to September 30, 2020, the Company estimated the total unconstrained transaction price to be $145 million, based on a high probability of achieving certain underlying milestones, and had recognized $18.3 million of cumulative revenue to date. As of September 30, 2020, the Company has constrained $282 million of variable consideration which relate to milestones that do not meet the criteria necessary under ASC 606 to be included in the transaction price. The Company recognized no collaboration revenue for the three and nine months ended September 30, 2020, and during the three months ended September 30, 2020, the Company recorded a credit loss reserve against a previously recorded $8.3 million contract asset in connection with the Cannabinoid Agreement. See Contract Assets and Liabilities below for further information.

DSM Ingredients Collaboration

In September 2017, the Company entered into a collaboration agreement with DSM (DSM Collaboration Agreement) to jointly develop a new molecule in the Clean Health market using the Company’s technology (DSM Ingredient), which the Company would have the sole right to manufacture, and DSM would commercialize. Pursuant to the DSM Collaboration Agreement, DSM provides funding for the development of the DSM Ingredients in the form of milestone-based payments and, upon commercialization, the parties would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredient from the Company at prices agreed by the parties. The development services are directed by a joint steering committee with equal representation by DSM and the Company and are governed by a milestone project plan. The timing of milestone achievements is subject to review and revision as agreed by the joint steering committee. In addition, the parties will share profit margin from DSM’s sales of products that incorporate the DSM Ingredient subject to the DSM Collaboration Agreement.

The DSM Collaboration Agreement is accounted for as a revenue contract under ASC 606, and has a total transaction price of $14.1 million, 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 three performance obligations of research and development services that are delivered over time and that revenue recognition is based on an input measure of progress as labor hours are expended in the achievement of each milestone. The Company recognized $0.8 million and $5.0 million of collaboration revenue for the three and nine months, respectively, ended September 30, 2020, and $9.9 million of cumulative-to-date collaboration revenues.

Yifan Collaborations

From September 2018 to December 2019, the Company entered into a series of license and collaboration agreements, culminating in a master services agreement for research and development services, with a subsidiary of Yifan Pharmaceutical Co., Ltd. (Yifan), a leading Chinese pharmaceutical company. Upon execution of the master services agreement in December 2019 (the Collaboration Agreement), the Company evaluated and concluded that the series of agreements should be combined and accounted for as a single revenue contract under ASC 606.

The Yifan Collaboration Agreement has a total transaction price of $21.0 million, 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 obligation. The Company concluded the Collaboration Agreement contained a single performance obligation of research and development services provided continuously over time. The Collaboration Agreement provides for upfront and periodic payments based on project milestones. The Company concluded the performance obligation is delivered

36

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 $1.9 million and $6.7 million of collaboration revenue in the three and nine months, respectively, ended September 30, 2020, and $12.8 million of cumulative-to-date collaboration revenue. At September 30, 2020, the Company also recorded a $1.8 million contract asset in connection with the Collaboration Agreement.

DSM Value Sharing Agreement

The original December 2017 DSM 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 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 refunded and reduces the refund liability by recording additional license and royalty revenue as the Company’s estimate of the refund obligation decreases. The Company recorded $8.8 million of license and royalty revenue in the fourth quarter of 2019 related to a change in the estimated refund liability and recorded the remaining $3.8 million in the three months ended March 31, 2020 related to a change in the Company’s estimate of the refund liability.

In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K), the Company recognized the following revenues for the three and nine months ended September 30, 2020 and 2019:

	Three Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	88	$	—	$	750	$	838	$	—	$	—	$	844	$	844
Sephora	3,501		—		—		3,501		2,625		—		—		2,625
Firmenich	5,099		3,563		—		8,662		4,556		2,305		400		7,261
Givaudan	2,059		—		—		2,059		3,312		—		—		3,312
Subtotal revenue from significant revenue agreements	10,747		3,563		750		15,060		10,493		2,305		9,482		22,280
Revenue from all other customers	16,830		—		2,368		19,198		6,870		—		5,803		12,673
Total revenue from all customers	$	27,577	$	3,563	$	3,118	$	34,258	$	17,363	$	2,305	$	15,285	$	34,953
	Nine Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	193	$	3,750	$	5,019	$	8,962	$	2	$	40,302	$	3,886	$	44,190
Sephora	10,389		—		—		10,389		6,369		—		—		6,369
Firmenich	7,308		5,964		454		13,726		6,439		3,085		1,413		10,937
Givaudan	5,328		—		—		5,328		6,127		—		—		6,127
Subtotal revenue from significant revenue agreements	23,218		9,714		5,473		38,405		18,937		43,387		17,041		79,365
Revenue from all other customers	47,401		—		7,587		54,988		22,430		—		10,226		32,656
Total revenue from all customers	$	70,619	$	9,714	$	13,060	$	93,393	$	41,367	$	43,387	$	27,267	$	112,021

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.

37

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 condensed consolidated balance sheets, net of the allowance for doubtful accounts. Trade receivables are recorded for the sale of goods or the performance of services 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.

Contract Balances

The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers:

(In thousands)	September 30, 2020		December 31, 2019
Accounts receivable, net	$	27,365	$	16,322
Accounts receivable - related party, net	$	419	$	3,868
Contract assets	$	2,082	$	8,485
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Contract liabilities	$	4,430	$	1,353
Contract liabilities, noncurrent(1)	$	111	$	1,449

(1)As of September 30, 2020 and December 31, 2019, contract liabilities, noncurrent is presented in Other noncurrent liabilities in the condensed consolidated balance sheets.

During the three months ended September 30, 2020, the collaboration partner in the Cannabinoid Agreement filed certain litigation claims and, among other things, alleging breach of contract. As a result, the Company concluded that realization and recoverability of an $8.3 million contract asset recorded in connection with the Cannabinoid Agreement was no longer probable. The Company recorded an $8.3 million credit loss reserve against this contract asset during the three months ended September 30, 2020.

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 September 30, 2020.

(In thousands)	As of September 30, 2020
Remaining 2020	$	1,928
2021	5,052
2022	1,630
2023 and thereafter	571
Total from all customers	$	9,181

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, approximately $302.1 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

10. Related Party Transactions

Related Party Debt

See Note 4, "Debt," for details of these related party debt transactions during the nine months ended September 30, 2020:

•Debt equitization – Foris

38

•$5 million unsecured loan - Foris

•2014 Rule 144A Note exchange, extensions and conversion – Total

•LSA Amendment - Foris

Related party debt was as follows:

	September 30, 2020								December 31, 2019
In thousands	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Foris notes	$	55,041	$	—	$	8,426	$	63,467	$	115,351	$	(9,516)	$	—	$	105,835
DSM notes	33,000		(3,007)		—		29,993		33,000		(4,621)		—		28,379
Naxyris note	23,914		(575)		—		23,339		24,437		(822)		—		23,615
Total 2014 Rule 144A convertible note	—		—		—		—		10,178		—		—		10,178
	$	111,955	$	(3,582)	$	8,426	$	116,799	$	182,966	$	(14,959)	$	—	$	168,007

Related Party Equity

See Note 6, "Stockholders' Deficit," for details of these related party equity transactions during the nine months ended September 30, 2020:

•Foris warrant exercises for cash

•Foris warrant exercise, common stock purchase and debt equitization

•January 2020 private placement, in which Foris purchased 5,226,481 shares of common stock

•June 2020 private placement, in which Foris and affiliated entities purchased 30,000 shares of Series E convertible preferred stock, which automatically converted into 9,999,999 shares of common stock in August 2020 after stockholders approved the conversion of the Series E convertible preferred stock and corresponding issuance of underlying common shares

•June 2020 private placement, in which Vivo Capital LLC and affiliated entities purchased 3,689,225 shares of common stock and 8,932.32 shares of Series E convertible preferred stock, which automatically converted into 2,977,442 shares of common stock in August 2020 after stockholders approved the conversion of the Series E convertible preferred stock and corresponding issuance of underlying common shares

Related Party Accounts Receivable, Unbilled Receivables and Accounts Payable

Related party accounts receivable, unbilled receivables and accounts payable were as follows:

(In thousands)	September 30, 2020		December 31, 2019
Accounts receivable - related party	$	419	$	3,868
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Accounts payable	$	5,789	$	13,957

39

11. Stock-based Compensation

The Company’s stock option activity and related information for the nine months ended September 30, 2020 was as follows:

	Quantity of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years	Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Granted	1,258,298	$	3.76
Exercised	(5,227)	$	2.99
Forfeited or expired	(301,787)	$	39.38
Outstanding - September 30, 2020	6,571,703	$	7.69	7.8	$	50
Vested or expected to vest after September 30, 2020	6,024,158	$	7.96	7.8	$	46
Exercisable at September 30, 2020	1,440,934	$	18.26	6.3	$	4

The Company’s restricted stock units (RSUs) activity and related information for the nine months ended September 30, 2020 was as follows:

	Quantity of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Awarded	4,333,999	$	3.74
Released	(1,830,077)	$	4.88
Forfeited	(563,943)	$	4.35
Outstanding - September 30, 2020	7,722,630	$	4.19	1.6
Vested or expected to vest after September 30, 2020	7,060,040	$	4.21	1.6

Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and nine months ended September 30, 2020 and 2019 was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Research and development	$	928	$	663	$	2,774	$	2,002
Sales, general and administrative	2,492		2,571		7,081		8,058
Total stock-based compensation expense	$	3,420	$	3,234	$	9,855	$	10,060

As of September 30, 2020, there was unrecognized compensation expense of $33.6 million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of 2.6 years.

Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan

In February 2020, 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 (Evergreen Shares). This increase is equal to approximately 5.0% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020. These shares in connection with the Purchase Plan represented an automatic annual increase in the number of shares reserved for issuance under the Purchase Plan of 588,713 shares. This increase is equal to approximately 0.5% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020.

40

In May 2020, the Company’s stockholders approved the Company’s 2020 Equity Incentive Plan (the New Plan) to replace the Equity Plan that expired in June 2020. The shares available for grant and issuance under the New Plan represent 9,896,751 shares of common stock previously reserved but unissued under the Equity Plan, including the Evergreen Shares. No additional stock awards will be granted under the Equity Plan, and, (a) shares that are subject to stock options or other awards granted under the Equity Plan that cease to be subject to such stock options or other awards by forfeiture or otherwise, (b) shares issued under the Equity Plan pursuant to the exercise of stock options that are forfeited, (c) shares issued under the Equity Plan that are repurchased by the Company at the original issue price and (d) shares that are subject to stock options or other awards under the Equity Plan that are used to pay the exercise price of an option or withheld to satisfy the tax withholding obligations related to any award will be available for future grant and issuance under the New Plan.

12. Subsequent Events

The Company has evaluated subsequent events through the November 6, 2020 issuance of these condensed consolidated financial statements. No subsequent events have occurred that require disclosure.

41

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis should be read in conjunction with our condensed consolidated financial statements and the related notes that appear elsewhere in this Quarterly Report on Form 10-Q. These discussions contain forward-looking statements reflecting our current expectations that involve risks and uncertainties which are subject to safe harbors under the Securities Act of 1933, as amended (the Securities Act), and the Securities Exchange Act of 1934 (the Exchange Act). These forward-looking statements include, but are not limited to, statements concerning our strategy of achieving a significant reduction in net cash outflows in 2020 and 2021, aspects of our future operations, our future financial position, expectations for our future revenues, margins and projected costs, expectations regarding demand and acceptance for our technologies and products, introductions of new products, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part II, Item 1A, “Risk Factors” in this Quarterly Report on Form 10-Q, in Part I, Item 1A, “Risk Factors” in our Annual Report on Form 10-K for the fiscal year ended December 31, 2019 (the 2019 Form 10-K) and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

Overview

As a leading synthetic biotechnology company, we apply our technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Clean Health & 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 platform, combined with our proprietary fermentation process, replaces existing complex and oftentimes 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 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 ingredients portfolio of products through a sales network provided by our commercial partners that represent leading companies for our target market sectors as well as via direct sales and distributors. We market our wholly owned Consumer brands in brick and mortar retail as well as through various ecommerce platforms. Via our collaboration model, our partners invest in the development of molecules that we bring 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, a precursor of artemisinin, an effective anti-malarial drug. 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. The commercialization of farnesene pushed us to create a more cost-efficient, faster and accurate development process in the lab and to 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.

Several years ago, we made the strategic decision to transition our business model from collaborating and commercializing molecules in lower-margin mature markets to higher-margin specialty ingredients markets. We began the transition by first commercializing and supplying farnesene-derived squalane as a cosmetic ingredient sold to formulators and

42

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, PurecaneTM, which is a superior sweetener and sugar replacement. 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 DSM for use in the Vitamin E field. We also sold our subsidiary Amyris Brasil Ltda. (Amyris Brasil), which operated our purpose-built, large-scale manufacturing facility located in Brotas, Brazil, to DSM in December 2017. The Brotas facility was built to batch manufacture one commodity product at a time (originally for high-volume production of biofuels, a business Amyris had exited), which is an inefficient manufacturing process that is not suited for the high-margin specialty markets in which we operate today. As a result, we are building a new large-scale plant focused solely on specialty ingredients 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 become fully operational by the end of 2021. During construction, we are manufacturing our products at four contract manufacturing sites in Brazil, the U.S. and Spain. Finally, 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; 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 perform research and development activities and Lavvan is responsible for the commercialization of the cannabinoids developed. 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. Additionally, the Cannabinoid Agreement provides for profit share to Amyris on Lavvan's gross profit margin once products are commercialized.

On April 24, 2020, the Food and Drug Administration (FDA) granted us full Over-the-Counter approval for product listing in the U.S. of our alcohol-based hand sanitizer. Sold through our PipetteTM brand, this hand sanitizer addresses critical public and institutional health needs during the current COVID-19 pandemic. We also became authorized to sell this hand sanitizer in Portugal and are currently pursuing additional authorizations in other European markets. The Company’s Reb M sweetener, PurecaneTM, achieved national approvals by the Columbian INVIMA Food Safety, Brazilian ANVISA and Health Canada Authorities on January 29, April 15, and April 17, 2020. Additionally, the product was authorized in Costa Rica on July 20, 2020. Each of these approvals allows for immediate distribution of Amyris’s sweetener product in these markets. On April 28, 2020, Amyris’s Aprinnova joint venture received new chemical approval for its hemisqualane ingredient by China's Ministry of Environment; this approval authorizes importation to supply China's cosmetic manufacturing industry. Finally, on May 5, 2020, our infant nutritional ingredient (known as HMO (2'-FL)), received validation by a medical Panel of Experts as Generally Recognized As Safe (“GRAS”), and we have submitted a petition for FDA GRAS approval of this ingredient.

We have invested over $700 million in infrastructure and technology to create microbes that produce molecules from sugar or other feedstocks at commercial scale. We have focused on accessing Brazilian sugarcane for our large-scale production because of its renewability, low cost and relative price stability. Our time to market for molecules has decreased from seven years to less than a year for our most recent molecules, mainly due to our ability to leverage the technology platform we have built. 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. 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

43

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 products.

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 through 2018 and 2019 we signed a collaboration agreement for four vitamins that we expect will contribute to our collaboration revenue and ultimately product sales. 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 our 2019 Form 10-K for additional information.

All our non-government partnerships include commercial terms for the supply of molecules that 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 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 and $3.8 million was recognized as royalty revenue in 2020. See Note 9, “Revenue Recognition,” and Note 10, "Related Party Transactions" in Part I, Item 1 of this Quarterly Report on Form 10-Q and Part II, Item 8 of our 2019 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 for arrangements with service delivery over time and 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

44

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

For more information about our critical accounting estimates and policies, see Note 1, "Basis of Presentation and Summary of Significant Accounting Policies" in Part I, Item 1 of this Quarterly Report on Form 10-Q and in Part II, Item 8 of our 2019 Form 10-K.

Results of Operations

Revenue

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Revenue
Renewable products	$	27,577	$	17,363	$	70,619	$	41,367
Licenses and royalties	3,563		2,305		9,714		43,387
Grants and collaborations	3,118		15,285		13,060		27,267
Total revenue	$	34,258	$	34,953	$	93,393	$	112,021

Three months ended September 30, 2020

Total revenue decreased by 2% to $34.3 million for the three months ended September 30, 2020 compared to the same period in 2019. The decrease was the result of a $12.2 million decrease in grants and collaborations revenue, mostly offset by a $10.2 million increase in renewable products revenue and a $1.3 million increase in licenses and royalties revenue.

Renewable products revenue increased by 59% to $27.6 million for the three months ended September 30, 2020 compared to the same period in 2019, primarily driven by increased sales in our consumer product lines.

Licenses and royalties revenue increased by 55% to $3.6 million for the three months ended September 30, 2020 compared to the same period in 2019, due to product sales growth from our customer Firmenich.

Grants and collaborations revenue decreased by 80% to $3.1 million for the three months ended September 30, 2020 compared to the same period in 2019, due to no collaboration revenue in 2020 from Lavvan, and a substantial reduction in collaboration revenue in 2020 from Yifan.

Nine months ended September 30, 2020

Total revenue decreased by 17% to $93.4 million for the nine months ended September 30, 2020 compared to the same period in 2019. The decrease was comprised of a $33.7 million decrease in licenses and royalties revenue and a $14.2 million decrease in grants and collaborations revenue, partly offset by a $29.3 million increase in renewable products revenue. The nine months ended September 30, 2020 included one-off Vitamin E revenue of $3.8 million, and the nine months ended September 30, 2019 included one-off Vitamin E revenue of $40.3 million. Excluding Vitamin E, total revenue would have increased by 23% from $71.7 million in 2019 to $88.2 million in 2020.

Renewable products revenue increased by 71% to $70.6 million for the nine months ended September 30, 2020 compared to the same period in 2019, primarily driven by increased sales in our consumer product lines.

Licenses and royalties revenue decreased by 78% to $9.7 million for the nine months ended September 30, 2020 compared to the same period in 2019, primarily due to $40.3 million of royalty revenue in 2019 from DSM related to the assignment of a value sharing agreement.

Grants and collaborations revenue decreased by 52% to $13.1 million for the nine months ended September 30, 2020 compared to the same period in 2019, primarily due to no collaboration revenue in 2020 from Lavvan, and a reduction in grant revenue in 2020 from DARPA.

45

Costs and Operating Expenses

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Cost and operating expenses
Cost of products sold	$	25,822	$	20,654	$	60,710	$	53,482
Research and development	18,197		19,032		52,288		56,093
Sales, general and administrative	38,321		33,341		100,838		92,456
Total cost and operating expenses	$	82,340	$	73,027	$	213,836	$	202,031

Cost of Products Sold

Cost of products sold includes raw materials, labor and overhead, amounts paid to contract manufacturers, inventory write-downs, and costs related to production scale-up. Because of our diverse consumer and business-to-business product mix and the timing and quantities of product sales, our overall cost of products sold can, but sometimes does not change in proportion to or directionally with changes in our renewable product revenues.

Three months ended September 30, 2020

Cost of products sold increased by 25% to $25.8 million for the three months ended September 30, 2020 compared to the same period in 2019, primarily due to a 59% increase in product revenue. The significant improvement in gross profit margin was driven primarily by improved manufacturing efficiencies coupled with higher sales volumes across our consumer product lines. Also contributing to the improvement was a reduction in Reb M sweetener ingredient production costs.

Nine months ended September 30, 2020

Cost of products sold increased by 14% to $60.7 million for the nine months ended September 30, 2020 compared to the same period in 2019, primarily due to a 71% increase in product revenue. The significant improvement in gross profit margin was driven primarily by improved manufacturing efficiencies coupled with higher sales volumes across our consumer product lines and a reduction in Reb M sweetener ingredient production costs.

Research and Development Expenses

Three months ended September 30, 2020

Research and development expenses decreased by 4% to $18.2 million for the three months ended September 30, 2020 compared to the same period in 2019, primarily due to decreases in laboratory equipment and supplies expenses.

Nine months ended September 30, 2020

Research and development expenses decreased by 7% to $52.3 million for the nine months ended September 30, 2020 compared to the same period in 2019, primarily due to decreases in laboratory equipment and supplies expenses.

Sales, General and Administrative Expenses

Three months ended September 30, 2020

Sales, general and administrative expenses increased by 15% to $38.3 million for the three months ended September 30, 2020 compared to the same period in 2019, primarily due to increases in marketing and employee compensation costs related to our consumer product lines and $8.3 million of credit loss reserves recorded against one of our contract assets.

Nine months ended September 30, 2020

Sales, general and administrative expenses increased by 9% to $100.8 million for the nine months ended September 30, 2020 compared to the same period in 2019, primarily due to increases in marketing expense and employee compensation costs related to our consumer product lines and $8.3 million of credit loss reserves recorded against one of our contract assets, partly offset by reduced audit and legal fees.

46

Other Expense, Net

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Other income (expense):
Interest expense	(6,627)		(16,857)		(41,747)		(44,608)
Gain (loss) from change in fair value of derivative instruments	1,999		(398)		(6,498)		(2,437)
Gain (loss) from change in fair value of debt	34,360		(2,055)		2,908		(18,629)
Loss upon extinguishment of debt	(2,606)		(2,721)		(51,954)		(8,596)
Other income (expense), net	(49)		1,076		1,452		920
Total other expense, net	$	27,077	$	(20,955)	$	(95,839)	$	(73,350)

Three months ended September 30, 2020

Total other income, net was $27.1 million for the three months ended September 30, 2020, compared to total other expense, net of $21.0 million for the same period in 2019. The $48.0 million change was primarily due to a $36.4 million change from loss to gain from change in fair value of debt, and a $10.2 million decrease in interest expense. See Note 3, “Fair value Measurements” and Note 4, “Debt” in Part 1, Item 1 of this Form 10-Q for more information on the individual transactions giving rise to these charges in the three months ended September 30, 2020.

Nine months ended September 30, 2020

Total other expense, net was $95.8 million for the nine months ended September 30, 2020, compared to $73.4 million for the same period in 2019. The $22.5 million increase was primarily due to a $43.4 million increase in loss upon extinguishment of debt, partly offset by a $21.5 million change from loss to gain from change in fair value of debt. See Note 3, “Fair value Measurements” and Note 4, “Debt” in Part 1, Item 1 of this Form 10-Q for more information on the individual transactions giving rise to these charges in the nine months ended September 30, 2020.

Provision for Income Taxes

Three and nine months ended September 30, 2020

For the three and nine months ended September 30, 2020, we recorded provisions of $0.1 million and $0.3 million for income taxes related to accrued interest on uncertain tax positions. For the three and nine months ended September 30, 2019, the provision for income taxes was $0.5 million.

Liquidity and Capital Resources

(In thousands)	September 30, 2020		December 31, 2019
Working capital (working capital deficit)	$	27,657	$	(87,526)
Cash and cash equivalents	$	38,280	$	270
Debt and lease obligations	$	195,619	$	289,065
Accumulated deficit	$	(1,977,075)	$	(1,755,653)

	Nine Months Ended September 30,
(In thousands)	2020		2019
Net cash (used in) provided by:
Operating activities	$	(165,813)	$	(113,467)
Investing activities	$	(9,619)	$	(9,013)
Financing activities	$	213,338	$	78,742

Liquidity. 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 filing of this Quarterly Report on Form 10-Q.

47

As of September 30, 2020, we had working capital of $27.7 million (compared to negative working capital of $87.5 million as of December 31, 2019), and an accumulated deficit of $2.0 billion.

As of September 30, 2020, our outstanding debt principal (including related party debt) totaled $175.3 million, of which $36.2 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 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 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. At December 31, 2019, we failed to meet certain covenants under several credit arrangements, including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. Further, at March 31, 2020, we failed to meet certain covenants and provisions under several credit arrangements, including those associated with cross-default provisions. In March 2020 and again in May 2020, most of these lenders provided permanent waivers to us for breaches of all past covenant violations and cross-default payment failures through May 8, 2020 under the respective credit agreements. We cured these defaults with the closing of the $200 million equity offering described below and the repayment of these past due amounts. As of September 30, 2020, we failed to achieve the minimum revenue thresholds under the Foris Convertible Note, Naxyris LSA and Senior Convertible Notes Due 2022, which are described in more detail in Note 4, “Debt”, Part 1, Item 1 of this Form 10-Q, and obtained a waiver from each of these lenders to cure the September 30, 2020 minimum revenue covenant violations. The minimum revenue threshold test is based on 4-quarters trailing revenue and has been significantly impacted by the elimination of a $37.5 million royalty from the measurement period that was recorded in April 2020 related to the DSM Value Sharing Agreement. See Note 9, “Revenue” for more information.

Beginning in May 2020 and continuing through June 2020, we executed a series of financial transactions to minimize cash outflows related to debt service payments and to increase operating cash. On May 1, 2020, we amended the Senior Convertible Notes Due 2022 to eliminate the monthly amortization payments and change the interest payment frequency from monthly to quarterly. On May 7, 2020, we received a $10 million Paycheck Protection Plan loan (PPP Loan). On June 1, 2020, we amended the Foris LSA to eliminate the quarterly principal payments and defer all interest payments until maturity on July 1, 2022, and to provide for the conversion of all outstanding indebtedness under the LSA at a $3.00 per share conversion price, which conversion was approved by our stockholders on August 14, 2020. Further, on June 1, 2020 and June 4, 2020, we entered into securities purchase agreements with investors for the private placement of an aggregate of $200 million of common and preferred stock, resulting in our receiving approximately $190 million of net proceeds. A portion of the proceeds from the offering was used to pay down approximately $37.1 million of debt principal (which included $10 million to repay the PPP Loan) and $6.1 million of accrued interest. Also, on June 2, 2020, Total Raffinage Chimie (Total) converted approximately $9.3 million of debt principal and accrued interest into common stock under the terms of the 2014 Rule 144A Convertible Note, further reducing our outstanding indebtedness. On August 10, 2020, we and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Second Amendment to Promissory Note and Partnership Agreement to reduce the frequency of partnership payments from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022. See Note 4, “Debt.” for more information. As a result of closing the equity offering, making past due payments, converting the $9.1 million 2014 Rule 144A Convertible Note principal into equity, and executing amendments to the Foris LSA, the Senior Convertible Notes Due 2022, and the Ginkgo Note, we cured all payment defaults and other events of default, including cross-defaults under our various debt instruments as of June 30, 2020. Although we have been able to obtain waivers in the past for substantially all our prior defaults to date and were able to cure the existing minimum revenue covenant default, we may not be able to cure or obtain a waiver for any defaults in the future.

Further, our cash and cash equivalents of $38.3 million as of September 30, 2020 will not be sufficient to fund expected future negative cash flows from operations and cash debt service obligations through November 2021. These factors raise substantial doubt about our ability to continue as a going concern within one year after the date these condensed consolidated financial statements are issued. The condensed consolidated 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 eliminate or minimize the anticipated negative cash flows from operations during the 12 months from the date of this filing, and to either raise additional cash proceeds through financings or refinance the debt maturities that will occur in December 2020 and June 2021, all of which are uncertain and outside our control. Further, our operating plan for the remainder of 2020 contemplates (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, (iv) continued cash inflows from collaborations and grants, and (v) the monetization of certain contractual assets. 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 over the next 12 months. This could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and we 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 assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these condensed consolidated financial statements.

48

If we do not achieve our planned operating results, our ability to continue as a going concern would be jeopardized and we may need to take the following actions to support our liquidity needs during the next 12 months:

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

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

•Reduce or delay uncommitted capital expenditures, including expenditures related to the construction and commissioning of the new production facility in Brazil, non-essential facility 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.

We expect to fund operations for the foreseeable future with cash and investments currently on hand and cash inflows from collaborations, grants, product sales, licenses and royalties, and debt and equity financings. All our research and development collaboration milestone payments are subject to risks that we may not meet milestones. Our planned working capital and capital expenditure needs for the next 12 months are dependent on significant inflows of cash from renewable product sales, license and royalties and existing and new collaborations, as well as additional debt financing for the construction of our new specialty ingredients fermentation facility in Brazil.

Cash Flows during the Nine Months Ended September 30, 2020 and 2019

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are costs related to the production and sale of our products and personnel-related expenditures, offset by cash received from renewable product sales, licenses and royalties, and grants and collaborations.

For the nine months ended September 30, 2020, net cash used in operating activities was $165.8 million, consisting primarily of a $217.6 million net loss, partially offset by $97.9 million of non-cash adjustments that were primarily comprised of a $52.0 million loss upon extinguishment of debt, $10.5 million of non-cash interest expense, $9.9 million of stock-based compensation expense, an $8.3 million credit loss, and a $6.5 million loss from change in fair value of derivative instruments. Additionally, there was a $46.1 million net increase in working capital.

For the nine months ended September 30, 2019, net cash used in operating activities was $113.5 million, consisting of a $163.9 million net loss, partially offset by $68.7 million of favorable non-cash adjustments, and a $18.3 million increase in working capital. The non-cash adjustments were primarily comprised of an $18.6 million loss from change in fair value of debt, $10.2 million of amortization of right-of-use assets under operating leases, $10.1 million of stock-based compensation expense, and $9.7 million of debt discount accretion.

Cash Flows from Investing Activities

For the nine months ended September 30, 2020 and September 30, 2019, net cash used in investing activities was $9.6 million, and $9.0 million, respectively, comprised of property, plant and equipment purchases.

Cash Flows from Financing Activities

For the nine months ended September 30, 2020, net cash provided by financing activities was $213.3 million, primarily comprised of $247.4 million of net proceeds from common and preferred stock issuances and $15.3 million of net proceeds from debt issuance, partly offset by $46.8 million of debt principal payments.

49

For the nine months ended September 30, 2019, net cash provided by financing activities was $78.7 million, primarily comprised of $53.6 million of net proceeds from common stock issuances and $89.2 million of net proceeds from debt issuance, partly offset by $63.7 million of debt principal payments.

Off-Balance Sheet Arrangements

At September 30, 2020, we did not have any material off-balance sheet arrangements, as defined in Item 303(a)(4)(ii) of Regulation S-K.

Contractual Obligations

The following is a summary of our contractual obligations as of September 30, 2020:

Payable by year ending December 31, (In thousands)	Total		2020		2021		2022		2023		2024		Thereafter
Principal payments on debt	$	175,296	$	5,133	$	56,174	$	99,235	$	12,793	$	307	$	1,654
Interest payments on debt(1)	32,646		2,734		13,449		16,050		106		91		216
Financing leases	5,654		1,086		4,568		—		—		—		—
Operating leases	20,570		1,960		7,480		7,657		3,322		151		—
Partnership payment obligation	11,578		292		878		10,408		—		—		—
Contract termination fee	3,973		3,973		—		—		—		—		—
Total	$	249,717	$	15,178	$	82,549	$	133,350	$	16,221	$	549	$	1,870

____________________

(1)Fixed and variable interest rates are described in Note 4, "Debt" in Part II, Item 8 of the 2019 Form 10-K. Future interest payments shown above for variable-rate debt instruments are measured on the basis of interest rates for such instruments as of September 30, 2020. The fixed interest rates are more fully described in Note 4, "Debt" in Part II, Item 8 of the 2019 Form 10-K.

50

ITEM 4. CONTROLS AND PROCEDURES

Evaluation of Disclosure Controls and Procedures

We maintain disclosure controls and procedures, as such term is defined under Rule 13a-15(e) promulgated under the Exchange Act. In designing and evaluating the disclosure controls and procedures, management recognizes that any disclosure controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and management necessarily is required to apply its judgment in evaluating the cost-benefit of possible controls and procedures.

Under the supervision and with the participation of management, including our principal executive officer and principal financial officer, we conducted an evaluation of the effectiveness of our disclosure controls and procedures as of the end of the period covered by this report. Based on this evaluation, our principal executive officer and principal financial officer have concluded that our disclosure controls and procedures were not effective at the reasonable assurance level as of September 30, 2020. This conclusion was based on the material weaknesses in our internal control over financial reporting described in Part II, Item 9A, “Controls and Procedures” of our 2019 Form 10-K. The material weaknesses have not been remediated as of September 30, 2020.

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 the Company’s annual or interim consolidated financial statements will not be prevented or detected on a timely basis. If not remediated, the material weaknesses in our internal control over financial reporting described in the 2019 Form 10-K could result in a material misstatement of our annual or interim consolidated financial statements that would not be prevented or detected on a timely basis.

Changes in Internal Control over Financial Reporting

During the fiscal quarter ended September 30, 2020, there were no changes in our internal control over financial reporting that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Inherent Limitations on Effectiveness of Controls

Our management, including our principal executive officer and principal financial officer, does not expect that our disclosure controls and procedures or our internal control over financial reporting will prevent or detect all errors and all fraud. A control system, no matter how well-designed and operated, can provide only reasonable, not absolute, assurance that the control system’s objectives will be met. The design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Further, because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that misstatements due to error or fraud will not occur or that all control issues and instances of fraud, if any, have been detected. The design of any system of controls is based in part on certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Projections of any evaluation of the effectiveness of controls to future periods are subject to risks. Over time, controls may become inadequate because of changes in conditions or deterioration in the degree of compliance with policies or procedures.

51

PART II

ITEM 1. 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, which was denied by the court on October 5, 2020. The Company filed its answer to the securities class action complaint on October 26, 2020. 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 naming 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.

On July 24, 2020, a securities class action complaint was filed against Amyris and the members of our Board in the Court of Chancery of the State of Delaware (Flatischler v. Melo, et. al.). The complaint alleged a breach of fiduciary obligation to disclose material information to stockholders in the proxy statement filed with the Securities and Exchange Commission on July 6, 2020 (Proxy), with respect to the Company’s special stockholders’ meeting held on August 14, 2020 (Special Meeting), at which stockholders were to vote to approve the conversion of all outstanding indebtedness under the Foris Convertible Note and of our Series E Preferred Stock issued in the June 2020 PIPE into shares of common stock, in accordance with Nasdaq Listing Standard Rule 5635(d). See Note 4, “Debt,” “Amendment No. 1 to Foris LSA — Foris, Related Party,” and Note 6, “Stockholders’ Deficit,” “June 2020 PIPE,” and “Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws” in Part I, Item 1 of this Quarterly Report on Form 10-Q for more information. The plaintiffs sought to enjoin the Special Meeting. On August 6, 2020, the plaintiffs withdrew their complaint as moot following the Company’s filing of a supplement to the Proxy on August 5, 2020. The Proxy supplement provided additional information regarding the approval process of the LSA Amendment and the June 2020 PIPE, and the relationships between the Company and its financial advisors to the June 2020 PIPE. The plaintiffs currently seek an amount for their attorney’s fees and certain legal expenses related to filing the complaint, which the parties are negotiating. Three substantially similar complaints were filed: one on July 28, 2020, in the United States District Court of Delaware (Sabatini v. Amyris, Inc.); one on July 31, 2020, in the Northern District of California (Nair v. Amyris); and another on August 4, 2020, in the Southern District of New York (Chamorro v. Amyris). Amyris answered the Chamorro case on October 19, 2020. The Sabatini and Nair cases were voluntarily dismissed by the plaintiffs on October 8, and October 22, 2020, respectively. For this matter, as of September 30, 2020, the Company has accrued a liability for the plaintiffs’ legal fees and expenses, which are not material.

On September 10, 2020, LAVVAN, Inc. (Lavvan) filed a suit against the Company in the United States District Court for the Southern District of New York alleging breach of contract, patent infringement, and trade secret misappropriation in connection with that certain Research, Collaboration and License Agreement between Lavvan and Amyris, dated March 18, 2019, as amended (Cannabinoid Agreement). Amyris filed motions to compel arbitration or to dismiss on October 2, 2020. On October 30, Lavvan filed its opposition to our motions. We believe the suit 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 therefrom.

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.

52

ITEM 1A. RISK FACTORS

In addition to the risk described below, the risks described in Part I, Item 1A, "Risk Factors" in our 2019 Form 10-K could materially and adversely affect our business, financial condition and results of operations, and the trading price of our common stock could decline. These risk factors do not identify all risks that we face; our operations could also be affected by factors that are not presently known to us or that we currently consider to be immaterial to our operations. Due to risks and uncertainties, known and unknown, our past financial results may not be a reliable indicator of future performance, and historical trends should not be used to anticipate results or trends in future periods. The “Risk Factors” section of the 2019 Form 10-K remains current in all material respects.

Our operations and financial results could be adversely impacted by the COVID-19 pandemic, and governmental measures taken in relation thereto, in the United States and the rest of the world.

On May 18, 2020, the health department of Alameda County, California (the County) revised its March 17, 2020 shelter-in-place order covering our corporate headquarters, primary research and development laboratories and employees. The order is in effect indefinitely, and has been amended in its scope on personal and business activities numerous times through October 23, 2020. In order to maintain our facilities, support ongoing critical production campaigns, and provide information to facilitate our employees working from home, we are currently conducting our operations in compliance with local county guidelines. Accordingly, we have instituted policies for those of our employees working on-site such as limiting the number of non-laboratory staff at our facilities, temperature and symptom confirmations, mandatory wearing of masks, and social distancing. As the COVID-19 pandemic continues to evolve, we may experience disruptions that could severely impact our financial condition, financial controls, business operations, research and development processes, manufacturing, commercialization and other activities, including:

•delays or disruptions in our supply chain due to staffing shortages, production slowdowns or stoppages and disruptions in delivery systems;

•delays or disruptions in the manufacture and/or shipment of our products, including facilities we rely upon in Brazil;

•delays or disruptions with respect to our activities in China;

•a decline in demand for our consumer goods products (including our Clean Beauty products) due to any measures put in place in response to the pandemic or any related economic downturn;

•store closings of our retail partners as mandated or recommended by federal, state or city governments;

•interruption of key research and development activities due to restricted or limited operations at our facilities and/or limitations on travel imposed or recommended by federal or state governments, employers and others;

•delays in receiving the supplies and materials needed to conduct our research and development and interruption in global shipping that may affect the transport of materials;

•interruption or delays to our development pipeline; limitations on employee resources that would otherwise be focused on the conduct of our business, including because of sickness of employees or their families or the responsibility of employees to manage family obligations while working from home;

•interruptions or delays in the operations of regulatory authorities, which may impact review or approval timelines;

•delays in necessary interactions with other agencies and contractors due to limitations in employee resources or forced furlough of government employees;

•termination of, or difficulties in procuring or maintaining, arrangements with third parties upon whom we depend such as manufacturers, including contract manufacturing organizations, suppliers and other strategic partners;

•delays in, or limited access to, the capital markets or other sources of funding; and

•disruptions or restrictions on our ability to travel, pursue partnerships and other business transactions.

The COVID-19 pandemic and the resulting mitigation measures may have an adverse impact on global economic conditions which could have an adverse effect on our business and financial condition. In addition, the COVID-19 pandemic has impacted, and may continue to impact, the trading price of shares of our common stock and could further impact our ability to raise additional capital on a timely basis or at all.

The full extent to which the COVID-19 pandemic impacts our business, financial condition, financial controls or results of operations will depend on future developments, which are highly uncertain and cannot be accurately predicted. New information may emerge concerning the severity of the COVID-19 pandemic and the actions to contain the pandemic or treat COVID-19, such as the ultimate geographic spread of the disease, the duration of the pandemic, continued travel restrictions and social distancing, business closures or disruptions as well as the effectiveness of actions taken to contain or treat COVID-19, in the United States and other countries. The COVID-19 pandemic could also result in social, political, economic, and labor instability in the countries in which we, or third parties with whom we engage, operate.

53

To the extent the COVID-19 pandemic adversely affects our business and financial results, it may also have the effect of impacting other risks described in Part I, Item 1A, "Risk Factors" in our 2019 Form 10-K.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

See Note 4, “Debt” and Note 6, “Stockholders’ Deficit,” in Part I, Item 1 of this Quarterly Report on Form 10-Q for information regarding unregistered sales of equity securities during the nine months ended September 30, 2020.

No underwriters or agents were involved in the issuance or sale of such securities, except that each of Jefferies LLC and Cowen and Company, LLC served as joint lead placement agents and Oppenheimer & Co. Inc. served as a co-placement agent with respect to the June 2020 PIPE offering of shares of common stock and Series E Preferred Stock, and we paid an aggregate of $9 million in fees in connection therewith. The securities were issued in private placements pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act, or in private exchanges pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The investors participating in the offerings or exchanges acquired the applicable securities for investment purposes only and without intent to resell, were able to fend for themselves in these transactions, and are accredited investors as defined in Rule 501 of Regulation D promulgated under the Securities Act. These purchasers had adequate access, through their relationships with us, to information about us.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

None.

ITEM 5. OTHER INFORMATION

None.

54

ITEM 6. EXHIBITS

Exhibit No.	Description	Incorporation by Reference
		Form	File No.	Exhibit	Filing Date	Filed Herewith
10.01	Second Amendment to Promissory Note and Partnership Agreement, dated August 10, 2020, between registrant and Ginkgo Bioworks, Inc.					x
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					x
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					x
32.01a	Certification of 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					x
32.02a	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					x
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 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.

55

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this Quarterly Report on Form 10-Q 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 (Principal Executive Officer)
	November 6, 2020
By:	/s/ Han Kieftenbeld
	Han Kieftenbeld
	Chief Financial Officer (Principal Financial Officer)
	November 6, 2020

56

EX-10.01

Exhibit 10.01

SECOND AMENDMENT TO PROMISSORY NOTE AND PARTNERSHIP AGREEMENT

This Second Amendment to Promissory Note and Partnership Agreement (this “SecondAmendment”) is made as of August 10, 2020 by and between Amyris, Inc., a Delaware corporation (the “Company”), and Ginkgo Bioworks, Inc., a Delaware corporation (“Ginkgo”), pursuant to the terms of (i) that certain Promissory Note, dated October 20, 2017 (as amended, the “Note”), issued by the Company to Ginkgo, (ii) that certain Partnership Agreement, dated October 20, 2017 (as amended, the “Partnership Agreement”), by and between the Company and Ginkgo, (iii) that certain Waiver Agreement and Amendment to Promissory Note Issued October 20, 2017, dated September 29, 2019 (the “First Note Amendment”), by and between the Company and Ginkgo, (iv) that certain Waiver Agreement and Amendment, dated March 11, 2020 (the “First Partnership Amendment”), by and between the Company and Ginkgo, and (v) that certain Waiver Agreement, dated May 6, 2020 (the “Waiver”), by and between the Company and Ginkgo. Capitalized terms used but not otherwise defined herein shall have the meanings given to such terms in the Note, the Partnership Agreement or the Waiver, as applicable.

RECITALS

A.    Pursuant to Section 2.1(b) of the Note, the Company is required to make monthly interest payments to Ginkgo beginning on November 30, 2017 and continuing on the last day of each month thereafter, through and including the Maturity Date (each, an “Interest Payment”).

B.    Pursuant to Section 4.3(a) of the Partnership Agreement, the Company is required to pay Ginkgo monthly fees beginning on March 31, 2020 and continuing on the last day of each month thereafter, through and including October 31, 2021 (each, a “Partnership Payment”).

C.    The Company and Ginkgo desire to amend the Note, the Partnership Agreement and the Waiver in order to adjust the payment terms of these agreements effective as of May 31, 2020.

D.     Pursuant to Section 10.7 of the Note, any modification to the Partnership Agreement shall only be effective if made in a writing signed by the Company and Ginkgo.

E.    Pursuant to Section 9.4 of the Partnership Agreement, any modification to the Partnership Agreement shall only be effective if made in a writing signed by the Company and Ginkgo.

AGREEMENT

In consideration of the mutual covenants and agreements set forth herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto, intending to be legally bound, agree as follows:

1.    Note Amendment. Effective May 31, 2020, the following amendments are hereby made to the Note:

a.The definition of “Applicable Rate” in the Note is hereby amended to read as follows:

“Applicable Rate” means (i) from October 20, 2017 to September 30, 2019 (inclusive), a rate equal to the lower of: (a) the Highest Lawful Rate; and (b) ten and one half of one percent (10.5%) per annum; (ii)

from and after October 1, 2019, a rate equal to the lower of: (a) the Highest Lawful Rate; and (b) twelve percent (12%) per annum; and (iii) conditioned upon timely Payment of Interest on September 30, 2020 and December 31, 2020, from and after January 1, 2021, a rate equal to the lower of: (a) the Highest Lawful Rate; and (b) nine percent (9%) per annum.

b.The definition of “Default Rate” in the Note is hereby amended to read as follows:

“Default Rate” (i) from October 20, 2017 to September 30, 2019 (inclusive), a rate equal to the lower of (a) the Highest Lawful Rate; and (b) fifteen and one half of one percent (15.5%) per annum; (ii) from and after October 1, 2019, a rate equal to the lower of: (a) the Highest Lawful Rate; and (b) seventeen percent (17%) per annum; and (iii) conditioned upon timely Payment of Interest on September 30, 2020 and December 31, 2020, from and after January 1, 2021, a rate equal to the lower of: (a) the Highest Lawful Rate; and (b) fourteen percent (14%) per annum.

c.Section 2.1 (b) of the Note is hereby amended to read as follows:

Payment of Interest.

(i)Beginning on November 30, 2017 and continuing on the last day of each month thereafter, through and including February 29, 2019, the Company shall pay monthly payments of interest in the amount of $105,000 (subject to Section 2.1(c), below), or such lower amount as represents payment of interest at a fixed per annum rate equal to the Applicable Rate.

(ii)Between March 31, 2019 and August 10, 2020, the Company shall make one payment of interest in the aggregate amount of $2,756,671 (subject to Section 2.1(c), below).

(iii)On each of September 30, 2020 and December 31, 2020, the Company shall pay interest in the amount of $360,000 (subject to Section 2.1(c), below), or such lower amount as represents payment of interest at a fixed per annum rate equal to the Applicable Rate.

(iv)Beginning on March 31, 2021 and continuing on the last day of each quarter thereafter, through the Maturity Date, the Company shall pay quarterly payments of interest at the Applicable Rate (subject to Section 2.1(c), below).

d.Section 2.1 (c) of the Notes is hereby amended to read as follows:

Default Rate of Interest. Immediately upon the occurrence and during the continuance of an Event of Default, the Company shall pay monthly interest at a fixed per annum rate equal to the Default Rate. Payment or acceptance of the increased interest rate provided in this Section 2.1(c) is not a permitted alternative to timely payment and shall not constitute a waiver of any Event of Default or otherwise prejudice or limit any rights or remedies of the Holder.

2.    Partnership Agreement Amendment. Effective May 31, 2020, the following amendments are hereby made to the Partnership Agreement:

e.Section 4.3, “Partnership Payments,” is hereby amended so that the first paragraph thereof reads as follows:

(a) Regardless of whether the Parties terminate this Agreement pursuant to Section 5.2 (or for any other reason), the Company shall pay directly to Ginkgo an aggregate of $4,188,610 on or before August 10, 2020, for unpaid Partnership Payments, interest, and any fees accrued through that date. The Parties further agree that the Company shall pay directly to Ginkgo an

2

aggregate of $2,120,625 in quarterly Partnership Payments, beginning on September 30, 2020 and continuing on the last day of each quarter thereafter, through and including September 30, 2022 (“Partnership Payment Term”), with Partnership Payments in the amount of $292,500 through and including December 31, 2020, and of $219,375 thereafter during the Partnership Payment Term provided that, if Amyris does not make timely payment of any Partnership Payment due by December 31, 2020, the quarterly Partnership Payments due beginning January 1, 2021 shall be $292,500; and (iii) an aggregate of $9,750,000 on October 19, 2022 (the “End of Term Payment”); provided that, if Amyris does not prepay the entire Balance of the Note, as amended, by April 19, 2022, the End of Term Payment shall be in the amount of $10,350,00.

3.    Waiver Amendment. Effective May 31, 2020, the following amendments are hereby made to the Waiver:

a.Section 3, “May 2020 Payment,” is hereby deleted, and the payments set forth in Section 3 of the Waiver are replaced by the payments set forth in Sections 1 and 2 of this Second Amendment.

4.    Full Force and Effect.Except as expressly modified by this Second Amendment, the terms of the Note (as amended), the Partnership Agreement (as amended), and the Waiver (as amended) shall remain in full force and effect.

5.    Release.In consideration of the agreements contained in this Second Amendment and other good and valuable consideration, the Company unconditionally and irrevocably releases, waives, and forever discharges Ginkgo, together with its respective predecessors, successors, assigns, subsidiaries, affiliates, agents, employees, directors, officers, attorneys, and attorneys’ consultants (collectively, the “Released Parties”), from (x) any and all liabilities, obligations, duties, promises, or indebtedness of any kind (if any) of the Released Parties to the Company or any of its affiliates, which existed, arose, or occurred at any time from the beginning of the world to the date of this Second Amendment; and (y) all claims, offsets, causes of action, suits, or defenses of any kind whatsoever (if any), which the Company or any of its affiliates might otherwise have against the Released Parties, or any of them; in either case of (x) or (y) on account of any condition, act, omission, event, contract, liability, obligation, indebtedness, claim, cause of action, defense, circumstance, or matter of any kind, which existed, arose, or occurred at any time from the beginning of the world to the date of this Second Amendment, whether at law or in equity, whether based upon statute, common law or otherwise, whether matured, contingent or non-contingent, whether direct or indirect, whether known or unknown, whether suspected or unsuspected, which the Company ever had, now has, or may claim to have against, arising out of, based on, asserted in, or in connection with any agreement or event.

6.    Section 1542 Waiver. In consideration of the agreements contained in this Second Amendment and other good and valuable consideration, the Company unconditionally and irrevocably waives any rights it has or may have pursuant to California Civil Code Section 1542, which provides as follows:

A general release does not extend to claims that the creditor or releasing party does not know or suspect to exist in his or her favor at the time of executing the release and that, if known by him or her, would have materially affected his or her settlement with the debtor or released party.

3

7.    Attorneys’ Fees. The Company promises to pay to Ginkgo immediately upon receipt of an invoice any and all reasonable attorneys’ and other professionals’ fees and expenses incurred by Ginkgo in connection with the Note (as amended), the Partnership Agreement (as amended), and Second Amendment, including, without limitation, with respect to the administration, collection, enforcement, amendment or modification of any of them; and with respect to any waiver, consent, release, termination, litigation, administrative proceeding, arbitration, bankruptcy proceeding, or dispute resolution. Any failure by the Company to make timely payment as set forth in this Section 7 shall render all waivers set forth in this Second Amendment null and void.

8.    Acknowledgement. Ginkgo hereby acknowledges and agrees that the defaults described in the First Note Amendment, the First Partnership Amendment and the Waiver have been cured as of this date.

9.    Integration.This Second Amendment, the Note (as amended), the Partnership Agreement (as amended), and the Waiver (as amended) shall constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between the parties hereto with respect to the specific subject matter hereof.

10.    Counterparts.This Second Amendment may be executed 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. This Second Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf) or other electronic format, and delivery of any signature page by any such method will be deemed to have the same effect as if the original signature page had been delivered to the other party.

[Signature pages follow]

4

IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment as of the date first above written.

AMYRIS, INC.

By: /s/ Han Kieftenbeld

Name: Han Kieftenbeld

Title: Chief Financial Officer

[Signature Page - Second Amendment]

IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment as of the date first above written.

GINKGO BIOWORKS, INC.

By: /s/ Jason Kelly

Name: Jason Kelly

Title: CEO

[Signature Page - Second Amendment]

EX-31.01

Exhibit 31.01

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, John G. Melo, certify that:

    1.    I have reviewed this Quarterly Report on Form 10-Q 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.

Date: November 6, 2020	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer

1

EX-31.02

Exhibit 31.02

CERTIFICATION OF CHIEF FINANCIAL OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, Han Kieftenbeld, certify that:

    1.    I have reviewed this Quarterly Report on Form 10-Q 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.

Date: November 6, 2020	/s/ Han Kieftenbeld
	Han Kieftenbeld
	Chief Financial Officer

1

EX-32.01

Exhibit 32.01

Certification of CEO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended September 30, 2020, as filed with the Securities and Exchange Commission on the date hereof, I, John G. Melo, Chief Executive Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended September 30, 2020 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: November 6, 2020	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

1

EX-32.02

Exhibit 32.02

Certification of CFO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended September 30, 2020, as filed with the Securities and Exchange Commission on the date hereof, I, Han Kieftenbeld, Chief Financial Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended September 30, 2020 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: November 6, 2020	/s/ Han Kieftenbeld
	Han Kieftenbeld
	Chief Financial Officer
	(Principal Financial Officer)

1

XML

Cover Page - shares	9 Months Ended
	Sep. 30, 2020	Nov. 04, 2020
Cover [Abstract]
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 Emerging Growth Company	false
Entity Small Business	true
Entity Shell Company	false
Entity Common Stock, Shares Outstanding (in shares)		239,211,413
Document Type	10-Q
Document Period End Date	Sep. 30, 2020
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q3
Amendment Flag	false
Document Quarterly Report	true
Document Transition Report	false
Entity File Number	001-34885
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	55-0856151
Entity Address, Address Line One	5885 Hollis Street
Entity Address, Address Line Two	Suite 100
Entity Address, City or Town	Emeryville
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94608
Title of 12(b) Security	Common Stock, $0.0001 par value per share
Trading Symbol	AMRS
Security Exchange Name	NASDAQ
City Area Code	510
Local Phone Number	450-0761
Entity Interactive Data Current	Yes

XML

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 38,280	$ 270
Restricted cash	329	469
Accounts receivable, net of allowance of $102 and $45, respectively	27,365	16,322
Accounts receivable - related party, net of allowance of $0 and $0, respectively	419	3,868
Contract assets	2,082	8,485
Contract assets - related party	1,203	0
Inventories	37,212	27,770
Deferred cost of products sold - related party	9,454	3,677
Prepaid expenses and other current assets	14,894	12,750
Total current assets	131,238	73,611
Property, plant and equipment, net	29,791	28,930
Contract assets, noncurrent - related party	0	1,203
Deferred cost of products sold, noncurrent - related party	11,858	12,815
Restricted cash, noncurrent	960	960
Recoverable taxes from Brazilian government entities	5,127	7,676
Right-of-use assets under financing leases, net	10,702	12,863
Right-of-use assets under operating leases	10,904	13,203
Other assets	5,359	9,705
Total assets	205,939	160,966
Current liabilities:
Accounts payable	30,357	51,234
Accrued and other current liabilities	28,430	36,655
Financing lease liabilities	3,882	3,465
Operating lease liabilities	5,051	4,625
Contract liabilities	4,430	1,353
Debt, current portion (includes instrument measured at fair value of $25,349 and $24,392, respectively)	31,431	45,313
Due to related parties, current	0	18,492
Total current liabilities	103,581	161,137
Long-term debt, net of current portion (includes instrument measured at fair value of $0 and $26,232, respectively)	26,176	48,452
Related party debt, net of current portion (includes instrument measured at fair value of $58,466 and $0, respectively)	116,799	149,515
Financing lease liabilities, net of current portion	1,171	4,166
Operating lease liabilities, net of current portion	11,109	15,037
Derivative liabilities	3,834	9,803
Other noncurrent liabilities	21,996	23,024
Total liabilities	284,666	411,134
Commitments and contingencies
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of September 30, 2020 and December 31, 2019; 8,280 shares issued and outstanding as of September 30, 2020 and December 31, 2019	0	0
Common stock - $0.0001 par value, 350,000,000 and 250,000,000 shares authorized as of September 30, 2020 and December 31, 2019, respectively; 239,185,985 and 117,742,677 shares issued and outstanding as of September 30, 2020 and December 31, 2019, respectively	24	12
Additional paid-in capital	1,938,411	1,543,668
Accumulated other comprehensive loss	(49,505)	(43,804)
Accumulated deficit	(1,977,075)	(1,755,653)
Total Amyris, Inc. stockholders’ deficit	(88,145)	(255,777)
Noncontrolling interest	4,418	609
Total stockholders' deficit	(83,727)	(255,168)
Total liabilities, mezzanine equity and stockholders' deficit	205,939	160,966
Contingently redeemable common stock
Current liabilities:
Contingently redeemable common stock	$ 5,000	$ 5,000

XML

Condensed Consolidated Balance Sheets (Parentheticals) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Statement of Financial Position [Abstract]
Accounts receivable, allowance	$ 102	$ 45
Accounts receivable, allowance, related parties	0	0
Fair value of debt	25,349	24,392
Fair value of long-term debt	0	26,232
Related party debt, net, fair value	$ 58,466	$ 0
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized (in shares)	5,000,000	5,000,000
Preferred stock, shares issued (in shares)	8,280
Preferred stock, shares outstanding (in shares)	8,280
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (in shares)	350,000,000	250,000,000
Common stock, shares issued (in shares)	239,185,985	117,742,677
Common stock, shares outstanding (in shares)	239,185,985	117,742,677

XML

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Revenues [Abstract]
Revenue	$ 34,258	$ 34,953	$ 93,393	$ 112,021
Cost and operating expenses:
Cost of products sold	25,822	20,654	60,710	53,482
Research and development	18,197	19,032	52,288	56,093
Sales, general and administrative	38,321	33,341	100,838	92,456
Total cost and operating expenses	82,340	73,027	213,836	202,031
Loss from operations	(48,082)	(38,074)	(120,443)	(90,010)
Other income (expense):
Interest expense	(6,627)	(16,857)	(41,747)	(44,608)
Gain (loss) from change in fair value of derivative instruments	1,999	(398)	(6,498)	(2,437)
Gain (loss) from change in fair value of debt	34,360	(2,055)	2,908	(18,629)
Loss upon extinguishment of debt	(2,606)	(2,721)	(51,954)	(8,596)
Other income (expense), net	(49)	1,076	1,452	920
Total other expense, net	27,077	(20,955)	(95,839)	(73,350)
Loss before income taxes and loss from investment in affiliate	(21,005)	(59,029)	(216,282)	(163,360)
Provision for income taxes	(83)	(533)	(273)	(533)
Loss from investment in affiliate	(366)	0	(1,058)	0
Net loss	(21,454)	(59,562)	(217,613)	(163,893)
Less: income attributable to noncontrolling interest in Aprinnova	(1,702)	0	(3,809)	0
Net loss	(23,156)	(59,562)	(221,422)	(163,893)
Less: deemed dividend to preferred stockholder on issuance and modification of common stock warrants	0	0	0	(34,964)
Less: deemed dividend to preferred stockholders upon conversion of Series E preferred stock	(67,151)	0	(67,151)	0
Add: losses allocated to participating securities	6,832	1,655	15,369	6,233
Net loss attributable to Amyris, Inc. common stockholders, basic	$ (83,475)	$ (57,907)	$ (273,204)	$ (192,624)
Earnings Per Share, Basic [Abstract]
Loss per share attributable to common stockholders, basic (in dollars per share)	$ (0.37)	$ (0.56)	$ (1.44)	$ (2.11)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic (in shares)	227,267,553	103,449,612	189,192,973	91,344,150
Earnings Per Share, Diluted [Abstract]
Loss per share attributable to common stockholders, diluted (in dollars per share)	$ (0.41)	$ (0.56)	$ (1.46)	$ (2.11)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted (in shares)	242,732,234	103,449,612	191,506,499	91,344,150
Product
Revenues [Abstract]
Revenue	$ 27,577	$ 17,363	$ 70,619	$ 41,367
Licenses and Royalties
Revenues [Abstract]
Revenue	3,563	2,305	9,714	43,387
Grants and Collaborations
Revenues [Abstract]
Revenue	$ 3,118	$ 15,285	$ 13,060	$ 27,267

XML

Condensed Consolidated Statements of Operations (Parentheticals) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Revenues, related party	$ 838	$ 844	$ 8,962	$ 44,190
ASU 2017-11			us-gaap:ProductMember
Product
Revenues, related party	88	0	$ 193	2
Licenses and Royalties
Revenues, related party	0	0	3,750	40,302
Grants and Collaborations
Revenues, related party	$ 750	$ 844	$ 5,019	$ 3,886

XML

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Comprehensive loss:
Net loss	$ (21,454)	$ (59,562)	$ (217,613)	$ (163,893)
Foreign currency translation adjustment	(797)	(1,066)	(5,701)	(1,202)
Total comprehensive loss	(22,251)	(60,628)	(223,314)	(165,095)
Less: income attributable to noncontrolling interest in Aprinnova	(1,702)	0	(3,809)	0
Comprehensive loss attributable to Amyris, Inc.	$ (23,953)	$ (60,628)	$ (227,123)	$ (165,095)

XML

Consolidated Statements of Stockholders' Deficit and Mezzanine Equity - USD ($) $ in Thousands	Total	Preferred Stock	Common Stock	Additional Paid-in Capital	Additional Paid-in Capital Cumulative Effect, Period of Adoption, Adjustment	Accumulated Other Comprehensive Loss	Accumulated Deficit	Accumulated Deficit Cumulative Effect, Period of Adoption, Adjustment	Noncontrolling Interest	Total Stockholders' Deficit	Total Stockholders' Deficit Cumulative Effect, Period of Adoption, Adjustment	Mezzanine Equity - Common Stock
Balance (in shares) at Dec. 31, 2018		14,656	76,564,829
Balance at Dec. 31, 2018		$ 0	$ 8	$ 1,346,996	$ 32,512	$ (43,343)	$ (1,521,417)	$ 8,531	$ 937	$ (216,819)	$ 41,043	$ 5,000
Issuance of common stock upon exercise of warrants (in shares)			450,568
Issuance of common stock upon exercise of warrants				1						1
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock (in shares)			191,672
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				(9)						(9)
Issuance of common stock upon exercise of stock options (in shares)			3,612
Issuance of common stock upon exercise of stock options				13						13
Fair value of bifurcated embedded conversion feature in connection with debt modification				398						398
Stock-based compensation				3,452						3,452
Foreign currency translation adjustment						964				964
Net loss							(66,243)			(66,243)
Balance (in shares) at Mar. 31, 2019		14,656	77,210,681
Balance at Mar. 31, 2019		$ 0	$ 8	1,383,363		(42,379)	(1,579,129)		937	(237,200)		5,000
Balance (in shares) at Dec. 31, 2018		14,656	76,564,829
Balance at Dec. 31, 2018		$ 0	$ 8	1,346,996	$ 32,512	(43,343)	(1,521,417)	$ 8,531	937	(216,819)	$ 41,043	5,000
Net loss	$ (163,893)
Net loss	(163,893)
Balance (in shares) at Sep. 30, 2019		14,656	103,400,207
Balance at Sep. 30, 2019		$ 0	$ 10	1,507,298		(44,545)	(1,676,779)		937	(213,079)		5,000
Balance (in shares) at Mar. 31, 2019		14,656	77,210,681
Balance at Mar. 31, 2019		$ 0	$ 8	1,383,363		(42,379)	(1,579,129)		937	(237,200)		5,000
Issuance of common stock in private placement (in shares)			3,610,944
Issuance of common stock in private placement			$ 1	14,221						14,222
Issuance of common stock in private placement - related party (in shares)			10,478,338
Issuance of common stock in private placement - related party				39,499						39,499
Issuance of common stock upon exercise of warrants (in shares)			2,064,606
Issuance of common stock upon exercise of warrants				0						0
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock (in shares)			589,241
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				(347)						(347)
Issuance of common stock upon ESPP purchase (in shares)			131,460
Issuance of common stock upon ESPP purchase				464						464
Issuance of common stock upon conversion of debt (in shares)			7,101,468
Issuance of common stock upon conversion of debt			$ 1	34,650						34,651
Issuance of warrants in connection with debt accounted for at fair value				4,428						4,428
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock				34,964						34,964
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock				(34,964)						(34,964)
Stock-based compensation				3,375						3,375
Other				(238)						(238)
Foreign currency translation adjustment						(1,100)				(1,100)
Net loss							(38,088)			(38,088)
Balance (in shares) at Jun. 30, 2019		14,656	101,186,738
Balance at Jun. 30, 2019		$ 0	$ 10	1,479,415		(43,479)	(1,617,217)		937	(180,334)		5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest (in shares)			1,767,632
Issuance of common stock and warrants upon conversion of debt principal and accrued interest				7,829						7,829
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock (in shares)			445,837
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				(271)						(271)
Issuance of warrants in connection with related party debt issuance				13,279						13,279
Issuance of warrants in connection with related party debt modification				2,882						2,882
Issuance of warrants in connection with debt accounted for at fair value				930						930
Stock-based compensation				3,234						3,234
Foreign currency translation adjustment						(1,066)				(1,066)
Net loss	(59,562)						(59,562)			(59,562)
Net loss	$ (59,562)
Balance (in shares) at Sep. 30, 2019		14,656	103,400,207
Balance at Sep. 30, 2019		$ 0	$ 10	1,507,298		(44,545)	(1,676,779)		937	(213,079)		5,000
Balance (in shares) at Dec. 31, 2019	117,742,677	8,280	117,742,677
Balance at Dec. 31, 2019	$ (255,168)	$ 0	$ 12	1,543,668		(43,804)	(1,755,653)		609	(255,168)		5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest (in shares)			6,337,594
Issuance of common stock and warrants upon conversion of debt principal and accrued interest			$ 1	21,259						21,260
Issuance of common stock in private placement (in shares)			3,484,321
Issuance of common stock in private placement				10,000						10,000
Issuance of common stock in private placement - related party (in shares)			10,505,652
Issuance of common stock in private placement - related party			$ 1	27,188						27,189
Issuance of common stock upon exercise of warrants (in shares)			1,160,929
Issuance of common stock upon exercise of warrants				3,332						3,332
Issuance of common stock upon exercise of warrants - related party (in shares)			24,165,166
Issuance of common stock upon exercise of warrants - related party			$ 2	68,763						68,765
Exercise of common stock rights warrant - related party				15,000						15,000
Issuance of common stock right warrant - related party				8,904						8,904
Modification of previously issued common stock warrants				1,286						1,286
Derecognition of liability warrants to equity				5,200						5,200
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock (in shares)			495,581
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				(8)						(8)
Stock-based compensation				3,504						3,504
Foreign currency translation adjustment						(2,549)				(2,549)
Net loss							(87,844)			(87,844)
Balance (in shares) at Mar. 31, 2020		8,280	163,891,920
Balance at Mar. 31, 2020		$ 0	$ 16	1,708,096		(46,353)	(1,843,497)		609	(181,129)		5,000
Balance (in shares) at Dec. 31, 2019	117,742,677	8,280	117,742,677
Balance at Dec. 31, 2019	$ (255,168)	$ 0	$ 12	1,543,668		(43,804)	(1,755,653)		609	(255,168)		5,000
Issuance of common stock upon exercise of warrants (in shares)	30,694,457
Issuance of common stock upon exercise of stock options (in shares)	5,227
Net loss	$ (221,422)
Net loss	(217,613)
Balance (in shares) at Sep. 30, 2020		8,280	239,185,985
Balance at Sep. 30, 2020	$ (83,727)	$ 0	$ 24	1,938,411		(49,505)	(1,977,075)		4,418	(83,727)		5,000
Balance (in shares) at Mar. 31, 2020		8,280	163,891,920
Balance at Mar. 31, 2020		$ 0	$ 16	1,708,096		(46,353)	(1,843,497)		609	(181,129)		5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest (in shares)		30,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest				30,000						30,000
Issuance of common stock upon exercise of warrants (in shares)			132,746
Issuance of common stock upon exercise of warrants				0						0
Derecognition of liability warrants to equity				6,550						6,550
Fair value of modification to previously issued common stock warrants				1,067						1,067
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock (in shares)			720,100
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				(98)						(98)
Issuance of common stock upon exercise of stock options (in shares)			5,227
Issuance of common stock upon exercise of stock options				16						16
Issuance of common stock upon ESPP purchase (in shares)			144,523
Issuance of common stock upon ESPP purchase				421						421
Issuance of preferred and common stock in private placement, net of issuance costs (in shares)	72,156		32,614,573
Issuance of preferred and common stock in private placement, net of issuance costs			$ 3	160,014						160,017
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)			5,226,481
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party			$ 1	(1)						0
Fair value of pre-delivery shares released to holder in connection with debt amendment				10,478						10,478
Return of pre-delivery shares previously issued in connection with debt agreement (in shares)			(1,363,636)
Return of pre-delivery shares previously issued in connection with debt agreement										0
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity (in shares)			3,246,489
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity				15,778						15,778
Stock-based compensation				2,931						2,931
Foreign currency translation adjustment						(2,355)				(2,355)
Net loss							(110,422)		2,107	(108,315)
Balance (in shares) at Jun. 30, 2020		110,436	204,618,423
Balance at Jun. 30, 2020		$ 0	$ 20	1,935,252		(48,708)	(1,953,919)		2,716	(64,639)		5,000
Issuance of common stock upon exercise of warrants (in shares)
Issuance of common stock upon exercise of warrants				20						20
Derecognition of liability warrants to equity				(67,151)						(67,151)
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock (in shares)			515,478
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				(295)						(295)
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)		(102,156)	34,052,084
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party			$ 4	(4)						0
Fair value of pre-delivery shares released to holder in connection with debt amendment				67,151						67,151
Stock-based compensation				3,438						3,438
Foreign currency translation adjustment						(797)				(797)
Net loss	$ (23,156)						(23,156)		1,702	(21,454)
Net loss	(21,454)
Balance (in shares) at Sep. 30, 2020		8,280	239,185,985
Balance at Sep. 30, 2020	$ (83,727)	$ 0	$ 24	$ 1,938,411		$ (49,505)	$ (1,977,075)		$ 4,418	$ (83,727)		$ 5,000

XML

Consolidated Statements of Stockholders' Deficit and Mezzanine Equity (Parenthetical)	12 Months Ended
	Dec. 31, 2018
Statement of Stockholders' Equity [Abstract]
Accounting standards update [extensible list]	us-gaap:AccountingStandardsUpdate201711Member

XML

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Operating activities
Net loss	$ (217,613)	$ (163,893)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss upon extinguishment of debt	51,954	8,596
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	10,478	0
Stock-based compensation	9,873	10,061
Contract asset credit loss reserve	8,342	0
Depreciation and amortization	6,740	2,691
Loss from change in fair value of derivative instruments	6,498	2,437
Accretion of debt discount	3,119	9,701
Amortization of right-of-use assets under operating leases	2,103	10,237
Non-cash interest expense in connection with modification of warrants	1,066	0
Loss in equity-method investee	1,058	0
Non-cash interest expense added to debt principal	100	0
Impairment of property, plant and equipment	13	1,263
Loss (gain) on disposal of property, plant and equipment	42	122
Expense for warrants issued for debt covenant waivers	0	5,358
Gain on foreign currency exchange rates	(583)	(361)
(Gain) loss from change in fair value of debt	(2,908)	18,629
Changes in assets and liabilities:
Accounts receivable	(7,736)	(3,482)
Contract assets	(1,939)	(2,567)
Accounts receivable, unbilled - related party	0	8,021
Inventories	(10,561)	(6,609)
Deferred cost of products sold - related party	(4,820)	(13,545)
Prepaid expenses and other assets	696	(4,445)
Accounts payable	(20,201)	(2,050)
Accrued and other liabilities	(1,259)	22,310
Lease liabilities	(3,352)	(12,453)
Contract liabilities	3,077	(3,488)
Net cash used in operating activities	(165,813)	(113,467)
Investing activities
Purchases of property, plant and equipment	(9,619)	(9,013)
Net cash used in investing activities	(9,619)	(9,013)
Financing activities
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs	170,037	14,221
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs - related party	45,000	39,500
Proceeds from issuance of debt, net of issuance costs	15,279	89,217
Proceeds from exercise of common stock rights warrant - related party	15,000	0
Proceeds from exercises of warrants - related party	13,998	0
Proceeds from exercises of warrants	3,332	1
Proceeds from issuance of common stock upon ESPP purchase	421	464
Proceeds from exercises of common stock options	16	13
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(401)	(627)
Principal payments on financing leases	(2,578)	(372)
Principal payments on debt	(46,766)	(63,675)
Net cash provided by financing activities	213,338	78,742
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(36)	(248)
Net increase (decrease) in cash, cash equivalents and restricted cash	37,870	(43,986)
Cash, cash equivalents and restricted cash at beginning of period	1,699	47,054
Cash, cash equivalents and restricted cash at end of the period	39,569	3,068
Cash and cash equivalents	38,280	1,632
Restricted cash, current	329	476
Restricted cash, noncurrent	960	960
Total cash, cash equivalents and restricted cash	39,569	3,068
Supplemental disclosures of cash flow information:
Cash paid for interest	13,858	10,390
Supplemental disclosures of non-cash investing and financing activities:
Accrued interest added to debt principal	2,056	986
Unpaid property, plant and equipment balances in accounts payable and accrued liabilities at end of period	2,100	134
Acquisition of right-of-use assets under operating leases	0	2,361
Cumulative effect of change in accounting principle	0	41,043
Derecognition of derivative liabilities to equity upon extinguishment of debt	6,461	0
Derecognition of derivative liabilities upon authorization of shares	6,550	0
Derecognition of derivative liabilities upon exercise of warrants	5,200	0
Exercise of common stock warrants in exchange for debt principal and accrued interest reduction	69,918	0
Fair value of embedded features in connection with private placement	2,962	0
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances	188	8,965
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances - related party	747	16,155
Fair value of warrants recorded as debt discount in connection with debt modification	0	398
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	27,650	42,479
Lease liabilities recorded upon adoption of ASC 842	0	33,552
Right-of-use assets under operating leases recorded upon adoption of ASC 842	$ 0	$ 29,713

XML

Basis of Presentation and Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Presentation and Summary of Significant Accounting Policies

Basis of Presentation and Summary of Significant Accounting Policies

Amyris, Inc. (Amyris or the Company) is a leading synthetic biotechnology company in Clean Health and Beauty markets through its consumer brands, and is a supplier of sustainable and natural ingredients. Amyris applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Clean Health & Beauty, and Flavor & Fragrance markets. The Company's technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume ingredients. This platform, combined with our proprietary fermentation process, replaces existing complex and oftentimes expensive manufacturing processes, resulting in our successful development and production of many distinct molecules at commercial volumes.

The accompanying unaudited condensed consolidated financial statements of Amyris, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2019 (the 2019 Form 10-K), from which the condensed consolidated balance sheet as of December 31, 2019 is derived. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the accompanying interim condensed consolidated financial statements do not include all the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Raizen Joint Venture Agreement

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into a joint venture agreement for 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 for 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. Due to the COVID-19 pandemic, the parties have agreed to extend the previous July 2020 deadline to conduct the relevant analysis of the sweetener production data in order to determine potential next steps for the joint venture. In addition, notwithstanding the satisfaction of 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. The Company will conclude its evaluation of the accounting treatment for its future interest in the joint venture under ASC 810, Consolidations and ASC 323, Equity Method and Joint Ventures when the economic participation structure and related corporate governance is finalized and the formation of the joint venture is consummated.

Potential Impact of COVID-19 on the Company's Business

With the global spread of the COVID-19 pandemic beginning in the first quarter of 2020 and anticipated continuation throughout 2020, and the resulting shelter-in-place orders covering the Company’s corporate headquarters, primary research and development laboratories, and employees, the Company has implemented policies and procedures to conduct its operations in compliance with local county guidelines. The extent to which the COVID-19 pandemic impacts the Company’s business, financial condition or results of operations will depend on future developments, which are highly uncertain and cannot be accurately predicted. New information may emerge concerning the severity of the COVID-19 pandemic and the actions to contain the pandemic or treat COVID-19, such as the ultimate geographic spread of the disease, the duration of the pandemic, continued travel restrictions, social distancing, business closures or disruptions, and the effectiveness of actions taken to contain or treat COVID-19 in the United States and in other countries. As the COVID-19 pandemic continues to evolve, to the extent it adversely affects our business and financial results, it may also impact other risks to which the Company is subject as set forth in the “Risk Factors” section (Part I, Item 1A) of the 2019 Form 10-K.

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 over the course of at least the next 12 months following the issuance of these condensed consolidated financial statements. As of September 30, 2020, the Company had working capital of $27.7 million (compared to negative working capital of $87.5 million as of December 31, 2019), and an accumulated deficit of $2.0 billion.

As of September 30, 2020, the Company's outstanding debt principal (including related party debt) totaled $175.3 million, of which $36.2 million is classified as current. 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, including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. Further, at March 31, 2020, the Company failed to meet certain covenants and provisions under several credit arrangements, including those associated with cross-default provisions. In March 2020 and again in May 2020, most of these lenders provided waivers to the Company for breaches of all past covenant violations and cross-default payment failures, under the respective credit agreements through the earlier of the closing of a significant equity offering or May 31, 2020. The Company cured these defaults with the closing of the $200 million equity offering described below and the repayment of these past due amounts. As of September 30, 2020, the Company failed to achieve the minimum revenue thresholds under the Foris LSA, Naxyris LSA and Senior Convertible Notes Due 2022, which are described in more detail in Note 4, “Debt”, and obtained a waiver from each of these lenders to cure the September 30, 2020 minimum revenue covenant violations. The minimum revenue threshold test is based on 4-quarters trailing revenue and has been significantly impacted by the elimination of a $37.5 million royalty from the measurement period that was recorded in April 2020 related to the DSM Value Sharing Agreement. See Note 9, “Revenue” for more information.

Beginning in May 2020 and continuing through June 2020, the Company executed a series of financial transactions to minimize cash outflows related to debt service payments and to increase operating cash. On May 1, 2020, the Company amended the Senior Convertible Notes Due 2022 to eliminate the monthly amortization payments and change the interest payment frequency from monthly to quarterly. On May 7, 2020, the Company received a $10 million Paycheck Protection Plan loan (PPP Loan). On June 1, 2020, the Company amended the Foris LSA to eliminate the quarterly principal payments and defer all interest payments until maturity on July 1, 2022, and to provide for the conversion of all outstanding indebtedness under the LSA at a $3.00 per share conversion price, which conversion was approved by the Company’s stockholders on August 14, 2020. Further, on June 1, 2020 and June 4, 2020, the Company entered into securities purchase agreements with investors for the private placement of an aggregate of $200 million of common and preferred stock, resulting in the Company receiving approximately $190 million of net proceeds. A portion of the proceeds from the offering was used to pay down approximately $37.1 million of debt principal (which included $10 million to repay the PPP Loan) and $6.1 million of accrued interest. Also, on June 2, 2020, Total Raffinage Chimie (Total) converted approximately $9.3 million of debt principal and accrued interest into common stock under the terms of the 2014 Rule 144A Convertible Note, further reducing the Company’s outstanding indebtedness. On August 10, 2020, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Second Amendment to Promissory Note and Partnership Agreement to reduce the frequency of partnership payments from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022. See Note 4, “Debt.” for more information. As a result of closing the equity offering, making past due payments, converting the $9.1 million 2014 Rule 144A Convertible Note principal into equity, and executing amendments to the Foris LSA, the Senior Convertible Notes Due 2022, and the Ginkgo Note, the Company cured all payment defaults and other events of default, including cross-defaults under the Company’s various debt instruments as of June 30, 2020. Although the Company has been able to obtain waivers in the past for substantially all its prior defaults to date and was able to cure the existing minimum revenue covenant default, it may not be able to cure or obtain a waiver for any defaults in the future.

Further, the Company's cash and cash equivalents of $38.3 million as of September 30, 2020 will not be sufficient to fund expected cash flows requirements from operations and cash debt service obligations through November 2021. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date these condensed consolidated financial statements are issued. The condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to eliminate or minimize the anticipated negative cash flows from operations during the 12 months from the date of this filing and to either raise additional cash proceeds through financings or refinance the debt maturities occurring in December 2020 and June 2021, all of which are uncertain and outside the control of the Company. Further, the Company's operating plan for the remainder of 2020 contemplates (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, (iv) continued cash inflows from collaborations and grants, and (v) the monetization of certain contractual assets. If the Company is unable to complete these actions, it may be unable to meet its operating cash flow needs and its obligations under its existing debt facilities over the next 12 months. 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 condensed consolidated financial statements.

Significant Accounting Policies

Note 1, "Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the 2019 Form 10-K includes a discussion of the significant accounting policies and estimates used in the preparation of the Company’s consolidated financial statements. There have been no material changes to the Company's significant accounting policies and estimates during the nine months ended September 30, 2020.

Accounting Standards or Updates Recently Adopted

In the nine months ended September 30, 2020, the Company adopted these accounting standards or updates:

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. ASU 2018-13 became effective in the first quarter of fiscal 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements.

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. ASU 2018-18 became effective in the first quarter of fiscal year 2020 retrospectively. The adoption of this standard did not have any impact on the Company’s condensed consolidated financial statements.

Accounting Standards or Updates Not Yet Adopted

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 is effective for the Company in the first quarter of 2023. The Company is currently evaluating the impact this standard will have on its condensed consolidated financial statements.

Accounting for Income Taxes In December 2019, the FASB issued ASU 2019-12, “Simplifying the Accounting for Income Taxes” (“ASU 2019-12”). The amendments in ASU 2019-12 simplify the accounting for income taxes by removing certain exceptions to the general principles in ASC Topic 740, Income Taxes. The amendments also improve consistent application of and simplify U.S. GAAP for other areas of ASC Topic 740 by clarifying and amending existing guidance. ASU 2019-12 will be effective for the Company commencing in the first quarter of fiscal year 2021. The transition requirements are dependent upon each amendment within this update and will be applied either prospectively or retrospectively. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Convertible Debt, and Derivatives and Hedging On August 5, 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, to improve financial reporting associated with accounting for convertible instruments and contracts in an entity’s own equity. ASU 2020-06 is effective for the

Company in the first quarter of 2022. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

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 condensed consolidated 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 condensed consolidated financial statements.

XML

Balance Sheet Details

9 Months Ended

Sep. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Balance Sheet Details

Balance Sheet Details

Allowance for Doubtful Accounts

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Period
Nine months ended September 30, 2020	$	45	$	57	$	—	$	102
Year ended December 31, 2019	$	642	$	110	$	(707)	$	45

Inventories

(In thousands)	September 30, 2020		December 31, 2019
Raw materials	$	7,136	$	3,255
Work-in-process	12,083		7,204
Finished goods	17,993		17,311
Inventories	$	37,212	$	27,770

Deferred cost of products sold - related party

(In thousands)	September 30, 2020		December 31, 2019
Deferred cost of products sold - related party	$	9,454	$	3,677
Deferred cost of products sold, noncurrent - related party	11,858		12,815
Total	$	21,312	$	16,492

In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for sweetener production through December 2022. See Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K for information regarding the November 2018 Supply Agreement Amendment. As part of the amendment, the Company made a series of manufacturing capacity fee payments from November 2018 to March 31, 2020. Of these payments $17.4 million was recorded as deferred cost of products sold. In June 2020, the Company paid an additional $6.9 million manufacturing capacity fee, which represents the final payment under the amendment. The capitalized 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 produced and sold over the five-year term of the supply agreement. Each quarter, the Company evaluates its estimated future production volumes through the end of the agreement and adjusts the unit cost to be expensed over the remaining estimated production volume. During the three and nine months ended September 30, 2020, the Company expensed $0.7 million and $2.0 million, respectively, of the deferred cost of products sold asset to cost of products sold. Inception-to-date amortization through September 30, 2020 totaled $3.0 million.

Prepaid expenses and other current assets

(In thousands)	September 30, 2020		December 31, 2019
Prepayments, advances and deposits	$	6,117	$	4,726
Non-inventory production supplies	3,746		5,376
Recoverable taxes from Brazilian government entities	1,978		—
Other	3,053		2,648
Total prepaid expenses and other current assets	$	14,894	$	12,750

Property, Plant and Equipment, Net

(In thousands)	September 30, 2020		December 31, 2019
Machinery and equipment	$	48,893	$	48,041
Leasehold improvements	43,198		41,478
Computers and software	10,589		9,822
Furniture and office equipment, vehicles and land	3,485		3,510
Construction in progress	7,369		9,752
	113,534		112,603
Less: accumulated depreciation and amortization	(83,743)		(83,673)
Property, plant and equipment, net	$	29,791	$	28,930

During the three and nine months ended September 30, 2020 and 2019, depreciation and amortization expense was as follows:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Depreciation and amortization expense	$	1,905	$	969	$	5,300	$	2,691

Leases

Operating Leases

The Company has operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 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 ROU assets under operating leases on the Company's condensed consolidated balance sheets 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 "Lease liabilities" and "Lease liabilities, net of current portion" on the Company's condensed consolidated balance sheets. Operating lease right-of-use assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. The Company had $10.9 million and $13.2 million of right-of-use assets as of September 30, 2020 and December 31, 2019, respectively. Operating lease liabilities were $16.2 million and $19.7 million as of September 30, 2020 and December 31, 2019, respectively. During the three and nine months ended September 30, 2020 and 2019, respectively, the Company recorded $1.5 million, $4.6 million, $5.9 million and $14.1 million of operating lease amortization that was charged to expense, of which $0, $0, $0.9 million and $5.2 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:

	Nine Months Ended September 30,
	2020	2019
Cash paid for operating lease liabilities, in thousands	$5,759	$15,908
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$—	$32,074
Weighted-average remaining lease term	2.7	2.6
Weighted-average discount rate	18.0%	17.5%

(1) 2019 amount includes $29.7 million for operating leases existing on January 1, 2019 and $2.4 million for operating leases that commenced during the nine months ended September 30, 2019.

Financing Leases

The Company has 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 condensed 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. Accumulated amortization of assets under financing leases totaled $3.9 million and $1.7 million as of September 30, 2020 and December 31, 2019, respectively.

Maturities of Financing and Operating Leases

Maturities of lease liabilities as of September 30, 2020 were as follows:

Years ending December 31: (In thousands)	Financing Leases		Operating Leases		Total Leases
2020 (remaining three months)	$	1,086	$	1,960	$	3,046
2021	4,568		7,480		12,048
2022	—		7,657		7,657
2023	—		3,322		3,322
2024	—		151		151
Total lease payments	5,654		20,570		26,224
Less: amount representing interest	(601)		(4,410)		(5,011)
Total lease liability	$	5,053	$	16,160	$	21,213
Current lease liability	$	3,882	$	5,051	$	8,933
Noncurrent lease liability	1,171		11,109		12,280
Total lease liability	$	5,053	$	16,160	$	21,213

Other Assets

(In thousands)	September 30, 2020		December 31, 2019
Equity-method investment	$	4,054	$	4,734
Deposits	126		295
Contingent consideration	—		3,303
Other	1,179		1,373
Total other assets	$	5,359	$	9,705

In connection with the December 2017 sale of its subsidiary Amyris Brasil Ltda. (Amyris Brasil), the Company recorded a long-term receivable related to certain contingent consideration to be received from DSM upon DSM’s realization of certain Brazilian value-added tax benefits it acquired with its purchase of Amyris Brasil. In the three months ended June 30, 2020, the Company received the $3.3 million remaining balance of contingent consideration due to the Company under the 2017 asset purchase agreement.

Accrued and Other Current Liabilities

(In thousands)	September 30, 2020		December 31, 2019
Accrued interest	$	8,116	$	8,209
Payroll and related expenses	7,063		7,296
Contract termination fees	4,315		5,347
Asset retirement obligation	2,603		3,184
Professional services	1,804		2,968
Ginkgo partnership payments	951		4,319
Tax-related liabilities	550		1,685
Other	3,028		3,647
Total accrued and other current liabilities	$	28,430	$	36,655

Other noncurrent liabilities

(In thousands)	September 30, 2020		December 31, 2019
Liability for unrecognized tax benefit	$	7,440	$	7,204
Liability in connection with acquisition of equity-method investment	6,354		5,249
Ginkgo partnership payments, net of current portion	7,098		4,492
Contract liabilities, net of current portion	111		1,449
Refund liability(1)	—		3,750
Other	993		880
Total other noncurrent liabilities	$	21,996	$	23,024

(1) In April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" in Part II, Item 8 of the 2019 Form 10-K for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in $12.5 million of prepaid variable consideration to the Company. The $12.5 million was recorded as a refund liability. During the three months ended March 31, 2020, the Company concluded that it would not be required to return any portion of the remaining refund liability to DSM, and recorded $3.8 million of royalty revenue related to this change in estimate and reduction of the refund liability.

Ginkgo Partnership Payments Modification

On August 10, 2020, the Company and Ginkgo entered into a Second Amendment to Promissory Note and Partnership Agreement (Second Amendment) to reduce the partnership payments frequency from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022 (the “End of Term Payment”), provided that, if the Ginkgo Promissory Note is not fully repaid by April 19, 2022, the End of Term Payment shall be of $10.4 million. See Note 4, “Debt.” for more information.

As a result of changes to key provisions in the partnership payments, the Company analyzed the combined before and after cash flows under the Promissory Note and Partnership Agreement that resulted from (i) the reduced interest rate on the Promissory Note, (ii) reduced payment frequency under the Promissory Note and Partnership Agreement, and (iii) changes in the periodic and total payment amounts under the Partnership Agreement, to determine whether these changes resulted in a modification or extinguishment of the obligations under the Second Amendment. Based on the combined before and after cash flows of the Promissory Note and Partnership Agreement, the change was significantly different. Consequently, the modifications resulting from the Second Amendment were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $0.1 million loss upon extinguishment of the partnership payment obligation, related to the write-off of the unamortized debt discount. Further, since the partnership payment obligation does not contain an explicit interest rate, the Company recorded the $11.9 million of total payments at its net present value of $8.1 million in other liabilities, with the $3.8 million difference recorded as a discount that is accreted to interest expense over the repayment term using the effective interest method.

XML

Fair Value Measurement

9 Months Ended

Sep. 30, 2020

Fair Value Disclosures [Abstract]

Fair Value Measurement

Fair Value Measurement

Liabilities Measured and Recorded at Fair Value on a Recurring Basis

The following tables summarize liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	September 30, 2020								December 31, 2019
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Foris Convertible Note (LSA Amendment)	$	—	$	—	$	58,467	$	58,467	$	—	$	—	$	—	$	—
Senior Convertible Notes	—		—		25,349		25,349		—		—		50,624		50,624
Embedded derivatives bifurcated from debt instruments	—		—		597		597		—		—		2,832		2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		3,237		3,237		—		—		6,971		6,971
Total liabilities measured and recorded at fair value	$	—	$	—	$	87,650	$	87,650	$	—	$	—	$	60,427	$	60,427

The Company did not hold any financial assets to be measured and recorded at fair value on a recurring basis as of September 30, 2020 and December 31, 2019. Also, there were no transfers between the levels during the three months ended September 30, 2020 or the year ended December 31, 2019.

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 embedded derivative liabilities is described subsequently in this note. Market risk associated with embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

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".

Fair Value of Debt — Foris Convertible Note (LSA Amendment)

On June 1, 2020, the Company and 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, entered into an Amendment No. 1 to the Amended and Restated Foris LSA (LSA Amendment), pursuant to which, among other provisions, Foris has the option, in its sole discretion, to convert all or a portion of the secured indebtedness under the LSA Amendment, including accrued interest, into shares of Common Stock at a $3.00 conversion price (Conversion Option), which Conversion Option was approved by the Company’s stockholders on August, 14, 2020. See Note 4, “Debt” for further information regarding the LSA Amendment and related extinguishment accounting treatment. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). The LSA Amendment also contains certain change in control embedded derivatives and a contingent beneficial conversion feature and management believes the fair value option best reflects the underlying economics of new convertible note. 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 LSA Amendment.

At June 30, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $81.6 million. The Company measured the initial fair value of the LSA Amendment using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $4.27 stock price, (ii) 25% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. At September 30, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $58.5 million. The Company remeasured the fair value of the LSA Amendment using the following inputs: (i) $2.92 stock price, (ii) 21% discount yield, (iii) 0.13% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. At both dates, the Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year. The Company recorded

gains of $23.1 million and $13.6 million related to change in fair value of the LSA Amendment for the three and nine months ended September 30, 2020, respectively.

Fair Value of Debt — Senior Convertible Notes

On January 14, 2020, the Company exchanged the $66 million Senior Convertible Notes (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), (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 (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). Due to the legal extinguishment and exchange of the Prior Notes and significantly different cash flows contained in the New Notes, the Company accounted for the exchange as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt, which was comprised of the $4.1 million fair value of the Warrants, the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and Rights over the $2.87 per share contractual value. See Note 4, "Debt” for further information regarding the transaction.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported as "Gain (loss) from change in fair value of debt" in the consolidated statements of operations in each reporting period subsequent to the issuance of the New Notes. At January 14, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $51.0 million and the fair value was $35.8 million. The Company measured the fair value at January 14, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $2.90 stock price, (ii) 226% discount yield, (iii) 1.59% risk free interest rate (iv) 45% equity volatility, (v) 25% / 75% probability of principal repayment in cash or stock, respectively and (vi) 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.

At September 30, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $30.0 million and the fair value was $25.3 million. The Company measured the fair value at September 30, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $2.92 stock price, (ii) 233% discount yield, (iii) 0.11% risk free interest rate (iv) 45% equity volatility, and (v) 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.

For the three and nine months ended September 30, 2020, the Company recorded an $11.3 million gain and a $10.7 million loss from change in fair value of debt, respectively, in connection with the fair value remeasurement of the Prior Notes and the New Senior Convertible Notes, as follows:

In thousands
Fair value at December 31, 2019	$	50,624
Less: principal paid	(35,980)
Loss from change in fair value	10,705
Fair value at September 30, 2020	$	25,349

A binomial lattice model was used to determine whether the LSA Amendment and the Senior Convertible Notes (Debt Instruments) 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 Debt Instruments using the "with-and-without method", where the fair value of the Debt Instruments including the embedded and freestanding features is defined as the "with," and the fair value of the Debt Instruments excluding the embedded and freestanding features is defined as the "without." This method estimates the fair value of the Debt Instruments by looking at the difference in the values of the Debt Instruments with the embedded and freestanding derivatives and the fair value of the Debt Instruments without the embedded and freestanding features. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility, estimated credit spread and other instrument-specific assumptions. The

Company remeasures the fair value of the Debt Instruments 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.

Derivative Liabilities Recognized in Connection with the Issuance of Debt 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 instruments, either freestanding or embedded, measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Derivative Liability
Balance at December 31, 2019	$	9,803
Fair value of derivative liabilities issued during the period	8,751
Change in fair value of derivative instruments	6,498
Derecognition on settlement or extinguishment	(21,218)
Balance at September 30, 2020	$	3,834

Freestanding Derivative Instruments

In connection with the January 14, 2020 issuance of the New Senior Convertible Notes as discussed above and in Note 4, “Debt” (which was accounted for as an extinguishment of the original $66 million Senior Convertible Notes), the Company issued warrants (the Warrants) to purchase up to an aggregate of 3.0 million shares of common stock (the Warrant Shares). Due to stock exchange ownership limitations, which if exceeded would require stockholder approval and possibly require cash settlement for failure to deliver shares upon exercise, the Company concluded that a portion of the Warrant Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Warrant Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Warrants had an initial fair value of $4.1 million, which was recorded as: (i) $4.1 million loss upon extinguishment of debt, (ii) $2.4 million additional paid in capital and (iii) $1.7 million derivative liability. The Warrant Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Warrants was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Warrant Shares derivative liability portion was $1.5 million, and the Company recorded a $0.2 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to remove the stock ownership limitations. As a result, the Company is able to physically deliver shares under the Warrants without the potential for cash settlement. In the three months ended June 30, 2020, the Company recorded a $1.3 million final mark-to-market loss on change in derivative liability, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and derecognized the $2.8 million derivative liability balance relate to this portion of the Warrant Shares into additional paid in capital.

In connection with the January 31, 2020 private placement transaction with Foris (an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock discussed in Note 6, “Stockholders’ Deficit”), the Company issued a right (the Right) to purchase up to an aggregate of 5.2 million shares of common stock (the Right Shares). Due to certain contractual provisions in the Right, the Company concluded that a portion of the Right Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Right Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Right had an initial fair value of $5.3 million, of which $2.3 million was recorded as additional paid in capital and $3.0 million was recorded as a derivative liability. The Right Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Right Shares derivative liability portion was $2.0 million, and the Company recorded a $1.0 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to increase its authorized common share count from 250 million to 350 million. As a result, the portion of the Right Shares initially accounting for as a derivative liability was no longer precluded from the derivative scope exception and met the criteria for equity classification. In the three months ended June 30, 2020, the Company recorded a $1.8 million final mark-to-market loss on change in fair value of derivative instruments using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and derecognized the $3.7 million derivative liability balance into additional paid in capital.

In connection with the January 31, 2020 Debt Equitization transaction with Foris, which was accounted for as a debt extinguishment as discussed in Note 4, “Debt” and Note 6, “Stockholders’ Deficit”, the Company issued rights (the Right) to purchase up to of 8.8 million shares of common stock at $2.87 per share for twelve months from the issuance date. The Company concluded that the Right met the derivative scope exception and criteria to be accounted for in equity. The Right had a fair value of $8.9 million which was recorded as additional paid in capital and a charge to loss upon extinguishment of debt. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below.

During the second half of 2019, the Company issued five freestanding liability warrants related to the September 2019 and November 2019 Schottenfeld Notes (the Schottenfeld Notes), which the Company recorded at fair value as a derivative liability and debt discount on the respective issuance dates (see Note 4, “Debt” for further information). These freestanding liability warrants had a collective fair value of $7.0 million at December 31, 2019. As a result of the Foris Debt Equitization transaction on January 31, 2020, the variability causing these instruments to be recorded as a derivative liability was eliminated and upon derecognition of this liability into equity, the Company recorded a $1.8 million gain on change in fair value of derivative instruments in the three months ended March 31, 2020, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and reclassified the derivative liability balance of $5.2 million to additional paid in capital.

On February 28, 2020, the Company entered into forbearance agreements with certain affiliates of the Schottenfeld Group LLC (the Lenders) related to certain defaults under the Schottenfeld Notes. The transaction was accounted for as a debt extinguishment. See Note 4, “Debt” for further information. In connection with entering into the forbearance agreements, the Company committed to issuing new warrants (the New Warrants) to the Lenders under certain contingent events for 1.9 million shares of common stock at a $2.87 purchase price and a two-year term. The contingent obligation to issue the New Warrants did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The contingently issuable New Warrants derivative liability had an initial fair value of $3.2 million and was recorded as a derivative liability with a $3.2 million charge to loss upon extinguishment of debt. The New Warrants derivative liability will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the New Warrants derivative liability was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At September 30, 2020, the fair value of the contingently issuable New Warrants derivative liability was $3.2 million, and for the three and nine months ended September 30, 2020, respectively, the Company recorded a $2.0 million gain and a $0.1 million loss on change in fair value of derivative instruments.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price from $56.16 to $2.87 per share. See Note 4, “Debt” for further information. Historically, the embedded conversion option was bifurcated and accounted for as a derivative liability, and at December 31, 2019 and March 31, 2020 had a $0 fair value due to the Note’s short maturity and the significant conversion price differential when compared to the Company’s current stock price. As a result of the conversion price reduction, the Company remeasured the fair value of the conversion option using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and recorded a $6.5 million loss on change in fair value of derivative instruments in the three months ended June 30, 2020. On June 2, 2020, Total elected to convert all the outstanding principal and interest under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $6.5 million liability was derecognized into additional paid in capital, along with the debt principal and interest balance.

Bifurcated Embedded Features in Debt Instruments

During the second half of 2019, the Company issued four debt instruments with embedded mandatory redemption features which were bifurcated from the debt host instruments and recorded at fair value as a derivative liability and debt discount. The collective fair value of the four bifurcated derivatives totaled $2.8 million at December 31, 2019. In January and February 2020, the Company again modified certain key terms in three of the four underlying debt instruments, resulting in a debt extinguishment of the three modified debt instruments. Consequently, in the three months ended March 31, 2020, the collective fair value of the three extinguished bifurcated derivatives totaling $2.3 million was recorded as a loss upon extinguishment of debt and the $0.9 million collective fair value of the new bifurcated embedded mandatory redemption features was recorded as a derivative liability and new debt discount at the modification date. The fair value of the bifurcated derivative liability was determined using a probability weighted discounted cash flow analysis which is discussed in the valuation methodology and approach section below. At September 30, 2020, the fair value of the bifurcated embedded mandatory redemption features totaled $0.6 million, and the Company recorded a $0.1 million gain on change in fair value derivative instruments during the nine months ended September 30, 2020. Also, one of the bifurcated features was embedded in the Foris LSA, which was modified and accounted for as an extinguishment in the three months ended June 30, 2020. As a result, the $0.7 million

derivative liability balance was derecognized and recorded into the initial fair value of the new Foris Convertible Note (see “Fair Value of Debt – Foris Convertible Note (LSA Amendment)” above).

Valuation Methodology and Approach to Measuring the Derivative Liabilities

The liabilities associated with the Company’s freestanding and embedded derivatives outstanding at September 30, 2020 and December 31, 2019 represent the fair value of freestanding equity instruments and mandatory redemption features embedded in certain debt 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 instruments or embedded derivatives using the Black-Scholes-Merton option pricing model or a probability weighted discounted cash flow analysis measuring the fair value of the debt instrument both with and without the embedded feature, both of which are discussed in more detail below.

The Company used the Black-Scholes-Merton option pricing model to determine the fair value of its liability classified warrants as of September 30, 2020 and December 31, 2019. Input assumptions for these freestanding instruments are as follows:

	Range for the Period
Input assumptions for liability classified warrants:	September 30, 2020		December 31, 2019
Fair value of common stock on issue date	$2.56 – $4.27		$3.09 – $4.76
Exercise price of warrants	$2.87 – $2.87		$3.87 – $3.90
Expected volatility	117% – 117%		94% – 105%
Risk-free interest rate	0.13% – 0.17%		1.58% – 1.67%
Expected term in years	1.75 – 2.26		1.51 – 2.00
Dividend yield	0.0	%	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 debt instruments. 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 market-based assumptions and estimates used in valuing the embedded derivative liabilities include amounts in the following ranges/amounts:

	September 30, 2020	December 31, 2019
Risk-free interest rate	0.09% - 0.17%	1.6% - 1.7%
Risk-adjusted discount yield	25.0% - 26.0%	20.0% - 27.0%
Probability of change in control	5.0%	5.0%
Credit spread	24.7% - 36.8%	18.4% - 25.4%
Estimated conversion dates	Not applicable	2022 - 2023

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, generally, an increase in the Company’s stock price, change of control probability, risk-adjusted yields term to maturity/conversion or stock price volatility increases the value of the derivative liability.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts 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. 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 September 30, 2020 and at December 31, 2019, excluding the debt instruments recorded at fair value, was $90.6 million and $195.8 million, respectively. The fair value of such debt at September 30, 2020 and at December 31, 2019 was $76.1 million and $194.8 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.

XML

Debt

9 Months Ended

Sep. 30, 2020

Debt Disclosure [Abstract]

Debt

Debt

Net carrying amounts of debt are as follows:

	September 30, 2020								December 31, 2019
(In thousands)	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Convertible notes payable
Senior convertible notes	$	30,020	$	—	$	(4,671)	$	25,349	$	66,000	$	—	$	(15,376)	$	50,624
	30,020		—		(4,671)		25,349		66,000		—		(15,376)		50,624
Related party convertible notes payable
Foris convertible note	50,041		—		8,426		58,467		—		—		—		—
2014 Rule 144A convertible notes	—		—		—		—		10,178		—		—		10,178
	50,041		—		8,426		58,467		10,178		—		—		10,178
Loans payable and credit facilities
Schottenfeld notes	12,500		(269)		—		12,231		20,350		(1,315)		—		19,035
Nikko notes	7,868		(794)		—		7,074		14,318		(901)		—		13,417
Ginkgo note	12,000		—		—		12,000		12,000		(3,139)		—		8,861
Other loans payable	953		—		—		953		1,828		—		—		1,828
	33,321		(1,063)		—		32,258		48,496		(5,355)		—		43,141
Related party loans payable
Foris notes	5,000		—		—		5,000		115,351		(9,516)		—		105,835
DSM notes	33,000		(3,007)		—		29,993		33,000		(4,621)		—		28,379
Naxyris note	23,914		(575)		—		23,339		24,437		(822)		—		23,615
	61,914		(3,582)		—		58,332		172,788		(14,959)		—		157,829
Total debt	$	175,296	$	(4,645)	$	3,755	174,406		$	297,462	$	(20,314)	$	(15,376)	261,772
Less: current portion							(31,431)								(63,805)
Long-term debt, net of current portion							$	142,975							$	197,967

Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (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 (the Rights Shares), (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 (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 Exchange Shares and Warrants were issued on January 14, 2020. The unpaid interest and cash fees were paid in accordance with the Exchange Agreements. The Rights were exercised by the Holder and common stock shares issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020.

The New Notes have substantially similar terms as the Prior Notes, except under the New Notes (i) the requirement to redeem an aggregate principal amount of $10 million on December 31, 2019 was eliminated, (ii) the Company would 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 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 stockholder approval for the Holders to exceed a 19.99% stock exchange ownership limitation (the Stockholder Approval) would be extended from January 31, 2020 to March 15, 2020.

Due to multiple changes in key provisions of the Prior Notes, the Company analyzed the before and after cash flows between the (i) fair value of the New Notes and (ii) reacquisition price of the Prior Notes resulting from the (A) decreased principal from $66 million to $51 million, (B) fair value of the Exchange Shares, (C) fair value of the Rights, (D) fair value of the Warrants and (E) cash fees to be paid prior to January 31, 2020 to determine whether these changes resulted in a modification or extinguishment of the Prior Notes. Based on the before and after cash flows of each note, the change was significantly different. Consequently, the Exchange Agreements were accounted for as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt in the three months ended March 31, 2020, which was comprised of the $4.1 million fair value of the Warrants (considered a non-cash fee paid to the lender), the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and the Rights Shares over the contractual value. See Note 6, “Stockholders’ Deficit” for further information on the accounting treatment of the Exchange Shares and the Rights Shares upon issuance of the New Notes. Also, see Note 3, “Fair Value Measurement” for more information regarding the valuation methodology used to determine the fair value of the Warrants.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, 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 New Notes. For the three months ended March 31, 2020, the Company recorded a loss of $1.1 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.

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 the $20.4 million of indebtedness outstanding under the Schottenfeld Credit Agreements (discussed under the Schottenfeld Forbearance Agreement below) 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 would be in the aggregate amount of $10.0 million (the Amortization Payment), split proportionally among the Holders, and that the Company would elect to pay such amortization payment in shares of Common Stock in accordance with the terms of the New Notes, provided however, that: (A) the Amortization Stock Payment Price (as defined in the New Notes) would be $3.00, (B) the Amortization Share Payment Period (as defined in the New Notes) with respect to the Amortization Payment would end on April 30, 2020 rather than March 31, 2020; and (C) in the event that Holder did not elect to receive the full Amortization Share Amount (as defined in the New Notes) during such Amortization Share Payment Period, then the Amortization Payment would be automatically reduced by the portion of such Amortization Payment not received by the Holder, (ii) there would be no amortization payment due on April 1, 2020, and (iii) the amortization payment due on May 1, 2020 would be in the aggregate amount of $8.9 million split proportionally among the Holders. The W&F Agreements were accounted for as a debt modification, as the before and after cash flows were not significantly different.

Amendment to Senior Convertible Notes Due 2022

On May 1, 2020, the Company and the holders of the New Senior Convertible Notes Due 2022 entered into separate amendments to the New Notes and the W&F Agreements (Note Amendment), pursuant to which the Company and the Holders agreed: (i) to amend the maturity date of the New Notes from September 30, 2022 to June 1, 2021 (Maturity Date); (ii) to remove from the New Notes all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances other than events of default; (iii) that the Company would no longer 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; (iv) that interest payments would be due quarterly (as opposed to monthly), starting on August 1, 2020; (v) that an aggregate amortization payment of approximately $16.4 million (split proportionally among the Holders) would be due on or before the earlier of May 31, 2020 and the date on which the Company receives at least $50 million of aggregate net proceeds in an offering of securities (Amended May Amortization), an amortization payment of $5 million (to the largest Holder) would be due on December 1, 2020 unless the Company receives at least $50 million of aggregate net cash proceeds from one or more financing transactions after May 1, 2020, and no other amortization payment would be due prior to the Maturity Date; (vi) to reduce the conversion price of the New Notes from $5.00 to $3.50; (vii) to reduce the redemption price with respect to optional redemptions by the Company prior to October 1, 2020 to 100%, prior to December 31, 2020 to 105% and to 110% thereafter (as opposed to 115%), of the amount being redeemed; and (viii) that an aggregate of 2,836,364 shares of Common Stock held by the Holders would not be considered as Pre-Delivery Shares (issued in connection with the November 15, 2019 Senior Convertible Notes Due 2022 and as defined in the New Notes) and would be subject to certain selling restrictions until June 15, 2020, and that an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders would be promptly returned to the Company. These Pre-Delivery Shares were returned to the Company on May 5, 2020 and May 6, 2020. The Company paid $16.4 million on June 1, 2020 to satisfy the required amortization payment and is no longer required to make the $5.0 million amortization payment on December 1, 2020. On June 4, 2020, the Company released an additional 700,000 Pre-Delivery Shares to the largest Holder in connection with the Second Amendment to New Notes and the W&F Agreements. The Company recorded $10.5 million of additional interest expense, representing the fair value of the 3,536,364 Pre-Delivery Shares released to the Holders.

Further, in connection with the Note Amendment, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share, from $3.25, with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s Common Stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share, from $5.02, and the exercise term of such warrant was extended to January 31, 2022, from May 10, 2021; and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s Common Stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022, from January 31, 2021. See Note 6, “Stockholders’ Deficit” for more information regarding the accounting treatment of these warrant modifications.

Debt Equitization – Foris, Related Party

As of December 31, 2019, the Company had two loans payable to Foris with a total principal balance of $110.0 million, excluding capitalized interest of $5.3 million. 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 first loan (Foris $19 million Note) was a $19 million unsecured borrowing that accrued interest at 12% per annum and matures on January 1, 2023. The second loan (Foris LSA) is a $91.0 million secured borrowing that accrues interest at 12.5% per annum and matured on March 1, 2023. The Foris LSA required quarterly principal payments and monthly interest payments. See Amendment No. 1 to Amended and Restated LSA — Foris, Related Party below for more information on the maturity date and payment terms of the Foris LSA.

On January 31, 2020, the Company completed a series of equity transactions with Foris that resulted in the Company (i) reducing its aggregate debt principal with Foris by $60.0 million and accrued interest and fees due to Foris by $9.9 million (including $5.4 million of capitalized interest), (ii) issuing an aggregate of 19,287,780 shares of common stock as a result of the exercise of outstanding warrants at a weighted average exercise price of approximately $2.84 per share for an aggregate of $54.8 million, (iii) issuing an aggregate of 5,279,171 shares of common stock at $2.87 per share for an aggregate of $15.1 million in a private placement, and (iv) issuing rights (the Rights) to purchase an aggregate of 8,778,230 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months. The exercise price of the outstanding warrants and the purchase price of the private placement common stock was paid through the cancellation of principal and accrued interest and fees totaling $69.9 million. See Note 6, “Stockholders’ Deficit” for information on the accounting treatment of the various equity related instruments.

As a result of the transaction described above, on January 31, 2020, the principal balance of the Foris $19 million Note and accrued but unpaid interest was fully settled through the exercise price of certain of outstanding warrants. Upon settlement of the Foris $19 million Note, the Company recorded a $5.7 million loss upon extinguishment debt, which was comprised of $6.1 million of unaccreted discount, less the $0.4 million fair value of the extinguished bifurcated derivative liability.

In addition, this series of equity transactions directly impacted the cash flows of the Foris LSA and, as a result, the Company analyzed the before and after cash flows resulting from the significant decrease in principal, the warrant exercise price modifications and the issuance rights to purchase additional shares of common stock at $2.87, to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was

significantly different. Consequently, the accelerated paydown of the Foris LSA loan balance through the exercise price of the remaining outstanding warrants and the purchase price of the private placement common stock was accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $10.4 million loss upon extinguishment of debt, which was comprised of $8.9 million fair value of the Rights and $3.1 million of unaccreted discount, less the $1.6 million fair value of the extinguished bifurcated derivative liability. See Note 6, “Stockholders’ Deficit” for further information on the valuation methodology and related accounting treatment of the Rights. In recording the new debt issuance, the Company capitalized $0.7 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

Amendment No. 1 to Foris LSA — Foris, Related Party

On June 1, 2020, the Company and Foris entered into Amendment No. 1 to the Foris LSA (LSA Amendment), pursuant to which: (i) the interest rate applicable to the then outstanding secured indebtedness (Secured Indebtedness) was amended from and after June 1, 2020 to a per annum rate of interest equal to 6.00% (previously 12.5%), (ii) the Company shall not be required to make any interest payments outstanding as of May 31, 2020 or accruing thereafter prior to July 1, 2022 (previously due monthly), (iii) the quarterly principal amortization payments were eliminated and all outstanding principal under the LSA Amendment became due on July 1, 2022, and (iv) Foris shall have the option, in its sole discretion, to convert all or portion of the Secured Indebtedness, including accrued interest, into shares of common stock at a $3.00 conversion price (Conversion Option), subject to the Company’s stockholder approval to issue shares of common stock upon exercise of the Conversion Option in accordance with applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d); for which stockholder approval was obtained on August 14, 2020.

The Company analyzed the before and after cash flows resulting from the LSA Amendment to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was significant. Consequently, the LSA Amendment was accounted for as a debt extinguishment and a new debt issuance. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). Management believes the fair value option best reflects the underlying economics of the LSA Amendment, which contains embedded derivatives, a conversion option requiring bifurcation and a beneficial conversion feature. 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 LSA Amendment. The Company also recorded gains of $23.1 million and $13.6 million for the three and nine months ended September 30, 2020 related to the change in fair value of the LSA Amendment after the June 1, 2020 issuance date, 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 LSA Amendment.

Schottenfeld Forbearance Agreement

The Company, Schottenfeld Group LLC (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 Schottenfeld Warrants) to purchase shares (the Warrant Shares) of the Company’s common stock. See Note 6, “Stockholders’ Deficit” for further information. Indebtedness under the September Notes totals $12.5 million, accrues interest at 12% per annum and matures on January 1, 2023. Indebtedness under the November Notes total $7.9 million, accrued interest at 12% per annum and originally matured on January 15, 2020. The Company failed to repay the $7.9 million November Notes by January 15, 2020.

On February 28, 2020, the Company entered into a forbearance agreement with the Lenders (Forbearance Agreement), 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 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) issue new warrants upon the occurrence of certain contingent events and (v) amend 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.

Due to multiple changes in key provisions of Schottenfeld Credit Agreements, the Company analyzed the before and after cash flows resulting from the warrant modification and forbearance fee 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 was significantly different. Consequently, the modifications resulting from the Forbearance Agreement were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $5.6 million loss upon extinguishment of debt, which was comprised of the $3.2 million fair value of contingent warrant issuance obligation, the $1.3 million incremental fair value of the modified warrants, $1.1 million of unaccreted discount and the forbearance fee, less the balance of the extinguished bifurcated derivative liability. In recording the new debt issuance, the Company capitalized $0.2 million of legal fees and $0.2 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

On April 19, 2020, the Company failed to pay the amounts due under the Forbearance Agreement, including the past due interest on the September Notes, and was unable to obtain a waiver or extension for the past due amounts. As a result, $20.4 million of principal outstanding under the Schottenfeld Notes was classified as a current liability on the condensed consolidated balance sheet as of March 31, 2020. On June 5, 2020, the Company repaid the past due November 2019 Notes totaling $7.9 million. Consequently, the September 2019 Notes due January 1, 2023 totaling $12.5 million were reclassified to a non-current liability as of September 30, 2020.

2014 Rule 144A Note Exchange and Extensions – Total, Related Party

On March 11, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement (the Extension Agreement) due to the Company’s failure to pay the $10.2 million principal amount due under the December 20, 2019 reissued 2014 Rule 144A Convertible Notes that matured on January 31, 2020. The Extension Agreement resulted in the reissuance and extension of the December 20, 2019 promissory note to March 31, 2020. Under the terms of the 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: (i) had a maturity date of March 31, 2020, (ii) had a $9.1 million principal amount due, (iii) accrued interest at a rate of 12.0% per annum, and (iv) had terms substantially identical to the December 20, 2019 promissory note. The Extension Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note to $2.87 per share. Effective April 30, 2020, the Company and Total entered into a subsequent Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The 2014 Rule 144A Convertible Note was reissued as a result of such extensions with terms substantially identical to the previously issued promissory notes. On June 2, 2020, Total elected to convert all the outstanding principal and interest due under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the fair value of the conversion option was derecognized into additional paid in capital. See Note 3, “Fair Value Measurement” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

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, pursuant to which Ginkgo agreed to (a) waive the Company’s failure to pay past due interest and partnership payments, including interest thereon of $6.7 million by December 15, 2019, and to comply with a reporting covenant prior to March 31, 2020, (b) to make a prior waiver fee payment of $0.5 million on

December 15, 2019, (c) waive any cross defaults due to events of default under other debt obligations by the Company, (d) 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, and (e) to defer all past due payments totaling $7.2 million until April 30, 2020. The Ginkgo Waiver was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On May 6, 2020, the Company entered into a waiver agreement under which the maturity date for all past due amounts to Ginkgo was extended to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The Company paid all past-due amounts to Ginkgo.

On August 10, 2020, the Company and Ginkgo entered into a Second Amendment to Promissory Note and Partnership Agreement (Second Amendment) to, among other things, (i) with respect to the Promissory Note, amend the interest payment frequency from monthly to quarterly beginning September 30, 2020 and reduce the interest rate from 12% to 9% beginning January 1, 2021, conditioned to the timely payment of interest on September 30, 2020 and December 31, 2020; and (ii) with respect to the Partnership Agreement, reduce the partnership payments frequency from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022 (the “End of Term Payment”), provided that, if the Promissory Note is not fully repaid by April 19, 2022, the End of Term Payment shall be of $10.4 million.

As a result of changes to key provisions of both the Promissory Note and Partnership Agreement, the Company analyzed the before and after cash flows resulting from (i) a reduced interest rate of the Promissory Note, (ii) reduced payment frequency for the Promissory Note interest and Partnership Agreement payments and (iii) changes in the periodic and total payment amounts under the Partnership Agreement, in order to determine whether these changes result in a modification or extinguishment of the obligations under the Second Amendment. Based on the combined before and after cash flows of the Promissory Note and Partnership Agreement, the change was significantly different. Consequently, the modifications resulting from the Second Amendment were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $2.5 million loss upon extinguishment of the Promissory Note and a $0.1 million loss upon extinguishment of the partnership payments, which was primarily related to the unamortized debt discounts. The $12.0 million principal amount due under the Promissory Note was unchanged and reflects the present value of the obligation after the modifications. See Note 2, “Balance Sheet Details”, for more information on the payments due under the Partnership Agreement.

Nikko Secured Loan Agreement Amendment

On March 12, 2020, the Company and Nikko Chemicals Co. Ltd. (Nikko), entered into an amendment to the secured loan agreement (Loan Agreement) under which the Company paid Nikko $0.5 million to reduce the principal balance of the Loan Agreement to $4.0 million, extended the maturity date of the loan from January 31, 2020 to March 31, 2020 and increased the interest rate to 8.0% per annum. The loan (i) matured on March 31, 2020, (ii) accrued interest at a rate of 2.75% per annum, and (iii) was secured by a first-priority lien on 27.2% of the Aprinnova JV interests owned by the Company. The Loan Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 3, 2020, the Company entered into a second amendment to the Loan Agreement under which the maturity date of the loan was extended to April 30, 2020. Subsequently, on May 7, 2020, the Company entered into a third amendment to the Loan Agreement under which the maturity date of the loan was extended to May 31, 2020. The Company fully repaid the $4.0 million loan on June 5, 2020.

Paycheck Protection Plan Loan

On April 7, 2020, the Company applied for a Paycheck Protection Plan loan (PPP Loan) established by the Coronavirus Aid, Relief, and Economic Security Act (CARES Act). On May 7, 2020, the Company received a $10 million loan pursuant to a promissory note issued by the Company. The PPP Loan accrued interest at an annual fixed rate of 1% and had a term of 2 years with no payments due in the first six months of such term; however, interest still accrued during this six-month period. Upon receipt of the PPP Loan, the Company applied the funds to payroll and building rent expenses. Following the completion of the private placement of its securities in early June 2020, the Company repaid the PPP Loan in full, including applicable interest, on June 12, 2020.

Foris $5 Million Note – Foris, Related Party

On April 29, 2020, the Company borrowed $5.0 million from Foris, an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock. The note is unsecured and accrues interest at 12% per annum. Principal and interest will be payable at maturity, on December 31, 2022.

Future Minimum Payments

Future minimum payments under the Company's debt agreements as of September 30, 2020 are as follows:

(In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020 (remaining three months)	$	375	$	5,945	$	—	$	1,547	$	7,867
2021	33,898		3,902		—		31,823		69,623
2022	—		14,768		59,578		40,939		115,285
2023	—		12,899		—		—		12,899
2024	—		398		—		—		398
Thereafter	—		1,870		—		—		1,870
Total future minimum payments	34,273		39,782		59,578		74,309		207,942
Less: amount representing interest	(4,253)		(6,460)		(9,537)		(12,396)		(32,646)
Present value of minimum debt payments	30,020		33,322		50,041		61,913		175,296
Less: current portion of debt principal	(30,020)		(5,236)		—		—		(35,256)
Noncurrent portion of debt principal	$	—	$	28,086	$	50,041	$	61,913	$	140,040

XML

Mezzanine Equity

9 Months Ended

Sep. 30, 2020

Temporary Equity Disclosure [Abstract]

Mezzanine Equity

Mezzanine Equity

Mezzanine equity at September 30, 2020 and December 31, 2019 is comprised of proceeds from shares of common stock sold on May 10, 2016 to the Bill & Melinda Gates Foundation (Gates Foundation). In connection with the stock sale, the Company and the Gates Foundation entered into an agreement under which the Company agreed to expend an aggregate amount not less than the proceeds from the stock sale 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. If the Company defaults in its obligation to use the proceeds from the stock sale as set forth above or defaults under certain other commitments in the agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party, the 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 September 30, 2020, the Company's remaining research and development obligation under this arrangement was $0.3 million.

XML

Stockholders' Deficit

9 Months Ended

Sep. 30, 2020

Equity [Abstract]

Stockholders' Deficit

Stockholders' Deficit

Foris Warrant Exercises for Cash

On January 13, 2020, 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. The Company received approximately $14.0 million from Foris in connection with the warrant exercise representing 4,877,386 shares of common stock issued and recorded $14.0 million as additional paid-in capital.

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. The Company and Foris agreed to defer the issuance of the shares until such time as stockholder approval has been obtained to increase the Company’s authorized share count. At March 31, 2020, the PIPE Rights exercise proceeds were recorded as additional paid-in capital as there is no contractual obligation to return the consideration if stockholder approval is not obtained. Stockholder approval was obtained on May 29, 2020 and the 5,226,481 shares of common stock were issued to Foris on June 2, 2020.

January 2020 Warrant Amendments and Exercises, Foris Debt Equitization and Private Placement

As described below in further detail, on January 31, 2020, the Company completed a series of equity 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 $9.9 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. See Note 4, “Debt,” for more information regarding the accounting treatment of the $60.0 million debt reduction.

Warrant Amendments and Exercises by Certain Holders

On January 31, 2020, the Company entered into separate warrant amendment agreements (the Warrant Amendments) with certain holders (the Warrant Holders) of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of certain warrants (the Amended Warrants) held by the Warrant Holders totaling 1.2 million shares was reduced to $2.87 per share. In connection with the entry into the Warrant Amendments, on January 31, 2020, the Warrant Holders exercised their Amended Warrants, representing an aggregate of 1,160,929 shares of common stock (the Warrant Amendment Shares), and the Company issued the Warrant Amendment Shares to the Holders along with a right 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 recorded the $3.3 million as additional paid in capital. The Company also measured the before and after fair value of the Amended Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Rights warrants met the derivative scope exception and equity classification criteria to be accounted for in equity.

Warrant Amendments and Exercises, Common Stock Purchase and Debt Equitization by Foris – Related Party

On January 31, 2020, the Company and Foris entered into certain warrant amendment agreements (the Foris Warrant Amendments) totaling 10.2 million shares of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of these certain warrants (the Amended Foris Warrants) was reduced to $2.87 per share. In connection with the Foris Warrant Amendments, on January 31, 2020 (i) Foris exercised all its then-outstanding common stock purchase warrants, including the Amended Foris Warrants, totaling 19,287,780 shares of common stock, at a weighted average exercise price of approximately $2.84 per share for an aggregate exercise price of $54.8 million (the Exercise Price), and purchased 5,279,171 shares of common stock (the Foris Shares) at $2.87 per share for a total purchase price of $15.1 million (Purchase Price), (ii) Foris paid the Exercise Price and the Purchase Price through the cancellation of $60 million of principal and $9.9 million of accrued interest and fees owed by the Company to Foris under the Foris $19 million Note and the Foris LSA (which was treated as a debt extinguishment as discussed in Note 4, "Debt") and (iii) the Company issued to Foris the Foris Shares and an additional right (the 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 execution of the warrant exercise agreement.

Upon exercise of the Amended Foris Warrants and issuance of the Foris Shares, the Company recorded a $69.9 million increase to additional paid-in capital. The Company also measured the before and after fair value of the Amended Foris Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Company concluded the Additional Rights met the derivative scope exception and criteria to be accounted for in equity and recorded the $8.9 million fair value of the Additional Rights to additional paid-in capital and loss upon extinguishment of debt. The fair value was determined using a Black-Scholes-Merton option pricing model based on the following input assumptions: (i) $2.56 stock price, (ii) 112% volatility, (iii) 1.45% risk free rate and (iv) 0% dividend.

January 2020 Private Placement

On January 31, 2020, the Company entered into separate Security Purchase Agreements with certain accredited investors and Foris, for the issuance and sale of an aggregate of 8,710,802 shares of common stock and rights to purchase an aggregate of 8,710,802 shares of common stock (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. The $25 million in proceeds was recorded as additional paid-in capital. See Note 3, “Fair Value Measurement,” for information regarding the valuation methodology used to determine fair value and the related accounting treatment of the PIPE rights.

Principal Conversion into Common Stock and New Warrants Issued in Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior

Convertible Notes), (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 (the Rights Shares), and (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, The New Notes, Exchange Shares, Rights and Warrants were issued on January 14, 2020. The Rights were exercised by the Holder and the Rights Shares were issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020. The contractual value of the Exchange Shares and the Rights Shares was $2.87 per share. Upon issuance of the New Notes, Exchange Shares and Rights, the $15.0 million of debt principal was extinguished and the $15.2 million fair value of the Exchange Shares and the Rights Shares was recorded as additional paid in capital. See Note 3, “Fair Value Measurement,” for more information regarding the valuation methodology used to determine the fair value and the related accounting treatment of the Warrants, and see Note 4, “Debt,” for further information on the accounting treatment and the terms of the note exchange.

Release of Pre-Delivery Shares and Amendment to Warrants Issued to Holders of Senior Convertible Notes Due 2022

Under the terms of the November 15, 2019 Senior Convertible Notes Due 2022 and the January 14, 2020 New Senior Convertible Notes, the Company was required to pre-deliver 7.5 million shares of common stock (the Pre-Delivery Shares) to the Holders, which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the 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 Holders 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 accounted for the fair value of the Pre-Delivery Shares within equity.

On May 1, 2020, in connection with the amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”, the Company and the Holders of the New Senior Convertible Notes Due 2022 agreed, among other provisions described in Note 4, “Debt”: (i) to remove all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances; (ii) to reduce the conversion price of the New Notes from $5.00 to $3.50; (iii) to release to the Holders an aggregate of 2,836,364 shares of common stock originally required to be returned under the Pre-Delivery Share arrangement, and (iv) return an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders to the Company. Further, on June 4, 2020, the Company agreed to release an additional 700,000 Pre-Delivery Shares to one of the Holders, in connection with the second amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”. After the release and return of the Pre-Delivery Shares on May 1, 2020 and June 4, 2020, the total number of Pre-Delivery Shares subject to the arrangement is 2,600,000 and must be returned to the Company following full redemption or repayment of the New Senior Convertible Notes Due 2022. As a result of releasing the 3,536,364 Pre-Delivery Shares to the Holders, the Company recorded $10.5 million of additional interest expense, representing the fair value of the released share.

Further, in connection with the May 1, 2020 amendment to the Senior Convertible Notes Due 2022, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share (from $3.25) with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s common stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share (from $5.02), and the exercise term of such warrant was extended to January 31, 2022 (from May 10, 2021); and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s common stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022 (from January 31, 2021). Each of these warrant instruments were previously accounted for in equity. As a result of the warrant amendments, the Company performed a before and after remeasurement of the warrants using the Black-Scholes-Merton option pricing model and recorded $1.1 million of incremental interest expense and a corresponding increase to additional paid in capital.

Increase in Authorized Common Stock

On May 29, 2020, through a proxy vote at the Company’s Annual Stockholder meeting, the Company’s stockholders approved an increase in the Company’s authorized common stock share count from 250 million to 350 million.

Total Conversion Price Reduction and Subsequent Conversion into Common Stock

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note from $56.16 to $2.87 per share. See Note 4, “Debt” for further information related to this debt instrument. On June 2, 2020, Total elected to convert all the outstanding principal and interest totaling $9.3 million due under the 2014 Rule 144A Convertible Note into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the conversion option was derecognized into additional paid-in capital. See Note 3, “Fair Value Measurement,” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

June 2020 PIPE

On June 1, 2020 and June 4, 2020, the Company entered into separate security purchase agreements (Purchase Agreements) with certain accredited investors (Investors), including Foris and Vivo Capital LLC, stockholders that beneficially own more than 5% of the Company’s outstanding common stock and are, respectively, owned by or affiliated with individuals serving on the Company’s Board of Directors, for the issuance and sale of an aggregate of 32,614,573 shares of the Company’s common stock, $0.0001 par value per share and 102,156 shares of the Company’s Series E Convertible Preferred Stock, $0.0001 par value per share, convertible into 34,052,070 shares of common stock, at a price of $3.00 per common share and $1,000 per preferred share, resulting in an aggregate purchase price of $200 million (Offering). The transaction closed on June 5, 2020, following the satisfaction of customary closing conditions. Upon closing, the Company received aggregate net proceeds of approximately $190 million after payment of the Offering expenses and placement agent fees. The Company used the proceeds from the Offering for the repayment of certain outstanding indebtedness and the remainder for general corporate purposes.

The Purchase Agreements included customary representations, warranties and covenants of the parties. In addition, the Company executed a letter agreement pursuant to which, subject to certain exceptions, the Company, the members of the Company’s Board of Directors, and the Company’s named executive officers agreed not to issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for common stock until September 2, 2020. The securities issued pursuant to the Purchase Agreements were sold in private placements pursuant to an exemption from registration under Section 4(a)(2) of the Securities Act of 1933, as amended (Securities Act) and Rule 506(b) of Regulation D promulgated under the Securities Act, without general solicitation, made only to and with accredited investors as defined in Regulation D.

Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws

On June 5, 2020, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series E Convertible Preferred Stock (Preferred Stock) with the Secretary of State of Delaware. Each share of Series E Preferred Stock issued in the June 2020 PIPE had a stated value of $1,000 and was convertible into 333.33 shares of common stock. All preferred shares automatically converted into common stock without any action by the holders on the first trading day after the Company obtains stockholder approval (as described below). Unless and until converted into common stock in accordance with its terms, the Preferred Stock had no voting rights, other than as required by law or with respect to matters specifically affecting the Preferred Stock.

The Company agreed to obtain stockholder approval for the issuance of common stock upon conversion of the Preferred Stock as is required by the applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d), and including the issuance of common stock upon conversion of the Preferred Shares in excess of 19.99% of the issued and outstanding common stock on the date of the Purchase Agreements. Pursuant to the Purchase Agreements, the Company was required to hold a special meeting of stockholders within 75 calendar days of the date of the Purchase Agreements for the purpose of obtaining stockholder approval. This special meeting of stockholders was held on August 14, 2020, at which the Company’s stockholders approved the conversion of the Series E Preferred Stock and as a result, 34,052,084 shares of common stock were issued on August 17, 2020 in exchange for the 102,156 shares of the Company’s Series E Convertible Preferred Stock.

The Company analyzed the automatic conversion provision related to the Series E Preferred Stock at the original commitment dates and determined the holders received a contingent beneficial conversion feature (BCF) equal to $67.2 million. This amount represents the difference between the Company’s closing stock price at the June 1, 2020 and June 4, 2020 commitment dates ($5.35 and $4.88, respectively) and the $3.00 conversion price. As the automatic conversion provision was contingent on stockholder approval on August 14, 2020, the BCF would be recognized when the contingency was resolved. Upon obtaining stockholder approval, the $67.2 million BCF was recognized in additional paid-in capital and reflected as a deemed dividend to the preferred stockholders in the September 30, 2020 condensed consolidated statement of operations, increasing the net loss attributable to common stockholders and increasing basic net loss per share.

Warrants and Rights Activity Summary

In connection with various debt and equity transactions (see Note 4, “Debt” above and Note 4, "Debt" and Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 2019 Form 10-K), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrants activity for the nine months ended September 30, 2020:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2019	Additional Warrants Issued	Exercises	Expired	Exercise Price per Share of Warrants Exercised		Number Outstanding as of September 30, 2020	Exercise Price per Share as of September 30, 2020
High Trail/Silverback warrants	2020	January 14, 2022	—	3,000,000	—	—	$	—	3,000,000	$2.87/$3.25
2020 PIPE right shares	2020	February 4, 2021	—	8,710,802	(5,226,481)	—	$	2.87	3,484,321	$	2.87
January 2020 warrant exercise right shares	2020	January 31, 2021 and January 31, 2022	—	9,939,159	—	—	$	—	9,939,159	$	2.87
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)	—	$	2.87	—	$	—
August 2019 Foris warrant	2019	August 28, 2021	4,871,795	—	(4,871,795)	—	$	2.87	—	$	—
April 2019 PIPE warrants	2019	April 26, 2021, April 29, 2021 and May 3, 2021	8,084,770	—	(4,712,781)	—	$	2.87	3,371,989	$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	$	2.87
Naxyris LSA warrants	2019	August 14, 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 14, 2021 and January 31, 2022	1,744,241	—	(784,016)	—	$	2.87	960,225	$	2.87
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	—	(4,877,386)	(7,219,778)	$	2.87	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,078,156	—	—	—	$	—	6,078,156	$	2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	—	3,968,116	$	2.87
May 2017 dilution warrants	2017	July 10, 2022	3,085,893	—	—	—	$	—	3,085,893	$	—
August 2017 dilution warrants	2017	May 23, 2023	3,028,983	—	—	—	$	—	3,028,983	$	—
February 2016 related party private placement	2016	February 12, 2021	171,429	—	(152,381)	—	$	0.15	19,048	$	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	72,650	—	(72,650)	—	$	0.15	—	$	—
July 2015 related party debt exchange	2015	July 29, 2025	58,690	—	—	—	$	—	58,690	$	0.15
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$	160.05
			65,755,629	21,649,961	(30,694,457)	(7,219,778)			49,491,355

XML

Loss Per Share

9 Months Ended

Sep. 30, 2020

Earnings Per Share [Abstract]

Loss Per Share

Loss per Share

For the three and nine months ended September 30, 2019, basic loss per share was the same as diluted loss per share, because the inclusion of all potentially dilutive securities outstanding was antidilutive.

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 loss per share:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Numerator:
Net loss attributable to Amyris, Inc.	$	(23,156)	$	(59,562)	$	(221,422)	$	(163,893)
Less: deemed dividend to preferred stockholder on issuance and modification of common stock warrants	—		—		—		(34,964)
Less: deemed dividend to preferred stockholders upon conversion of Series E preferred stock	(67,151)		—		(67,151)		—
Add: losses allocated to participating securities	6,832		1,655		15,369		6,233
Net loss attributable to Amyris, Inc. common stockholders, basic	$	(83,475)	$	(57,907)	$	(273,204)	$	(192,624)
Adjustment to earnings allocated to participating securities	744		—		120		—
Interest on convertible debt	1,081		—		317		—
Gain from change in fair value of debt	(17,221)		—		(5,945)		—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(98,871)	$	(57,907)	$	(278,712)	$	(192,624)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	227,267,553		103,449,612		189,192,973		91,344,150
Basic loss per share	$	(0.37)	$	(0.56)	$	(1.44)	$	(2.11)
Weighted-average shares of common stock outstanding	227,267,553		103,449,612		189,192,973		91,344,150
Effect of dilutive convertible debt	15,464,681		—		2,313,526		—
Weighted-average shares of common stock equivalents used in computing loss per share of common stock, diluted	242,732,234		103,449,612		191,506,499		91,344,150
Diluted loss per share	$	(0.41)	$	(0.56)	$	(1.46)	$	(2.11)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted loss per share of common stock because including them would have been antidilutive:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2020	2019	2020	2019
Period-end common stock warrants	43,298,741	52,612,330	43,298,741	52,612,330
Convertible promissory notes(1)	—	14,259,214	8,574,399	14,259,214
Period-end stock options to purchase common stock	6,571,703	5,398,834	6,571,703	5,398,834
Period-end restricted stock units	7,722,630	4,543,190	7,722,630	4,543,190
Period-end preferred stock	1,943,661	2,955,732	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted loss per share	59,536,735	79,769,300	68,111,134	79,769,300

______________

(1)    The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. 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.

XML

Commitments and Contingencies

9 Months Ended

Sep. 30, 2020

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

Contingencies

The Company has levied indirect taxes on sugarcane-based biodiesel sales that took place several years ago by Amyris Brasil Ltda. (see Note 12, “Divestiture” in Part II, Item 8 of the 2019 Form 10-K) to customers in Brazil, based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate the Company levied.

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, which was denied by the court on October 5, 2020. The Company filed its answer to the securities class action complaint on October 26, 2020. 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 naming 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.

On July 24, 2020, a securities class action complaint was filed against Amyris and the members of our Board in the Court of Chancery of the State of Delaware (Flatischler v. Melo, et. al.). The complaint alleged a breach of fiduciary obligation to disclose material information to stockholders in the proxy statement filed with the Securities and Exchange Commission on July 6, 2020 (Proxy), with respect to the Company’s special stockholders’ meeting held on August 14, 2020 (Special Meeting), at which stockholders were to vote to approve the conversion of all outstanding indebtedness under the Foris Convertible Note and of our Series E Preferred Stock issued in the June 2020 PIPE into shares of common stock, in accordance with Nasdaq Listing Standard Rule 5635(d). See Note 4, “Debt,” “Amendment No. 1 to Foris LSA — Foris, Related Party,” and Note 6, “Stockholders’ Deficit,” “June 2020 PIPE,” and “Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws” in Part I, Item 1 of this Quarterly Report on Form 10-Q for more information. The plaintiffs sought to enjoin the Special Meeting. On August 6, 2020, the plaintiffs withdrew their complaint as moot following the Company’s filing of a supplement to the Proxy on August 5, 2020. The Proxy supplement provided additional information regarding the approval process of the LSA Amendment and the June 2020 PIPE, and the relationships between the Company and its financial advisors to the June 2020 PIPE. The plaintiffs currently seek an amount for their attorney’s fees and certain legal expenses related to filing the complaint, which the parties are negotiating. Three substantially similar complaints were filed: one on July 28, 2020, in the United States District Court of Delaware (Sabatini v. Amyris, Inc.); one on July 31, 2020, in the Northern District of California (Nair v. Amyris); and another on August 4, 2020, in the Southern District of New York (Chamorro v. Amyris). Amyris answered the Chamorro case on October 19, 2020. The Sabatini and Nair cases were voluntarily dismissed by the plaintiffs on October 8 and October 22, 2020, respectively. For this matter, as of September 30, 2020, the Company has accrued a liability for the plaintiffs’ legal fees and expenses, which are not material.

On September 10, 2020, LAVVAN, Inc. (Lavvan) filed a suit against the Company in the United States District Court for the Southern District of New York alleging breach of contract, patent infringement, and trade secret misappropriation in connection with that certain Research, Collaboration and License Agreement between Lavvan and Amyris, dated March 18, 2019, as amended (Cannabinoid Agreement). Amyris filed motions to compel arbitration or to dismiss on October 2, 2020. On October 30, Lavvan filed its opposition to the Company’s motions. The Company believes that the suit lacks merit and intends to continue to defend itself vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result therefrom.

In addition, 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 that are not predictable with reasonable assurance, and therefore, an estimate of all the reasonably possible losses cannot be determined at this time. 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.

Other Matters

Certain conditions may exist as of the date the condensed consolidated 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.

XML

Revenue Recognition and Contract Assets and Liabilities

9 Months Ended

Sep. 30, 2020

Revenue from Contract with Customer [Abstract]

Revenue Recognition and Contract Assets and Liabilities

Revenue Recognition and Contract Assets and Liabilities

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	20,759	$	—	$	263	$	21,022	$	9,927	$	—	$	9,114	$	19,041
Europe	3,752		3,563		919		8,234		2,609		2,305		1,354		6,268
Asia	1,542		—		1,936		3,478		2,398		—		4,789		7,187
Brazil	1,298		—		—		1,298		2,272		—		28		2,300
Other	226		—		—		226		157		—		—		157
	$	27,577	$	3,563	$	3,118	$	34,258	$	17,363	$	2,305	$	15,285	$	34,953
	Nine Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	49,568	$	—	$	263	$	49,831	$	22,806	$	—	$	16,015	$	38,821
Europe	10,100		9,714		6,073		25,887		7,565		43,387		6,180		57,132
Asia	7,901		—		6,724		14,625		8,015		—		5,038		13,053
Brazil	2,546		—		—		2,546		2,787		—		34		2,821
Other	504		—		—		504		194		—		—		194
	$	70,619	$	9,714	$	13,060	$	93,393	$	41,367	$	43,387	$	27,267	$	112,021

Significant Revenue Agreements During the Nine Months Ended September 30, 2020

Cannabinoid Agreement

On March 18, 2019, the Company entered into a Research, Collaboration and License Agreement (as amended, the Cannabinoid Agreement) with LAVVAN, Inc., an investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids, subject to certain closing conditions. Under the Cannabinoid Agreement, the Company performs research and development activities, and Lavvan is responsible for manufacturing and commercialization, related to the cannabinoids developed in accordance with the Cannabinoid Agreement. The Cannabinoid Agreement principally funds milestones that include both technical R&D targets and completion of production campaigns, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. Additionally, the Cannabinoid

Agreement provides for profit share to the Company on Lavvan's gross profit margin once the cannabinoid products are commercialized. On May 2, 2019, the parties formed 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 Convertible Note (see Note 4, “Debt”). On March 11, 2020, the parties revised the agreement to reflect product specifications and cost assumptions.

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 obligation. The Company concluded the agreement contained a single performance obligation of research and development services. The Company also concluded that the performance obligation is continuously delivered over time and that revenue recognition is based on an input measure of progress of labor hours incurred compared to total estimated labor hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, based on changes in estimated project plan hours, with proportional performance adjustments to quarterly revenue as necessary. Prior to September 30, 2020, the Company estimated the total unconstrained transaction price to be $145 million, based on a high probability of achieving certain underlying milestones, and had recognized $18.3 million of cumulative revenue to date. As of September 30, 2020, the Company has constrained $282 million of variable consideration which relate to milestones that do not meet the criteria necessary under ASC 606 to be included in the transaction price. The Company recognized no collaboration revenue for the three and nine months ended September 30, 2020, and during the three months ended September 30, 2020, the Company recorded a credit loss reserve against a previously recorded $8.3 million contract asset in connection with the Cannabinoid Agreement. See Contract Assets and Liabilities below for further information.

DSM Ingredients Collaboration

In September 2017, the Company entered into a collaboration agreement with DSM (DSM Collaboration Agreement) to jointly develop a new molecule in the Clean Health market using the Company’s technology (DSM Ingredient), which the Company would have the sole right to manufacture, and DSM would commercialize. Pursuant to the DSM Collaboration Agreement, DSM provides funding for the development of the DSM Ingredients in the form of milestone-based payments and, upon commercialization, the parties would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredient from the Company at prices agreed by the parties. The development services are directed by a joint steering committee with equal representation by DSM and the Company and are governed by a milestone project plan. The timing of milestone achievements is subject to review and revision as agreed by the joint steering committee. In addition, the parties will share profit margin from DSM’s sales of products that incorporate the DSM Ingredient subject to the DSM Collaboration Agreement.

The DSM Collaboration Agreement is accounted for as a revenue contract under ASC 606, and has a total transaction price of $14.1 million, 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 three performance obligations of research and development services that are delivered over time and that revenue recognition is based on an input measure of progress as labor hours are expended in the achievement of each milestone. The Company recognized $0.8 million and $5.0 million of collaboration revenue for the three and nine months, respectively, ended September 30, 2020, and $9.9 million of cumulative-to-date collaboration revenues.

Yifan Collaborations

From September 2018 to December 2019, the Company entered into a series of license and collaboration agreements, culminating in a master services agreement for research and development services, with a subsidiary of Yifan Pharmaceutical Co., Ltd. (Yifan), a leading Chinese pharmaceutical company. Upon execution of the master services agreement in December 2019 (the Collaboration Agreement), the Company evaluated and concluded that the series of agreements should be combined and accounted for as a single revenue contract under ASC 606.

The Yifan Collaboration Agreement has a total transaction price of $21.0 million, 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 obligation. The Company concluded the Collaboration Agreement contained a single performance obligation of research and development services provided continuously over time. The Collaboration Agreement provides for upfront and periodic payments based on project milestones. The Company concluded 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 $1.9 million and $6.7 million of collaboration revenue in the three and nine months, respectively, ended September 30, 2020, and $12.8 million of cumulative-to-date collaboration revenue. At September 30, 2020, the Company also recorded a $1.8 million contract asset in connection with the Collaboration Agreement.

DSM Value Sharing Agreement

The original December 2017 DSM 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 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 refunded and reduces the refund liability by recording additional license and royalty revenue as the Company’s estimate of the refund obligation decreases. The Company recorded $8.8 million of license and royalty revenue in the fourth quarter of 2019 related to a change in the estimated refund liability and recorded the remaining $3.8 million in the three months ended March 31, 2020 related to a change in the Company’s estimate of the refund liability.

In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K), the Company recognized the following revenues for the three and nine months ended September 30, 2020 and 2019:

	Three Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	88	$	—	$	750	$	838	$	—	$	—	$	844	$	844
Sephora	3,501		—		—		3,501		2,625		—		—		2,625
Firmenich	5,099		3,563		—		8,662		4,556		2,305		400		7,261
Givaudan	2,059		—		—		2,059		3,312		—		—		3,312
Subtotal revenue from significant revenue agreements	10,747		3,563		750		15,060		10,493		2,305		9,482		22,280
Revenue from all other customers	16,830		—		2,368		19,198		6,870		—		5,803		12,673
Total revenue from all customers	$	27,577	$	3,563	$	3,118	$	34,258	$	17,363	$	2,305	$	15,285	$	34,953
	Nine Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	193	$	3,750	$	5,019	$	8,962	$	2	$	40,302	$	3,886	$	44,190
Sephora	10,389		—		—		10,389		6,369		—		—		6,369
Firmenich	7,308		5,964		454		13,726		6,439		3,085		1,413		10,937
Givaudan	5,328		—		—		5,328		6,127		—		—		6,127
Subtotal revenue from significant revenue agreements	23,218		9,714		5,473		38,405		18,937		43,387		17,041		79,365
Revenue from all other customers	47,401		—		7,587		54,988		22,430		—		10,226		32,656
Total revenue from all customers	$	70,619	$	9,714	$	13,060	$	93,393	$	41,367	$	43,387	$	27,267	$	112,021

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 condensed consolidated balance sheets, net of the allowance for doubtful accounts. Trade receivables are recorded for the sale of goods or the performance of services 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.

Contract Balances

The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers:

(In thousands)	September 30, 2020		December 31, 2019
Accounts receivable, net	$	27,365	$	16,322
Accounts receivable - related party, net	$	419	$	3,868
Contract assets	$	2,082	$	8,485
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Contract liabilities	$	4,430	$	1,353
Contract liabilities, noncurrent(1)	$	111	$	1,449

(1)As of September 30, 2020 and December 31, 2019, contract liabilities, noncurrent is presented in Other noncurrent liabilities in the condensed consolidated balance sheets.

During the three months ended September 30, 2020, the collaboration partner in the Cannabinoid Agreement filed certain litigation claims and, among other things, alleging breach of contract. As a result, the Company concluded that realization and recoverability of an $8.3 million contract asset recorded in connection with the Cannabinoid Agreement was no longer probable. The Company recorded an $8.3 million credit loss reserve against this contract asset during the three months ended September 30, 2020.

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 September 30, 2020.

(In thousands)	As of September 30, 2020
Remaining 2020	$	1,928
2021	5,052
2022	1,630
2023 and thereafter	571
Total from all customers	$	9,181

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, approximately $302.1 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

XML

Related Party Transactions

9 Months Ended

Sep. 30, 2020

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

Related Party Debt

See Note 4, "Debt," for details of these related party debt transactions during the nine months ended September 30, 2020:

•Debt equitization – Foris

•$5 million unsecured loan - Foris

•2014 Rule 144A Note exchange, extensions and conversion – Total

•LSA Amendment - Foris

Related party debt was as follows:

	September 30, 2020								December 31, 2019
In thousands	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Foris notes	$	55,041	$	—	$	8,426	$	63,467	$	115,351	$	(9,516)	$	—	$	105,835
DSM notes	33,000		(3,007)		—		29,993		33,000		(4,621)		—		28,379
Naxyris note	23,914		(575)		—		23,339		24,437		(822)		—		23,615
Total 2014 Rule 144A convertible note	—		—		—		—		10,178		—		—		10,178
	$	111,955	$	(3,582)	$	8,426	$	116,799	$	182,966	$	(14,959)	$	—	$	168,007

Related Party Equity

See Note 6, "Stockholders' Deficit," for details of these related party equity transactions during the nine months ended September 30, 2020:

•Foris warrant exercises for cash

•Foris warrant exercise, common stock purchase and debt equitization

•January 2020 private placement, in which Foris purchased 5,226,481 shares of common stock

•June 2020 private placement, in which Foris and affiliated entities purchased 30,000 shares of Series E convertible preferred stock, which automatically converted into 9,999,999 shares of common stock in August 2020 after stockholders approved the conversion of the Series E convertible preferred stock and corresponding issuance of underlying common shares

•June 2020 private placement, in which Vivo Capital LLC and affiliated entities purchased 3,689,225 shares of common stock and 8,932.32 shares of Series E convertible preferred stock, which automatically converted into 2,977,442 shares of common stock in August 2020 after stockholders approved the conversion of the Series E convertible preferred stock and corresponding issuance of underlying common shares

Related Party Accounts Receivable, Unbilled Receivables and Accounts Payable

Related party accounts receivable, unbilled receivables and accounts payable were as follows:

(In thousands)	September 30, 2020		December 31, 2019
Accounts receivable - related party	$	419	$	3,868
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Accounts payable	$	5,789	$	13,957

XML

Stock-based Compensation

9 Months Ended

Sep. 30, 2020

Share-based Payment Arrangement [Abstract]

Stock-based Compensation

Stock-based Compensation

The Company’s stock option activity and related information for the nine months ended September 30, 2020 was as follows:

	Quantity of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years	Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Granted	1,258,298	$	3.76
Exercised	(5,227)	$	2.99
Forfeited or expired	(301,787)	$	39.38
Outstanding - September 30, 2020	6,571,703	$	7.69	7.8	$	50
Vested or expected to vest after September 30, 2020	6,024,158	$	7.96	7.8	$	46
Exercisable at September 30, 2020	1,440,934	$	18.26	6.3	$	4

The Company’s restricted stock units (RSUs) activity and related information for the nine months ended September 30, 2020 was as follows:

	Quantity of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Awarded	4,333,999	$	3.74
Released	(1,830,077)	$	4.88
Forfeited	(563,943)	$	4.35
Outstanding - September 30, 2020	7,722,630	$	4.19	1.6
Vested or expected to vest after September 30, 2020	7,060,040	$	4.21	1.6

Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and nine months ended September 30, 2020 and 2019 was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Research and development	$	928	$	663	$	2,774	$	2,002
Sales, general and administrative	2,492		2,571		7,081		8,058
Total stock-based compensation expense	$	3,420	$	3,234	$	9,855	$	10,060

As of September 30, 2020, there was unrecognized compensation expense of $33.6 million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of 2.6 years.

Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan

In February 2020, 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 (Evergreen Shares). This increase is equal to approximately 5.0% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020. These shares in connection with the Purchase Plan represented an automatic annual increase in the number of shares reserved for issuance under the Purchase Plan of 588,713 shares. This increase is equal to approximately 0.5% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020.

In May 2020, the Company’s stockholders approved the Company’s 2020 Equity Incentive Plan (the New Plan) to replace the Equity Plan that expired in June 2020. The shares available for grant and issuance under the New Plan represent 9,896,751 shares of common stock previously reserved but unissued under the Equity Plan, including the Evergreen Shares. No additional stock awards will be granted under the Equity Plan, and, (a) shares that are subject to stock options or other awards granted under the Equity Plan that cease to be subject to such stock options or other awards by forfeiture or otherwise, (b) shares issued under the Equity Plan pursuant to the exercise of stock options that are forfeited, (c) shares issued under the Equity Plan that are repurchased by the Company at the original issue price and (d) shares that are subject to stock options or other awards under the Equity Plan that are used to pay the exercise price of an option or withheld to satisfy the tax withholding obligations related to any award will be available for future grant and issuance under the New Plan.

XML

Subsequent Events	9 Months Ended
	Sep. 30, 2020
Subsequent Events [Abstract]
Subsequent Events	Subsequent EventsThe Company has evaluated subsequent events through the November 6, 2020 issuance of these condensed consolidated financial statements. No subsequent events have occurred that require disclosure.

XML

Basis of Presentation and Summary of Significant Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of accounting

The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the accompanying interim condensed consolidated financial statements do not include all the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Accounting Standards or Updates Recently Adopted and Recent Accounting Standards or Updates Not Yet Effective

Accounting Standards or Updates Recently Adopted

In the nine months ended September 30, 2020, the Company adopted these accounting standards or updates:

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. ASU 2018-13 became effective in the first quarter of fiscal 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements.

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. ASU 2018-18 became effective in the first quarter of fiscal year 2020 retrospectively. The adoption of this standard did not have any impact on the Company’s condensed consolidated financial statements.

Accounting Standards or Updates Not Yet Adopted

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 is effective for the Company in the first quarter of 2023. The Company is currently evaluating the impact this standard will have on its condensed consolidated financial statements.

Accounting for Income Taxes In December 2019, the FASB issued ASU 2019-12, “Simplifying the Accounting for Income Taxes” (“ASU 2019-12”). The amendments in ASU 2019-12 simplify the accounting for income taxes by removing certain exceptions to the general principles in ASC Topic 740, Income Taxes. The amendments also improve consistent application of and simplify U.S. GAAP for other areas of ASC Topic 740 by clarifying and amending existing guidance. ASU 2019-12 will be effective for the Company commencing in the first quarter of fiscal year 2021. The transition requirements are dependent upon each amendment within this update and will be applied either prospectively or retrospectively. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Convertible Debt, and Derivatives and Hedging On August 5, 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, to improve financial reporting associated with accounting for convertible instruments and contracts in an entity’s own equity. ASU 2020-06 is effective for the

Company in the first quarter of 2022. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Use of Estimates and Judgements

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 condensed consolidated 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 condensed consolidated financial statements.

XML

Balance Sheet Details (Tables)

9 Months Ended

Sep. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Allowance for Doubtful Accounts

Allowance for Doubtful Accounts

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Period
Nine months ended September 30, 2020	$	45	$	57	$	—	$	102
Year ended December 31, 2019	$	642	$	110	$	(707)	$	45

Inventories

Inventories

(In thousands)	September 30, 2020		December 31, 2019
Raw materials	$	7,136	$	3,255
Work-in-process	12,083		7,204
Finished goods	17,993		17,311
Inventories	$	37,212	$	27,770

Deferred Cost of Products Sold

Deferred cost of products sold - related party

(In thousands)	September 30, 2020		December 31, 2019
Deferred cost of products sold - related party	$	9,454	$	3,677
Deferred cost of products sold, noncurrent - related party	11,858		12,815
Total	$	21,312	$	16,492

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets

(In thousands)	September 30, 2020		December 31, 2019
Prepayments, advances and deposits	$	6,117	$	4,726
Non-inventory production supplies	3,746		5,376
Recoverable taxes from Brazilian government entities	1,978		—
Other	3,053		2,648
Total prepaid expenses and other current assets	$	14,894	$	12,750

Property, Plant and Equipment, Net

Property, Plant and Equipment, Net

(In thousands)	September 30, 2020		December 31, 2019
Machinery and equipment	$	48,893	$	48,041
Leasehold improvements	43,198		41,478
Computers and software	10,589		9,822
Furniture and office equipment, vehicles and land	3,485		3,510
Construction in progress	7,369		9,752
	113,534		112,603
Less: accumulated depreciation and amortization	(83,743)		(83,673)
Property, plant and equipment, net	$	29,791	$	28,930

Schedule Of Depreciation and Amortization

During the three and nine months ended September 30, 2020 and 2019, depreciation and amortization expense was as follows:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Depreciation and amortization expense	$	1,905	$	969	$	5,300	$	2,691

Lease, Cost

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

	Nine Months Ended September 30,
	2020	2019
Cash paid for operating lease liabilities, in thousands	$5,759	$15,908
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$—	$32,074
Weighted-average remaining lease term	2.7	2.6
Weighted-average discount rate	18.0%	17.5%

(1) 2019 amount includes $29.7 million for operating leases existing on January 1, 2019 and $2.4 million for operating leases that commenced during the nine months ended September 30, 2019.

Lessee, Lease Liability, Maturity

Maturities of lease liabilities as of September 30, 2020 were as follows:

Years ending December 31: (In thousands)	Financing Leases		Operating Leases		Total Leases
2020 (remaining three months)	$	1,086	$	1,960	$	3,046
2021	4,568		7,480		12,048
2022	—		7,657		7,657
2023	—		3,322		3,322
2024	—		151		151
Total lease payments	5,654		20,570		26,224
Less: amount representing interest	(601)		(4,410)		(5,011)
Total lease liability	$	5,053	$	16,160	$	21,213
Current lease liability	$	3,882	$	5,051	$	8,933
Noncurrent lease liability	1,171		11,109		12,280
Total lease liability	$	5,053	$	16,160	$	21,213

Other Assets

Other Assets

(In thousands)	September 30, 2020		December 31, 2019
Equity-method investment	$	4,054	$	4,734
Deposits	126		295
Contingent consideration	—		3,303
Other	1,179		1,373
Total other assets	$	5,359	$	9,705

Accrued and Other Current Liabilities

Accrued and Other Current Liabilities

(In thousands)	September 30, 2020		December 31, 2019
Accrued interest	$	8,116	$	8,209
Payroll and related expenses	7,063		7,296
Contract termination fees	4,315		5,347
Asset retirement obligation	2,603		3,184
Professional services	1,804		2,968
Ginkgo partnership payments	951		4,319
Tax-related liabilities	550		1,685
Other	3,028		3,647
Total accrued and other current liabilities	$	28,430	$	36,655

Other Liabilities

Other noncurrent liabilities

(In thousands)	September 30, 2020		December 31, 2019
Liability for unrecognized tax benefit	$	7,440	$	7,204
Liability in connection with acquisition of equity-method investment	6,354		5,249
Ginkgo partnership payments, net of current portion	7,098		4,492
Contract liabilities, net of current portion	111		1,449
Refund liability(1)	—		3,750
Other	993		880
Total other noncurrent liabilities	$	21,996	$	23,024

(1) In April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" in Part II, Item 8 of the 2019 Form 10-K for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in $12.5 million of prepaid variable consideration to the Company. The $12.5 million was recorded as a refund liability. During the three months ended March 31, 2020, the Company concluded that it would not be required to return any portion of the remaining refund liability to DSM, and recorded $3.8 million of royalty revenue related to this change in estimate and reduction of the refund liability.

XML

Fair Value Measurement (Tables)

9 Months Ended

Sep. 30, 2020

Fair Value Disclosures [Abstract]

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis

The following tables summarize liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	September 30, 2020								December 31, 2019
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Foris Convertible Note (LSA Amendment)	$	—	$	—	$	58,467	$	58,467	$	—	$	—	$	—	$	—
Senior Convertible Notes	—		—		25,349		25,349		—		—		50,624		50,624
Embedded derivatives bifurcated from debt instruments	—		—		597		597		—		—		2,832		2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		3,237		3,237		—		—		6,971		6,971
Total liabilities measured and recorded at fair value	$	—	$	—	$	87,650	$	87,650	$	—	$	—	$	60,427	$	60,427

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation

In thousands
Fair value at December 31, 2019	$	50,624
Less: principal paid	(35,980)
Loss from change in fair value	10,705
Fair value at September 30, 2020	$	25,349

Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation

(In thousands)	Derivative Liability
Balance at December 31, 2019	$	9,803
Fair value of derivative liabilities issued during the period	8,751
Change in fair value of derivative instruments	6,498
Derecognition on settlement or extinguishment	(21,218)
Balance at September 30, 2020	$	3,834

Fair Value Measurement Inputs and Valuation Techniques

Input assumptions for these freestanding instruments are as follows:

	Range for the Period
Input assumptions for liability classified warrants:	September 30, 2020		December 31, 2019
Fair value of common stock on issue date	$2.56 – $4.27		$3.09 – $4.76
Exercise price of warrants	$2.87 – $2.87		$3.87 – $3.90
Expected volatility	117% – 117%		94% – 105%
Risk-free interest rate	0.13% – 0.17%		1.58% – 1.67%
Expected term in years	1.75 – 2.26		1.51 – 2.00
Dividend yield	0.0	%	0.0 %

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

	September 30, 2020	December 31, 2019
Risk-free interest rate	0.09% - 0.17%	1.6% - 1.7%
Risk-adjusted discount yield	25.0% - 26.0%	20.0% - 27.0%
Probability of change in control	5.0%	5.0%
Credit spread	24.7% - 36.8%	18.4% - 25.4%
Estimated conversion dates	Not applicable	2022 - 2023

XML

Debt (Tables)

9 Months Ended

Sep. 30, 2020

Debt Disclosure [Abstract]

Schedule of Debt

Net carrying amounts of debt are as follows:

	September 30, 2020								December 31, 2019
(In thousands)	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Convertible notes payable
Senior convertible notes	$	30,020	$	—	$	(4,671)	$	25,349	$	66,000	$	—	$	(15,376)	$	50,624
	30,020		—		(4,671)		25,349		66,000		—		(15,376)		50,624
Related party convertible notes payable
Foris convertible note	50,041		—		8,426		58,467		—		—		—		—
2014 Rule 144A convertible notes	—		—		—		—		10,178		—		—		10,178
	50,041		—		8,426		58,467		10,178		—		—		10,178
Loans payable and credit facilities
Schottenfeld notes	12,500		(269)		—		12,231		20,350		(1,315)		—		19,035
Nikko notes	7,868		(794)		—		7,074		14,318		(901)		—		13,417
Ginkgo note	12,000		—		—		12,000		12,000		(3,139)		—		8,861
Other loans payable	953		—		—		953		1,828		—		—		1,828
	33,321		(1,063)		—		32,258		48,496		(5,355)		—		43,141
Related party loans payable
Foris notes	5,000		—		—		5,000		115,351		(9,516)		—		105,835
DSM notes	33,000		(3,007)		—		29,993		33,000		(4,621)		—		28,379
Naxyris note	23,914		(575)		—		23,339		24,437		(822)		—		23,615
	61,914		(3,582)		—		58,332		172,788		(14,959)		—		157,829
Total debt	$	175,296	$	(4,645)	$	3,755	174,406		$	297,462	$	(20,314)	$	(15,376)	261,772
Less: current portion							(31,431)								(63,805)
Long-term debt, net of current portion							$	142,975							$	197,967

Schedule of Long-term Debt Instruments

Future minimum payments under the Company's debt agreements as of September 30, 2020 are as follows:

(In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020 (remaining three months)	$	375	$	5,945	$	—	$	1,547	$	7,867
2021	33,898		3,902		—		31,823		69,623
2022	—		14,768		59,578		40,939		115,285
2023	—		12,899		—		—		12,899
2024	—		398		—		—		398
Thereafter	—		1,870		—		—		1,870
Total future minimum payments	34,273		39,782		59,578		74,309		207,942
Less: amount representing interest	(4,253)		(6,460)		(9,537)		(12,396)		(32,646)
Present value of minimum debt payments	30,020		33,322		50,041		61,913		175,296
Less: current portion of debt principal	(30,020)		(5,236)		—		—		(35,256)
Noncurrent portion of debt principal	$	—	$	28,086	$	50,041	$	61,913	$	140,040

XML

Stockholders' Deficit (Tables)

9 Months Ended

Sep. 30, 2020

Equity [Abstract]

Schedule of Stockholders' Equity Note, Warrants or Rights

The following table summarizes warrants activity for the nine months ended September 30, 2020:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2019	Additional Warrants Issued	Exercises	Expired	Exercise Price per Share of Warrants Exercised		Number Outstanding as of September 30, 2020	Exercise Price per Share as of September 30, 2020
High Trail/Silverback warrants	2020	January 14, 2022	—	3,000,000	—	—	$	—	3,000,000	$2.87/$3.25
2020 PIPE right shares	2020	February 4, 2021	—	8,710,802	(5,226,481)	—	$	2.87	3,484,321	$	2.87
January 2020 warrant exercise right shares	2020	January 31, 2021 and January 31, 2022	—	9,939,159	—	—	$	—	9,939,159	$	2.87
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)	—	$	2.87	—	$	—
August 2019 Foris warrant	2019	August 28, 2021	4,871,795	—	(4,871,795)	—	$	2.87	—	$	—
April 2019 PIPE warrants	2019	April 26, 2021, April 29, 2021 and May 3, 2021	8,084,770	—	(4,712,781)	—	$	2.87	3,371,989	$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	$	2.87
Naxyris LSA warrants	2019	August 14, 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 14, 2021 and January 31, 2022	1,744,241	—	(784,016)	—	$	2.87	960,225	$	2.87
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	—	(4,877,386)	(7,219,778)	$	2.87	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,078,156	—	—	—	$	—	6,078,156	$	2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	—	3,968,116	$	2.87
May 2017 dilution warrants	2017	July 10, 2022	3,085,893	—	—	—	$	—	3,085,893	$	—
August 2017 dilution warrants	2017	May 23, 2023	3,028,983	—	—	—	$	—	3,028,983	$	—
February 2016 related party private placement	2016	February 12, 2021	171,429	—	(152,381)	—	$	0.15	19,048	$	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	72,650	—	(72,650)	—	$	0.15	—	$	—
July 2015 related party debt exchange	2015	July 29, 2025	58,690	—	—	—	$	—	58,690	$	0.15
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$	160.05
			65,755,629	21,649,961	(30,694,457)	(7,219,778)			49,491,355

XML

Loss Per Share (Tables)

9 Months Ended

Sep. 30, 2020

Earnings Per Share [Abstract]

Schedule of Earnings Per Share, Basic and Diluted

The following table presents the calculation of basic and diluted loss per share:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Numerator:
Net loss attributable to Amyris, Inc.	$	(23,156)	$	(59,562)	$	(221,422)	$	(163,893)
Less: deemed dividend to preferred stockholder on issuance and modification of common stock warrants	—		—		—		(34,964)
Less: deemed dividend to preferred stockholders upon conversion of Series E preferred stock	(67,151)		—		(67,151)		—
Add: losses allocated to participating securities	6,832		1,655		15,369		6,233
Net loss attributable to Amyris, Inc. common stockholders, basic	$	(83,475)	$	(57,907)	$	(273,204)	$	(192,624)
Adjustment to earnings allocated to participating securities	744		—		120		—
Interest on convertible debt	1,081		—		317		—
Gain from change in fair value of debt	(17,221)		—		(5,945)		—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(98,871)	$	(57,907)	$	(278,712)	$	(192,624)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic	227,267,553		103,449,612		189,192,973		91,344,150
Basic loss per share	$	(0.37)	$	(0.56)	$	(1.44)	$	(2.11)
Weighted-average shares of common stock outstanding	227,267,553		103,449,612		189,192,973		91,344,150
Effect of dilutive convertible debt	15,464,681		—		2,313,526		—
Weighted-average shares of common stock equivalents used in computing loss per share of common stock, diluted	242,732,234		103,449,612		191,506,499		91,344,150
Diluted loss per share	$	(0.41)	$	(0.56)	$	(1.46)	$	(2.11)

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 loss per share of common stock because including them would have been antidilutive:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2020	2019	2020	2019
Period-end common stock warrants	43,298,741	52,612,330	43,298,741	52,612,330
Convertible promissory notes(1)	—	14,259,214	8,574,399	14,259,214
Period-end stock options to purchase common stock	6,571,703	5,398,834	6,571,703	5,398,834
Period-end restricted stock units	7,722,630	4,543,190	7,722,630	4,543,190
Period-end preferred stock	1,943,661	2,955,732	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted loss per share	59,536,735	79,769,300	68,111,134	79,769,300

______________

(1)    The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. 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.

XML

Revenue Recognition and Contract Assets and Liabilities (Tables)

9 Months Ended

Sep. 30, 2020

Revenue from Contract with Customer [Abstract]

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	20,759	$	—	$	263	$	21,022	$	9,927	$	—	$	9,114	$	19,041
Europe	3,752		3,563		919		8,234		2,609		2,305		1,354		6,268
Asia	1,542		—		1,936		3,478		2,398		—		4,789		7,187
Brazil	1,298		—		—		1,298		2,272		—		28		2,300
Other	226		—		—		226		157		—		—		157
	$	27,577	$	3,563	$	3,118	$	34,258	$	17,363	$	2,305	$	15,285	$	34,953
	Nine Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	49,568	$	—	$	263	$	49,831	$	22,806	$	—	$	16,015	$	38,821
Europe	10,100		9,714		6,073		25,887		7,565		43,387		6,180		57,132
Asia	7,901		—		6,724		14,625		8,015		—		5,038		13,053
Brazil	2,546		—		—		2,546		2,787		—		34		2,821
Other	504		—		—		504		194		—		—		194
	$	70,619	$	9,714	$	13,060	$	93,393	$	41,367	$	43,387	$	27,267	$	112,021

Revenue in Connection with Significant Revenue Agreement

In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K), the Company recognized the following revenues for the three and nine months ended September 30, 2020 and 2019:

	Three Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	88	$	—	$	750	$	838	$	—	$	—	$	844	$	844
Sephora	3,501		—		—		3,501		2,625		—		—		2,625
Firmenich	5,099		3,563		—		8,662		4,556		2,305		400		7,261
Givaudan	2,059		—		—		2,059		3,312		—		—		3,312
Subtotal revenue from significant revenue agreements	10,747		3,563		750		15,060		10,493		2,305		9,482		22,280
Revenue from all other customers	16,830		—		2,368		19,198		6,870		—		5,803		12,673
Total revenue from all customers	$	27,577	$	3,563	$	3,118	$	34,258	$	17,363	$	2,305	$	15,285	$	34,953
	Nine Months Ended September 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	193	$	3,750	$	5,019	$	8,962	$	2	$	40,302	$	3,886	$	44,190
Sephora	10,389		—		—		10,389		6,369		—		—		6,369
Firmenich	7,308		5,964		454		13,726		6,439		3,085		1,413		10,937
Givaudan	5,328		—		—		5,328		6,127		—		—		6,127
Subtotal revenue from significant revenue agreements	23,218		9,714		5,473		38,405		18,937		43,387		17,041		79,365
Revenue from all other customers	47,401		—		7,587		54,988		22,430		—		10,226		32,656
Total revenue from all customers	$	70,619	$	9,714	$	13,060	$	93,393	$	41,367	$	43,387	$	27,267	$	112,021

Contract with Customer, Asset and Liability

The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers:

(In thousands)	September 30, 2020		December 31, 2019
Accounts receivable, net	$	27,365	$	16,322
Accounts receivable - related party, net	$	419	$	3,868
Contract assets	$	2,082	$	8,485
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Contract liabilities	$	4,430	$	1,353
Contract liabilities, noncurrent(1)	$	111	$	1,449

(1)As of September 30, 2020 and December 31, 2019, contract liabilities, noncurrent is presented in Other noncurrent liabilities in the condensed 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 September 30, 2020.

(In thousands)	As of September 30, 2020
Remaining 2020	$	1,928
2021	5,052
2022	1,630
2023 and thereafter	571
Total from all customers	$	9,181

XML

Related Party Transactions (Tables)

9 Months Ended

Sep. 30, 2020

Related Party Transactions [Abstract]

Schedule of Related Party Debt

Related party debt was as follows:

	September 30, 2020								December 31, 2019
In thousands	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Foris notes	$	55,041	$	—	$	8,426	$	63,467	$	115,351	$	(9,516)	$	—	$	105,835
DSM notes	33,000		(3,007)		—		29,993		33,000		(4,621)		—		28,379
Naxyris note	23,914		(575)		—		23,339		24,437		(822)		—		23,615
Total 2014 Rule 144A convertible note	—		—		—		—		10,178		—		—		10,178
	$	111,955	$	(3,582)	$	8,426	$	116,799	$	182,966	$	(14,959)	$	—	$	168,007

Schedule of Related Party Accounts Receivables

Related party accounts receivable, unbilled receivables and accounts payable were as follows:

(In thousands)	September 30, 2020		December 31, 2019
Accounts receivable - related party	$	419	$	3,868
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Accounts payable	$	5,789	$	13,957

XML

Stock-based Compensation (Tables)

9 Months Ended

Sep. 30, 2020

Share-based Payment Arrangement [Abstract]

Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity

The Company’s stock option activity and related information for the nine months ended September 30, 2020 was as follows:

	Quantity of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years	Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Granted	1,258,298	$	3.76
Exercised	(5,227)	$	2.99
Forfeited or expired	(301,787)	$	39.38
Outstanding - September 30, 2020	6,571,703	$	7.69	7.8	$	50
Vested or expected to vest after September 30, 2020	6,024,158	$	7.96	7.8	$	46
Exercisable at September 30, 2020	1,440,934	$	18.26	6.3	$	4

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity

The Company’s restricted stock units (RSUs) activity and related information for the nine months ended September 30, 2020 was as follows:

	Quantity of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Awarded	4,333,999	$	3.74
Released	(1,830,077)	$	4.88
Forfeited	(563,943)	$	4.35
Outstanding - September 30, 2020	7,722,630	$	4.19	1.6
Vested or expected to vest after September 30, 2020	7,060,040	$	4.21	1.6

Share-based Payment Arrangement, Expensed and Capitalized, Amount

Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and nine months ended September 30, 2020 and 2019 was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2020		2019		2020		2019
Research and development	$	928	$	663	$	2,774	$	2,002
Sales, general and administrative	2,492		2,571		7,081		8,058
Total stock-based compensation expense	$	3,420	$	3,234	$	9,855	$	10,060

XML

Basis of Presentation and Summary of Significant Accounting Policies (Details) - USD ($)						9 Months Ended
	Aug. 10, 2020	Jun. 02, 2020	Jun. 01, 2020	Mar. 11, 2020	Jan. 31, 2020	Sep. 30, 2020	Sep. 30, 2019	May 07, 2020	Dec. 31, 2019
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Working capital						$ 27,700,000			$ (87,500,000)
Accumulated deficit						1,977,075,000			1,755,653,000
Principal						175,296,000			297,462,000
Carrying value current long term debt						36,200,000
Repayments of debt			$ 37,100,000
Proceeds from issuance or sale of equity			190,000,000	$ 15,000,000.0	$ 28,300,000
Payment of accrued interest			6,100,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest						27,650,000	$ 42,479,000
Cash and cash equivalents						38,280,000	$ 1,632,000		$ 270,000
Paycheck Protection Plan Loan | Senior Notes
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, face amount								$ 10,000,000
Foris LSA
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Repayments of debt			$ 200,000,000			$ 200,000,000
Foris LSA | Senior Notes
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)								$ 3.00
Rule 144A Convertible Note | Senior Notes
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Issuance of common stock and warrants upon conversion of debt principal and accrued interest		$ 9,300,000
Induced conversion of convertible debt expense		$ 9,100,000
Second Amendment to Ginkgo Note and Partnership Agreement | Debt Instrument, Redemption, Period One
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, periodic payment	$ 2,100,000
Second Amendment to Ginkgo Note and Partnership Agreement | Debt Instrument, Redemption, Period Two
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, periodic payment	$ 9,800,000

XML

Balance Sheet Details - Allowance for Doubtful Accounts (Details) - USD ($) $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Balance at Beginning of Year	$ 45	$ 642
Provisions	57	110
Write-offs, Net	0	(707)
Accounts Receivable, Allowance for Credit Loss, Current	$ 102	$ 45

XML

Balance Sheet Details - Inventories (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials	$ 7,136	$ 3,255
Work-in-process	12,083	7,204
Finished goods	17,993	17,311
Inventories	$ 37,212	$ 27,770

XML

Balance Sheet Details - Deferred Cost of Products Sold - Related Party (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Deferred cost of products sold - related party	$ 9,454	$ 3,677
Deferred cost of products sold, noncurrent - related party	11,858	12,815
Total	$ 21,312	$ 16,492

XML

Balance Sheet Details - Additional Information (Details) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended		17 Months Ended	23 Months Ended
	Jan. 01, 2019	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Mar. 31, 2020	Sep. 30, 2020	Dec. 31, 2019	Apr. 30, 2019
Property, Plant and Equipment [Line Items]
Deferred cost of products sold, related party		$ 21,312		$ 21,312			$ 21,312	$ 16,492
Supply agreement term (years)				5 years
Deferred cost of products sold, amortization		700		$ 2,000			3,000
Right-of-use assets under operating leases		10,904		10,904			10,904	13,203
Operating lease liability		16,160		16,160			16,160	19,700
Operating lease expense		1,500	$ 5,900	4,600	$ 14,100
Lease, cost		0	$ 900	0	5,200
Acquisition of right-of-use assets under operating leases	$ 29,700			0	$ 2,361
Finance lease, right-of-use asset amortization		(3,900)		(3,900)			(3,900)	$ (1,700)
Proceeds from divestiture of interest in consolidated subsidiaries				3,300
Licenses and Royalties
Property, Plant and Equipment [Line Items]
Increase (decrease) in revenue				3,800
DSM International B.V.
Property, Plant and Equipment [Line Items]
Payments of reservation capacity fees						$ 17,400
Deferred cost of products sold, related party		$ 6,900		$ 6,900			$ 6,900
Minimum
Property, Plant and Equipment [Line Items]
Operating lease remaining lease term (years)		1 year		1 year			1 year
Operating lease renewal term (years)		1 year		1 year			1 year
Maximum
Property, Plant and Equipment [Line Items]
Operating lease remaining lease term (years)		5 years		5 years			5 years
Operating lease renewal term (years)		5 years		5 years			5 years
DSM International B.V.
Property, Plant and Equipment [Line Items]
Prepaid variable consideration		$ 12,500		$ 12,500			$ 12,500		$ 12,500

XML

Balance Sheet Details - Prepaid Expenses and Other Current Assets (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Prepayments, advances and deposits	$ 6,117	$ 4,726
Non-inventory production supplies	3,746	5,376
Recoverable taxes from Brazilian government entities	1,978	0
Other	3,053	2,648
Prepaid expenses and other current assets	$ 14,894	$ 12,750

XML

Balance Sheet Details - Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	$ 113,534	$ 112,603
Less: accumulated depreciation and amortization	(83,743)	(83,673)
Property, plant and equipment, net	29,791	28,930
Machinery and equipment
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	48,893	48,041
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	43,198	41,478
Computers and software
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	10,589	9,822
Furniture and office equipment, vehicles and land
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	3,485	3,510
Construction in progress
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	$ 7,369	$ 9,752

XML

Balance Sheet Details - Depreciation and Amortization (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Depreciation and amortization expense	$ 1,905	$ 969	$ 5,300	$ 2,691

XML

Balance Sheet Details - Right-of-use Assets and Related Lease Liabilities (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Cash paid for operating lease liabilities, in thousands	$ 5,759	$ 15,908
Right-of-use assets obtained in exchange for new operating lease obligations	$ 0	$ 32,074
Weighted-average remaining lease term	2 years 8 months 12 days	2 years 7 months 6 days
Weighted-average discount rate	18.00%	17.50%

XML

Balance Sheet Details - Maturities of Financing and Operating Leases (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Finance Lease, Liability, Payment, Due [Abstract]
2020 (remaining six months), finance leases	$ 1,086
2021, finance leases	4,568
2022, financing leases	0
2023, financing leases	0
2024, financing leases	0
Total lease payments, financing leases	5,654
Less: amount representing interest	(601)
Total lease liability, financing leases	5,053
Financing lease liabilities	3,882	$ 3,465
Financing lease liabilities, net of current portion	1,171	4,166
Lessee, Operating Lease, Liability, Payment, Due [Abstract]
2020 (remaining six months), operating leases	1,960
2021, operating leases	7,480
2022, operating leases	7,657
2023, operating leases	3,322
2024, operating leases	151
Total lease payments, operating leases	20,570
Less: amount representing interest	(4,410)
Total lease liability, operating leases	16,160	19,700
Operating lease liabilities	5,051	4,625
Operating lease liabilities, net of current portion	11,109	$ 15,037
2020 (remaining six months), total leases	3,046
2021, total leases	12,048
2022, total leases	7,657
2023, total leases	3,322
2024, total leases	151
Total lease payments, total leases	26,224
Less: amount representing interest	(5,011)
Total lease liability, total leases	21,213
Lease liabilities	8,933
Lease liabilities, net of current portion	$ 12,280

XML

Balance Sheet Details - Other Assets (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Equity-method investment	$ 4,054	$ 4,734
Contingent consideration	0	3,303
Deposits	126	295
Other	1,179	1,373
Total other assets	$ 5,359	$ 9,705

XML

Balance Sheet Details - Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Accrued interest	$ 8,116	$ 8,209
Ginkgo partnership payments	951	4,319
Payroll and related expenses	7,063	7,296
Contract termination fees	4,315	5,347
Professional services	1,804	2,968
Asset retirement obligation	2,603	3,184
Tax-related liabilities	550	1,685
Other	3,028	3,647
Total accrued and other current liabilities	$ 28,430	$ 36,655

XML

Balance Sheet Details - Other Noncurrent Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Liability for unrecognized tax benefit	$ 7,440	$ 7,204
Liability in connection with acquisition of equity-method investment	6,354	5,249
Ginkgo partnership payments, net of current portion	7,098	4,492
Contract liability, net of current portion	111	1,449
Refund liability	0	3,750
Other	993	880
Other noncurrent liabilities	$ 21,996	$ 23,024

XML

Balance Sheet Details - Ginkgo partnership payments modification (Details) - USD ($) $ in Thousands		9 Months Ended
	Aug. 10, 2020	Sep. 30, 2020	Sep. 30, 2019
Debt Instrument [Line Items]
Loss upon extinguishment of debt		$ 51,954	$ 8,596
Second Amendment to Ginkgo Note and Partnership Agreement | Debt Instrument, Redemption, Period One
Debt Instrument [Line Items]
Debt instrument, periodic payment	$ 2,100
Second Amendment to Ginkgo Note and Partnership Agreement | Debt Instrument, Redemption, Period Two
Debt Instrument [Line Items]
Debt instrument, periodic payment	9,800
Second Amendment to Ginkgo Note and Partnership Agreement | Debt Instrument, Redemption, Period Three
Debt Instrument [Line Items]
Debt instrument, periodic payment	10,400
Loss upon extinguishment of debt	100
Debt instrument, payment, net present value	11,900
Other liabilities	8,100
Debt instrument, discount accreted to interest expense	$ 3,800

XML

Fair Value Measurement - Fair Value, Assets, and Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	$ 25,349	$ 24,392
Fair Value, Measurements, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	597	2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	3,237	6,971
Total liabilities measured and recorded at fair value	87,650	60,427
Fair Value, Measurements, Recurring | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	58,467	0
Fair Value, Measurements, Recurring | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	25,349	50,624
Fair Value, Measurements, Recurring | Level 1
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, Measurements, Recurring | Level 1 | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 1 | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 2
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, Measurements, Recurring | Level 2 | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 2 | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 3
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	597	2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	3,237	6,971
Total liabilities measured and recorded at fair value	87,650	60,427
Fair Value, Measurements, Recurring | Level 3 | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	58,467	0
Fair Value, Measurements, Recurring | Level 3 | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	$ 25,349	$ 50,624

XML

Fair Value Measurement - Fair Value of Debt — Foris Convertible Note (LSA Amendment) (Details)		3 Months Ended		9 Months Ended
	Jun. 01, 2020 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Dec. 31, 2019 USD ($)
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Loss upon extinguishment of debt		$ (2,606,000)	$ (2,721,000)	$ (51,954,000)	$ (8,596,000)
Extinguishment of debt, gain (loss), net of tax	$ 72,100,000
Debt instrument fair value disclosure		76,100,000		76,100,000			$ 194,800,000
Gain (loss) from change in fair value of debt		34,360,000	$ (2,055,000)	2,908,000	$ (18,629,000)
Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability		25,349,000		25,349,000			$ 50,624,000
Foris Convertible Note (LSA Amendment)
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Gain (loss) from change in fair value of debt		$ (23,100,000)		$ (13,600,000)
Foris Convertible Note (LSA Amendment) | Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability						$ 81,600,000
Foris Convertible Note (LSA Amendment) | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, convertible, conversion ratio	3.00
Loss upon extinguishment of debt	$ (22,000,000.0)
Debt instrument fair value disclosure						$ 50,000,000.0
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Measurement Input, Stock Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		2.92		2.92		4.27
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Measurement Input, Discount Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.21		0.21		0.25
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.0013		0.0013		0.0016
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.45		0.45		0.45
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Probability of Change in Control
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.05		0.05		0.05

XML

Fair Value Measurement - Fair Value of Debt — Senior Convertible Notes (Details)			3 Months Ended		9 Months Ended
	May 01, 2020 $ / shares shares	Jan. 14, 2020 USD ($) $ / shares shares	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	May 09, 2020 $ / shares	Apr. 30, 2020 $ / shares	Mar. 11, 2020 $ / shares	Jan. 31, 2020 $ / shares shares	Jan. 13, 2020 $ / shares shares	Dec. 31, 2019 USD ($)	May 10, 2019 $ / shares
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares										1,200,000	4,877,386
Exercise price per share (in dollars per share) | $ / shares									$ 2.87	$ 2.87	$ 2.87
Gain (loss) on extinguishment of debt			$ 2,606,000	$ 2,721,000	$ 51,954,000	$ 8,596,000
Debt instrument fair value disclosure			76,100,000		76,100,000							$ 194,800,000
(Gain) loss from change in fair value of debt			(34,360,000)	$ 2,055,000	(2,908,000)	$ 18,629,000
Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability			25,349,000		25,349,000							$ 50,624,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Exercise price per share (in dollars per share) | $ / shares		$ 2.87
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount		$ 66,000,000
Gain (loss) on extinguishment of debt		(4,100,000)
Senior convertible notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
(Gain) loss from change in fair value of debt			11,300,000		10,700,000
Senior convertible notes | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount		$ 51,000,000	15,000,000.0		15,000,000.0
Debt conversion, converted instrument (in shares) | shares	2,836,364	2,742,160
Exercise price per share (in dollars per share) | $ / shares							$ 5.02						$ 2.87
Debt issuance costs, gross		$ 1,000,000.0
Gain (loss) on extinguishment of debt		5,300,000
Gain (loss) on extinguishment of debt, fair value warrants		4,100,000
Gain (loss) on extinguishment of debt, cash fee		1,000,000.0
Gain (loss) on extinguishment of debt, excess fair value		200,000
Debt instrument fair value disclosure		$ 35,800,000	$ 30,000,000.0		$ 30,000,000.0
Senior convertible notes | Convertible notes payable | Measurement Input, Stock Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		2.90	2.92		2.92
Senior convertible notes | Convertible notes payable | Measurement Input, Discount Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		2.26	2.33		2.33
Senior convertible notes | Convertible notes payable | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.0159	0.0011		0.0011
Senior convertible notes | Convertible notes payable | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.45	0.45		0.45
Senior convertible notes | Convertible notes payable | Probability of Principal Repayment in Cash
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.25
Senior convertible notes | Convertible notes payable | Probability of Principal Repayment in Stock
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.75
Senior convertible notes | Convertible notes payable | Probability of Change in Control
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.05	0.05		0.05
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	431,378	2,484,321
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares		3,000,000
Exercise price per share (in dollars per share) | $ / shares	$ 2.87	$ 3.25						$ 3.25
Class of warrant or right, term		2 years

XML

Fair Value Measurement - Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation (Details) - Long-term Debt $ in Thousands	9 Months Ended
	Sep. 30, 2020 USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	$ 50,624
Less: principal paid	(35,980)
Change in fair value of derivative liabilities	10,705
Fair value, ending balance	$ 25,349

XML

Fair Value Measurement - Reconciliation for Compound Embedded Derivative Liability (Details) - Debt-related Derivative Liability - Level 3 $ in Thousands	9 Months Ended
	Sep. 30, 2020 USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	$ 9,803
Fair value of derivative liabilities issued during the period	8,751
Change in fair value of derivative liabilities	6,498
Derecognition on settlement or extinguishment	(21,218)
Fair value, ending balance	$ 3,834

XML

Fair Value Measurement - Freestanding Derivative Instruments (Details) - USD ($)						3 Months Ended				9 Months Ended
	Jun. 02, 2020	Feb. 28, 2020	Jan. 31, 2020	Jan. 14, 2020	Jan. 13, 2020	Sep. 30, 2020	Jun. 30, 2020	Mar. 31, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	May 29, 2020	May 28, 2020	May 09, 2020	May 01, 2020	Apr. 30, 2020	Apr. 06, 2020	Apr. 05, 2020	Mar. 11, 2020	Dec. 31, 2019	May 10, 2019
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,200,000		4,877,386
Loss upon extinguishment of debt						$ (2,606,000)			$ (2,721,000)	$ (51,954,000)	$ (8,596,000)
Related party, percentage ownership in company			5.00%		5.00%
Common stock, shares authorized (in shares)						350,000,000				350,000,000		350,000,000	250,000,000							250,000,000
Exercise price per share (in dollars per share)			$ 2.87		$ 2.87														$ 2.87
Issuance of common stock and warrants upon conversion of debt principal and accrued interest										$ 27,650,000	$ 42,479,000
2014 Rule 144A Convertible Note
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative, fair value of embedded derivative liability								$ 0												$ 0
Private Placement - January 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			8,710,802
Warrants and rights outstanding			$ 8,900,000
Exercise price per share (in dollars per share)			$ 2.87
Class of warrant or right, term			12 months
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Warrants and rights outstanding				$ 4,100,000
Warrants and rights outstanding, additional paid in capital				2,400,000
Warrants and rights outstanding, derivative liability				$ 1,700,000			$ 2,800,000	1,500,000
Fair value adjustment of warrants							1,300,000	200,000
Exercise price per share (in dollars per share)				$ 2.87
Warrants Issued In Connection With Foris Ventures LLC
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			5,200,000
Warrants and rights outstanding			$ 5,300,000
Warrants and rights outstanding, additional paid in capital			2,300,000
Warrants and rights outstanding, derivative liability			3,000,000.0				37,500,000	2,000,000.0
Fair value adjustment of warrants							1,800,000	1,000,000.0
Common stock, shares authorized (in shares)												350,000,000	250,000,000
Derivative liability							3,700,000
Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		1,900,000
Warrants and rights outstanding		$ 3,200,000																		$ 7,000,000.0
Warrants and rights outstanding, additional paid in capital			$ 5,200,000
Warrants and rights outstanding, derivative liability		$ 3,200,000				$ 3,200,000				3,200,000
Fair value adjustment of warrants						2,000,000.0		$ 1,800,000		100,000
Exercise price per share (in dollars per share)		$ 2.87
Class of warrant or right, term		2 years
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount				$ 66,000,000
Loss upon extinguishment of debt				4,100,000
Senior convertible notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)															$ 3.50	$ 5.00
Senior convertible notes | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount				51,000,000		$ 15,000,000.0				$ 15,000,000.0
Loss upon extinguishment of debt				$ (5,300,000)
Exercise price per share (in dollars per share)														$ 5.02							$ 2.87
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000
Exercise price per share (in dollars per share)				$ 3.25											$ 2.87	$ 3.25
Class of warrant or right, term				2 years
Foris $19 Million Note | Private Placement - January 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			8,800,000
2014 Rule 144A Convertible Note
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount	$ 9,300,000
Debt instrument, convertible, conversion price (in dollars per share)																	$ 2.87	$ 56.16
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300,000
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity (in shares)	3,246,489
2014 Rule 144A Convertible Note | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Warrants and rights outstanding, derivative liability	$ 6,500,000
2014 Rule 144A Convertible Note | Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value adjustment of warrants							$ 6,500,000

XML

Fair Value Measurement - Bifurcated Embedded Features in Debt Instruments (Details) $ in Thousands	3 Months Ended			9 Months Ended
	Sep. 30, 2020 USD ($)	Mar. 31, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Feb. 28, 2020 USD ($)	Dec. 31, 2019 USD ($) derivative
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Loss upon extinguishment of debt	$ (2,606)		$ (2,721)	$ (51,954)	$ (8,596)
Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value adjustment of warrants	2,000	$ 1,800		100
Warrants and rights outstanding, derivative liability	3,200			3,200		$ 3,200
Four Derivative Liabilities
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative, fair value of embedded derivative liability	600			600			$ 2,800
Loss upon extinguishment of debt		2,300
Embedded derivative, fair value, collective amount		$ 900
Fair value adjustment of warrants				100
Four Derivative Liabilities | Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Warrants and rights outstanding, derivative liability	$ 700			$ 700
Maximum
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative, number of instruments held | derivative							4

XML

Fair Value Measurement - Market-based Assumption and Estimates for Compound Embedded Derivative Liabilities Valuation (Details)	Sep. 30, 2020	Dec. 31, 2019
Probability of Change in Control
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.050	0.050
Expected Diviend Yield
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000	0.000
Minimum | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000013	0.0158
Risk-free interest rate	0.0009	0.016
Minimum | Risk-adjusted Yields
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.250	0.200
Minimum | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	1.17	0.94
Minimum | Credit spread
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.247	0.184
Minimum | Share Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.56	3.09
Minimum | Measurement Input, Exercise Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.87	3.87
Minimum | Measurement Input, Expected Term
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	1.75	1.51
Maximum | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000017	0.0167
Risk-free interest rate	0.0017	0.017
Maximum | Risk-adjusted Yields
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.260	0.270
Maximum | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	1.17	1.05
Maximum | Credit spread
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.368	0.254
Maximum | Share Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	4.27	4.76
Maximum | Measurement Input, Exercise Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.87	3.90
Maximum | Measurement Input, Expected Term
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.26	2.00

XML

Fair Value Measurement - Financial Assets and Liabilities (Details) - USD ($) $ in Millions	Sep. 30, 2020	Dec. 31, 2019
Fair Value Disclosures [Abstract]
Combined debt amount	$ 90.6	$ 195.8
Debt instrument fair value disclosure	$ 76.1	$ 194.8

XML

Debt - Debt Components (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended	12 Months Ended
	Mar. 31, 2020	Sep. 30, 2020	Dec. 31, 2019	Feb. 18, 2020	Jan. 31, 2020
Debt Instrument [Line Items]
Principal		$ 175,296	$ 297,462
Unaccreted debt discount		(4,645)	(20,314)
Debt change in fair value gain loss	$ 1,100	3,755	(15,376)
Net		174,406	261,772		$ 60,000
Less: current portion		(31,431)	(63,805)
Long-term debt, net of current portion		142,975	197,967
Convertible notes payable
Debt Instrument [Line Items]
Principal		30,020	66,000
Unaccreted debt discount		0	0
Debt change in fair value gain loss		(4,671)	(15,376)
Net		25,349	50,624
Convertible notes payable | Senior convertible notes
Debt Instrument [Line Items]
Principal		30,020	66,000
Unaccreted debt discount		0	0
Debt change in fair value gain loss		(4,671)	(15,376)
Net		25,349	50,624
Related party convertible notes payable
Debt Instrument [Line Items]
Principal		50,041	10,178
Unaccreted debt discount		0	0
Debt change in fair value gain loss		8,426	0
Net		58,467	10,178
Related party convertible notes payable | Foris Convertible Note (LSA Amendment)
Debt Instrument [Line Items]
Principal		50,041	0
Unaccreted debt discount		0	0
Debt change in fair value gain loss		8,426	0
Net		58,467	0
Related party convertible notes payable | 2014 Rule 144A convertible notes
Debt Instrument [Line Items]
Principal		0	10,178
Unaccreted debt discount		0	0
Debt change in fair value gain loss		0	0
Net		0	10,178
Loans payable and credit facilities
Debt Instrument [Line Items]
Principal		33,321	48,496
Unaccreted debt discount		(1,063)	(5,355)
Debt change in fair value gain loss		0	0
Net		32,258	43,141
Loans payable and credit facilities | Schottenfeld notes
Debt Instrument [Line Items]
Principal		12,500	20,350	$ 20,400
Unaccreted debt discount		(269)	(1,315)
Debt change in fair value gain loss		0	0
Net		12,231	19,035
Loans payable and credit facilities | Nikko notes
Debt Instrument [Line Items]
Principal		7,868	14,318
Unaccreted debt discount		(794)	(901)
Debt change in fair value gain loss		0	0
Net		7,074	13,417
Loans payable and credit facilities | Ginkgo note
Debt Instrument [Line Items]
Principal		12,000	12,000
Unaccreted debt discount		0	(3,139)
Debt change in fair value gain loss		0	0
Net		12,000	8,861
Loans payable and credit facilities | Other loans payable
Debt Instrument [Line Items]
Principal		953	1,828
Unaccreted debt discount		0	0
Debt change in fair value gain loss		0	0
Net		953	1,828
Related party loans payable
Debt Instrument [Line Items]
Principal		61,914	172,788
Unaccreted debt discount		(3,582)	(14,959)
Debt change in fair value gain loss		0	0
Net		58,332	157,829
Related party loans payable | Foris notes
Debt Instrument [Line Items]
Principal		5,000	115,351
Unaccreted debt discount		0	(9,516)
Debt change in fair value gain loss		0	0
Net		5,000	105,835
Related party loans payable | DSM notes
Debt Instrument [Line Items]
Principal		33,000	33,000
Unaccreted debt discount		(3,007)	(4,621)
Debt change in fair value gain loss		0	0
Net		29,993	28,379
Related party loans payable | Naxyris note
Debt Instrument [Line Items]
Principal		23,914	24,437
Unaccreted debt discount		(575)	(822)
Debt change in fair value gain loss		0	0
Net		$ 23,339	$ 23,615

XML

Debt - Exchange of Senior Convertible Notes Due 2022 (Details) - USD ($)					3 Months Ended			9 Months Ended		12 Months Ended
	May 01, 2020	Mar. 01, 2020	Feb. 18, 2020	Jan. 14, 2020	Sep. 30, 2020	Mar. 31, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Dec. 31, 2019	May 09, 2020	Apr. 30, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	May 10, 2019
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)														1,200,000	4,877,386
Exercise price per share (in dollars per share)													$ 2.87	$ 2.87	$ 2.87
Gain (loss) on extinguishment of debt					$ 2,606,000		$ 2,721,000	$ 51,954,000	$ 8,596,000
Debt change in fair value gain loss						$ 1,100,000		3,755,000		$ (15,376,000)
Principal					175,296,000			175,296,000		297,462,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument [Line Items]
Exercise price per share (in dollars per share)				$ 2.87
Convertible notes payable
Debt Instrument [Line Items]
Debt change in fair value gain loss								(4,671,000)		(15,376,000)
Principal					30,020,000			30,020,000		66,000,000
Loans payable and credit facilities
Debt Instrument [Line Items]
Debt change in fair value gain loss								0		0
Principal					33,321,000			33,321,000		48,496,000
Senior convertible notes | Convertible notes payable
Debt Instrument [Line Items]
Debt instrument, face amount				$ 51,000,000	15,000,000.0			15,000,000.0
Debt conversion, converted instrument (in shares)	2,836,364			2,742,160
Exercise price per share (in dollars per share)											$ 5.02					$ 2.87
Debt issuance costs, gross				$ 1,000,000.0
Debt conversion, original debt, amount	$ 10,000,000			10,000,000						10,000,000
Debt instrument, redemption, aggregate net cash proceeds, minimum	80,000,000			$ 80,000,000
Debt instrument, redemption price, percentage				107.00%
Debt instrument, redemption, required aggregate net cash proceeds, minimum	50,000,000		$ 50,000,000
Gain (loss) on extinguishment of debt				$ 5,300,000
Gain (loss) on extinguishment of debt, fair value warrants				4,100,000
Gain (loss) on extinguishment of debt, cash fee				1,000,000.0
Gain (loss) on extinguishment of debt, excess fair value				$ 200,000
Debt change in fair value gain loss								(4,671,000)		(15,376,000)
Principal					30,020,000			30,020,000		66,000,000
Debt instrument, amortization stock payment price (in dollars per share)		$ 3.00
Debt instrument, amortization payment, amount	$ 8,900,000	$ 10,000,000.0
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000
Class of warrant or right, term				2 years
Exercise price per share (in dollars per share)	$ 2.87			$ 3.25								$ 3.25
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	431,378			2,484,321
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Debt Instrument [Line Items]
Debt instrument, face amount				$ 66,000,000
Stock exchange ownership percentage				19.99%
Gain (loss) on extinguishment of debt				$ (4,100,000)
Schottenfeld notes | Loans payable and credit facilities
Debt Instrument [Line Items]
Debt change in fair value gain loss								0		0
Principal			$ 20,400,000		$ 12,500,000			$ 12,500,000		$ 20,350,000

XML

Debt - Amendment to Senior Convertible Notes Due 2022 (Details) - USD ($)					9 Months Ended		12 Months Ended
	Jun. 04, 2020	May 01, 2020	Feb. 18, 2020	Jan. 14, 2020	Sep. 30, 2020	Sep. 30, 2019	Dec. 31, 2019	May 09, 2020	Apr. 30, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	May 10, 2019
Debt Instrument, Redemption [Line Items]
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment					$ 10,478,000	$ 0
Class of warrant or right, outstanding (in shares)					49,491,355		65,755,629
Exercise price per share (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)											1,200,000	4,877,386
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Exercise price per share (in dollars per share)				$ 2.87
Senior convertible notes
Debt Instrument, Redemption [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)		$ 3.50							$ 5.00
Debt conversion, converted instrument, pre-delivery (in shares)				7,500,000
Senior convertible notes | Convertible notes payable
Debt Instrument, Redemption [Line Items]
Debt conversion, original debt, amount		$ 10,000,000		$ 10,000,000			$ 10,000,000
Debt instrument, redemption, aggregate net cash proceeds, minimum		80,000,000		$ 80,000,000
Amortization of debt issuance costs		16,400,000
Debt instrument, redemption, required aggregate net cash proceeds, minimum		$ 50,000,000	$ 50,000,000
Debt instrument, redemption price, percentage				107.00%
Debt conversion, converted instrument (in shares)		2,836,364		2,742,160
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	1,363,636
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500,000
Class of warrant or right, outstanding (in shares)													960,225
Exercise price per share (in dollars per share)								$ 5.02					$ 2.87
Payments of Debt Issuance Costs		$ 16,400,000
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Class of warrant or right, outstanding (in shares)		2,000,000
Exercise price per share (in dollars per share)		$ 2.87		$ 3.25					$ 3.25
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		431,378		2,484,321
Senior convertible notes | Convertible notes payable | Debt Instrument, Redemption, Period One
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		100.00%
Senior convertible notes | Convertible notes payable | Debt Instrument, Redemption, Period Two
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		105.00%
Senior convertible notes | Convertible notes payable | Debt Instrument, Redemption, Period Three
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		110.00%
Senior convertible notes | Convertible notes payable | Minimum
Debt Instrument, Redemption [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)		$ 5.00
Senior convertible notes | Convertible notes payable | Maximum
Debt Instrument, Redemption [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)		3.50
Exercise price per share (in dollars per share)													$ 5.02
Senior convertible notes | Convertible notes payable | Maximum | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Exercise price per share (in dollars per share)		$ 3.25
Senior convertible notes | Convertible notes payable | Maximum | Debt Instrument, Redemption, Period Three
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		115.00%
Senior convertible notes | Convertible notes payable | Holders [Member]
Debt Instrument, Redemption [Line Items]
Amortization of debt issuance costs		$ 5,000,000.0
Payments of Debt Issuance Costs		$ 5,000,000
Second Amendment to New Notes and the W&F Agreements | Convertible notes payable
Debt Instrument, Redemption [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	700,000
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500,000

XML

Debt - Debt Equitization - Foris Related Party (Details) - USD ($)				3 Months Ended		9 Months Ended
	Jan. 31, 2020	Jan. 13, 2020	Dec. 31, 2019	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Mar. 11, 2020
Debt Instrument [Line Items]
Issuance of common stock upon exercise of warrants (in shares)	25,326,095	4,877,386				30,694,457
Exercise price per share (in dollars per share)	$ 2.87	$ 2.87						$ 2.87
Proceeds from exercises of warrants		$ 14,000,000.0				$ 3,332,000	$ 1,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,200,000	4,877,386
Loss upon extinguishment of debt				$ (2,606,000)	$ (2,721,000)	$ (51,954,000)	$ (8,596,000)
Private Placement - January 2020 Sale Of Stock To Foris
Debt Instrument [Line Items]
Issuance of common stock upon exercise of warrants (in shares)	10,200,000
Exercise price per share (in dollars per share)	$ 2.87
Number of shares issued in sale of stock (in shares)	5,279,171
Purchase price of sale of stock	$ 15,100,000
January 2020 Warrant Exercises
Debt Instrument [Line Items]
Issuance of common stock upon exercise of warrants (in shares)	19,287,780
Exercise price per share (in dollars per share)	$ 2.84
Proceeds from exercises of warrants	$ 54,800,000
January 2020 Rights Issued To Foris
Debt Instrument [Line Items]
Exercise price per share (in dollars per share)	$ 2.87
Purchase price of sale of stock	$ 69,900,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	8,778,230
Class of warrant or right, term	12 months
Foris notes | Related party loans payable
Debt Instrument [Line Items]
Debt instrument, face amount			$ 110,000,000.0
Debt instrument, capitalized interest			5,300,000
Foris $19 Million Note | Related party loans payable
Debt Instrument [Line Items]
Debt conversion, original debt, amount			$ 19,000,000
Debt instrument, interest rate, stated percentage			12.00%
Debt instrument, reduction in principal	$ 60,000,000.0
Debt instrument, reduction in principal, interest and fees	9,900,000
Debt instrument, reduction in principal, capitalized interest	5,400,000
Loss upon extinguishment of debt	(5,700,000)
Gain (loss) on extinguishment of debt, unaccredited discount	6,100,000
Gain (loss) on extinguishment of debt, fair value derivative liability	400,000
Foris LSA | Related party loans payable
Debt Instrument [Line Items]
Debt conversion, original debt, amount			$ 91,000,000.0
Debt instrument, interest rate, stated percentage			12.50%
Loss upon extinguishment of debt	10,400,000
Gain (loss) on extinguishment of debt, unaccredited discount	3,100,000
Gain (loss) on extinguishment of debt, fair value derivative liability	1,600,000
Gain (Loss) On Extinguishment Of Debt, Fair Value Of Rights	8,900,000
Capitalized Fair Value Of Embedded Mandatory Redemption Feature	$ 700,000

XML

Debt - Amendment No. 1 to Foris LSA — Foris, Related Party (Details) - USD ($)		3 Months Ended		9 Months Ended
	Mar. 11, 2020	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Jun. 01, 2020	May 31, 2020
Debt Instrument, Redemption [Line Items]
Debt instrument, interest rate during period	12.00%
Gain (loss) from change in fair value of debt		$ 34,360,000	$ (2,055,000)	$ 2,908,000	$ (18,629,000)
Foris LSA Amendment
Debt Instrument, Redemption [Line Items]
Debt instrument, interest rate, stated percentage						6.00%	12.50%
Debt instrument, convertible, conversion price (in dollars per share)						$ 3.00
Debt instrument, face amount						$ 22,000,000.0
Debt instrument, repurchase amount						$ 72,100,000
Gain (loss) from change in fair value of debt		$ 23,100,000		$ 13,600,000

XML

Debt - Schottenfeld Forbearance Agreement (Details) - USD ($)				3 Months Ended		9 Months Ended
	Jun. 05, 2020	Jun. 01, 2020	Feb. 28, 2020	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Apr. 19, 2020	Dec. 31, 2019	Nov. 14, 2019	Sep. 10, 2019	Aug. 14, 2019
Debt Instrument [Line Items]
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, partial payment of interest			$ 150,000
Forbearance agreement, forbearance fee			$ 150,000
Forbearance agreement, class of warrant or right, exercise price of warrants or rights (in dollars per share)			$ 2.87
Loss upon extinguishment of debt				$ (2,606,000)	$ (2,721,000)	$ (51,954,000)	$ (8,596,000)
Debt, current				31,431,000		31,431,000			$ 45,313,000
Repayments of debt		$ 37,100,000
Schottenfeld September 2019 Credit Agreements
Debt Instrument [Line Items]
Debt instrument, face amount				$ 12,500,000		12,500,000						$ 12,500,000
Debt instrument, interest rate, stated percentage											12.00%
Loss upon extinguishment of debt						(5,600,000)
Gain (loss) on extinguishment of debt, fair value warrants						3,200,000
Gain (loss) on extinguishment of debt, fair value modified warrants						1,300,000
Gain (loss) on extinguishment of debt, unaccredited discount						$ 1,100,000
Debt, current								$ 20,400,000
Repayments of debt	$ 7,900,000
Schottenfeld November 2019 Credit and Security Agreement
Debt Instrument [Line Items]
Debt instrument, additional face amount										$ 7,900,000
Debt instrument, fee amount										200,000
Embedded derivative, fair value of embedded derivative liability										$ 200,000

XML

Debt - 2014 Rule 144A Note Exchange and Extension - Total, Related Party (Details) - USD ($)			9 Months Ended
	Jun. 02, 2020	Mar. 11, 2020	Sep. 30, 2020	Sep. 30, 2019	Apr. 06, 2020	Jan. 31, 2020	Jan. 13, 2020
Debt Instrument, Redemption [Line Items]
Senior notes		$ 10,200,000
Repayments of senior debt, interest portion		1,500,000
Senior notes, principal amount		9,100,000
Repayments of senior debt		$ 1,100,000
Debt instrument, interest rate during period		12.00%
Exercise price per share (in dollars per share)		$ 2.87				$ 2.87	$ 2.87
Issuance of common stock and warrants upon conversion of debt principal and accrued interest			$ 27,650,000	$ 42,479,000
2014 Rule 144A Convertible Note
Debt Instrument, Redemption [Line Items]
Debt instrument, face amount	$ 9,300,000
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity (in shares)	3,246,489
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300,000
Derivative, fair value, net	$ 6,500,000
2014 Rule 144A Convertible Note
Debt Instrument, Redemption [Line Items]
Exercise price per share (in dollars per share)					$ 2.87

XML

Debt - Ginkgo Waiver Agreement (Details) - USD ($) $ in Thousands		9 Months Ended
	Aug. 10, 2020	Sep. 30, 2020	Sep. 30, 2019	Mar. 11, 2020
Debt Instrument [Line Items]
Waiver agreement, past due interest waived				$ 6,700
Waiver agreement, past due partnership payments plus interest waived				500
Waiver agreement, monthly payment amended				500
Senior notes, past due payments deferred				$ 7,200
Loss upon extinguishment of debt		$ 51,954	$ 8,596
Convertible promissory notes | Debt Instrument, Redemption, Period Three
Debt Instrument [Line Items]
Loss upon extinguishment of debt	$ 2,500

XML

Debt - Nikko Secured Loan Agreement Amendment (Details) - USD ($)	Jun. 01, 2020	Mar. 12, 2020	Mar. 11, 2020	Apr. 03, 2020
Debt Instrument [Line Items]
Repayments of debt	$ 37,100,000
Debt instrument, interest rate during period			12.00%
Nikko Loan Agreement
Debt Instrument [Line Items]
Repayments of debt		$ 500,000
Long term debt, principal amount		$ 4,000,000.0		$ 4,000,000.0
Debt instrument, interest rate during period		8.00%
Debt instrument, covenant, accrued interest rate		2.75%
Debt instrument, covenant, first priority lien		27.20%

XML

Debt - Paycheck Protection Plan Loan (Details) - Paycheck Protection Plan Loan	May 07, 2020 USD ($)
Debt Instrument, Redemption [Line Items]
Proceeds from notes payable	$ 10,000,000
Debt instrument, interest rate, stated percentage	1.00%
Debt instrument, term	2 years

XML

Debt - Future Minimum Payments (Details) $ in Thousands	Sep. 30, 2020 USD ($)
Debt Instrument [Line Items]
2020 (remaining three months)	$ 7,867
2021	69,623
2022	115,285
2023	12,899
2024	398
Thereafter	1,870
Total future minimum payments	207,942
Less: amount representing interest	(32,646)
Present value of minimum debt payments	175,296
Less: current portion of debt principal	(35,256)
Noncurrent portion of debt principal	140,040
Convertible notes payable
Debt Instrument [Line Items]
2020 (remaining three months)	375
2021	33,898
2022	0
2023	0
2024	0
Thereafter	0
Total future minimum payments	34,273
Less: amount representing interest	(4,253)
Present value of minimum debt payments	30,020
Less: current portion of debt principal	(30,020)
Noncurrent portion of debt principal	0
Loans Payable and Credit Facilities
Debt Instrument [Line Items]
2020 (remaining three months)	5,945
2021	3,902
2022	14,768
2023	12,899
2024	398
Thereafter	1,870
Total future minimum payments	39,782
Less: amount representing interest	(6,460)
Present value of minimum debt payments	33,322
Less: current portion of debt principal	(5,236)
Noncurrent portion of debt principal	28,086
Related party convertible notes payable
Debt Instrument [Line Items]
2020 (remaining three months)	0
2021	0
2022	59,578
2023	0
2024	0
Thereafter	0
Total future minimum payments	59,578
Less: amount representing interest	(9,537)
Present value of minimum debt payments	50,041
Less: current portion of debt principal	0
Noncurrent portion of debt principal	50,041
Related Party Loans Payable and Credit Facilities
Debt Instrument [Line Items]
2020 (remaining three months)	1,547
2021	31,823
2022	40,939
2023	0
2024	0
Thereafter	0
Total future minimum payments	74,309
Less: amount representing interest	(12,396)
Present value of minimum debt payments	61,913
Less: current portion of debt principal	0
Noncurrent portion of debt principal	$ 61,913

XML

Debt - Foris $5 Million Note – Foris, Related Party (Details) - Foris $5 Million Note - Foris notes	Apr. 29, 2020 USD ($)
Debt Instrument, Redemption [Line Items]
Debt instrument, face amount	$ 5,000,000.0
Related party ownership percentage	5.00%
Debt instrument, interest rate, stated percentage	12.00%

XML

Mezzanine Equity (Details Textual) - Gates Foundation Purchase Agreement $ / shares in Units, $ in Millions	9 Months Ended
	Sep. 30, 2020 USD ($) $ / shares
Subsidiary, Sale of Stock [Line Items]
Stock price (in dollars per share) | $ / shares	$ 17.10
Compound annual return (percentage)	10.00%
Research and development obligation, remaining amount | $	$ 0.3

XML

Stockholders' Deficit - Foris Warrant Exercises for Cash (Details) - USD ($) $ / shares in Units, $ in Thousands						1 Months Ended	9 Months Ended
	Jun. 02, 2020	Jun. 01, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Jan. 31, 2020	Sep. 30, 2020	Sep. 30, 2019
Class of Warrant or Right [Line Items]
Related party, percentage ownership in company				5.00%	5.00%
Class of warrant or right, number of securities called by warrants or rights (in shares)				1,200,000	4,877,386	1,200,000
Exercise price per share (in dollars per share)			$ 2.87	$ 2.87	$ 2.87	$ 2.87
Proceeds from exercises of warrants					$ 14,000		$ 3,332	$ 1
Issuance of common stock upon exercise of warrants (in shares)				25,326,095	4,877,386		30,694,457
Proceeds from issuance or sale of equity		$ 190,000	$ 15,000	$ 28,300
Foris notes
Class of Warrant or Right [Line Items]
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)						5,226,481
Foris notes
Class of Warrant or Right [Line Items]
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)	5,226,481

XML

Stockholders' Deficit - January 2020 Warrant Amendments and Exercises, Foris Debt Equitization and Private Placement (Details) - USD ($) $ / shares in Units, $ in Thousands					9 Months Ended
	Jun. 01, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Sep. 30, 2020	Dec. 31, 2019
Class of Warrant or Right [Line Items]
Proceeds from issuance or sale of equity	$ 190,000	$ 15,000	$ 28,300
Net			60,000		$ 174,406	$ 261,772
Interest Payable			$ 9,900
Issuance of common stock upon exercise of warrants (in shares)			25,326,095	4,877,386	30,694,457
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,200,000	4,877,386
Exercise price per share (in dollars per share)		$ 2.87	$ 2.87	$ 2.87
Private Placement
Class of Warrant or Right [Line Items]
Number of shares issued in sale of stock (in shares)			13,989,973
January 2020 Rights Issued
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			18,649,961
Exercise price per share (in dollars per share)			$ 2.87
Class of warrant or right, term			12 months

XML

Stockholders' Deficit - Warrant Amendments and Exercise by Certain Holders (Details) - USD ($) $ / shares in Units, $ in Thousands			9 Months Ended
	Jan. 31, 2020	Jan. 13, 2020	Sep. 30, 2020	Sep. 30, 2019	Mar. 11, 2020
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,200,000	4,877,386
Exercise price per share (in dollars per share)	$ 2.87	$ 2.87			$ 2.87
Issuance of common stock upon exercise of warrants (in shares)	25,326,095	4,877,386	30,694,457
Proceeds from exercises of warrants		$ 14,000	$ 3,332	$ 1
January 2020 Warrant Amendments
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,160,929
Exercise price per share (in dollars per share)	$ 2.87
Issuance of common stock upon exercise of warrants (in shares)	1,160,929
Class of warrant or right, term	12 months
Proceeds from exercises of warrants	$ 3,300

XML

Stockholders' Deficit - Warrant Amendments and Exercises, Common Stock Purchase and Debt Equitization by Foris- Related Party (Details)					3 Months Ended		9 Months Ended
	May 01, 2020 USD ($) $ / shares	Jan. 31, 2020 USD ($) $ / shares shares	Jan. 14, 2020 USD ($) $ / shares shares	Jan. 13, 2020 USD ($) $ / shares shares	Jun. 30, 2020 USD ($)	Mar. 31, 2020 USD ($)	Sep. 30, 2020 USD ($) $ / shares shares	Sep. 30, 2019 USD ($)	May 09, 2020 $ / shares	Apr. 30, 2020 $ / shares	Mar. 11, 2020 $ / shares	May 10, 2019 $ / shares
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares		25,326,095		4,877,386			30,694,457
Exercise price per share (in dollars per share) | $ / shares		$ 2.87		$ 2.87							$ 2.87
Proceeds from exercises of warrants | $				$ 14,000,000.0			$ 3,332,000	$ 1,000
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares		1,200,000		4,877,386
August Foris Credit Agreement | Foris notes
Class of Warrant or Right [Line Items]
Extinguishment of debt, amount | $		$ 60,000,000
Line of credit facility, maximum borrowing capacity | $		$ 19,000,000
Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share) | $ / shares									$ 5.02			$ 2.87
Senior convertible notes | Maximum | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share) | $ / shares												$ 5.02
Private Placement - January 2020 Sale Of Stock To Foris
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares		10,200,000
Exercise price per share (in dollars per share) | $ / shares		$ 2.87
Number of shares issued in sale of stock (in shares) | shares		5,279,171
Purchase price of sale of stock | $		$ 15,100,000
January 2020 Warrant Exercises
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares		19,287,780
Exercise price per share (in dollars per share) | $ / shares		$ 2.84
Proceeds from exercises of warrants | $		$ 54,800,000
January 2020 Rights Issued To Foris
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share) | $ / shares		$ 2.87
Purchase price of sale of stock | $		$ 69,900,000
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares		8,778,230
Class of warrant or right, term		12 months
Ammended Foris Warrants
Class of Warrant or Right [Line Items]
Fair value adjustment of warrants | $							69,900,000
Warrants and rights outstanding | $							$ 8,900,000
Ammended Foris Warrants | Share Price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares							2.56
Ammended Foris Warrants | Stock Price Volatility
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input							1.12
Ammended Foris Warrants | Expected Diviend Yield
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares							0
Ammended Foris Warrants | Risk-free Interest Rate
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input							0.0145
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share) | $ / shares			$ 2.87
Fair value adjustment of warrants | $					$ 1,300,000	$ 200,000
Warrants and rights outstanding | $			$ 4,100,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share) | $ / shares	$ 2.87		$ 3.25							$ 3.25
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares			3,000,000
Class of warrant or right, term			2 years
Fair value of modification to previously issued common stock warrants | $	$ 1,100,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Maximum | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share) | $ / shares	$ 3.25

XML

Stockholders' Deficit - Increase in Authorized Common Stock (Details) - shares	Sep. 30, 2020	May 29, 2020	May 28, 2020	Dec. 31, 2019
Equity [Abstract]
Common stock, shares authorized (in shares)	350,000,000	350,000,000	250,000,000	250,000,000

XML

Stockholders' Deficit - Total Conversion Price Reduction and Subsequent Conversion into Common Stock (Details) - USD ($)		9 Months Ended
	Jun. 02, 2020	Sep. 30, 2020	Sep. 30, 2019	Apr. 06, 2020	Apr. 05, 2020	Dec. 31, 2019
Debt Conversion [Line Items]
Common stock, shares outstanding (in shares)		239,185,985				117,742,677
Issuance of common stock and warrants upon conversion of debt principal and accrued interest		$ 27,650,000	$ 42,479,000
2014 Rule 144A Convertible Note
Debt Conversion [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)				$ 2.87	$ 56.16
Debt instrument, face amount	$ 9,300,000
Common stock, shares outstanding (in shares)	3,246,489
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300,000
Derivative, fair value, net	$ 6,500,000

XML

Stockholders' Deficit - June 2020 PIPE (Details) - USD ($) $ / shares in Units, $ in Millions	Aug. 17, 2020	Jun. 05, 2020	Sep. 30, 2020	Dec. 31, 2019
Class of Stock [Line Items]
Common stock, par value (in dollars per share)			$ 0.0001	$ 0.0001
June 2020 PIPE
Class of Stock [Line Items]
Stockholders' ownership of company stock		5.00%
Number of shares issued in sale of stock (in shares)		32,614,573
Common stock, par value (in dollars per share)		$ 0.0001
Purchase price of sale of stock		$ 190
June 2020 PIPE | Preferred Stock
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)		$ 1,000
Series E Convertible Preferred Stock
Class of Stock [Line Items]
Number of shares issued in sale of stock (in shares)	34,052,084	102,156
Common stock, par value (in dollars per share)		$ 0.0001
Conversion of stock, shares converted (in shares)	102,156	34,052,070
Sale of stock, consideration received per transaction		$ 200
Series E Convertible Preferred Stock | Common Stock
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)		$ 3.00
Series E Convertible Preferred Stock | Preferred Stock
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)		$ 1,000

XML

Stockholders' Deficit - January 2020 Private Placement (Details) - USD ($)					9 Months Ended
	Jun. 01, 2020	May 01, 2020	Jan. 31, 2020	Jan. 14, 2020	Sep. 30, 2020	May 09, 2020	Apr. 30, 2020	Mar. 11, 2020	Jan. 13, 2020	May 10, 2019
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,200,000						4,877,386
Exercise price per share (in dollars per share)			$ 2.87					$ 2.87	$ 2.87
Repayments of debt	$ 37,100,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)				$ 2.87
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Class of Warrant or Right [Line Items]
Debt instrument, face amount				$ 66,000,000
Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)						$ 5.02				$ 2.87
Debt instrument, face amount				$ 51,000,000	$ 15,000,000.0
Debt conversion, converted instrument (in shares)		2,836,364		2,742,160
Repayments of debt					$ 15,200,000
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		431,378		2,484,321
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000
Exercise price per share (in dollars per share)		$ 2.87		$ 3.25			$ 3.25
Class of warrant or right, term				2 years
Private Placement - January 2020
Class of Warrant or Right [Line Items]
Number of shares issued in sale of stock (in shares)			8,710,802
Class of warrant or right, number of securities called by warrants or rights (in shares)			8,710,802
Exercise price per share (in dollars per share)			$ 2.87
Class of warrant or right, term			12 months
Purchase price of sale of stock			$ 25,000,000

XML

Stockholders' Deficit - Release of Pre-Delivery Shares and Amendment to Warrants Issued to Holders of Senior Convertible Notes Due 2022 (Details) - USD ($) $ / shares in Units, $ in Thousands				3 Months Ended		9 Months Ended
	Jun. 04, 2020	May 01, 2020	Jan. 14, 2020	Jun. 30, 2020	Mar. 31, 2020	Sep. 30, 2020	Sep. 30, 2019	May 09, 2020	Apr. 30, 2020	Apr. 06, 2020	Apr. 05, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Dec. 31, 2019	May 10, 2019
Class of Warrant or Right [Line Items]
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment						$ 10,478	$ 0
Exercise price per share (in dollars per share)												$ 2.87	$ 2.87	$ 2.87
Class of warrant or right, outstanding (in shares)						49,491,355									65,755,629
Class of warrant or right, number of securities called by warrants or rights (in shares)													1,200,000	4,877,386
Senior convertible notes
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)			7,500,000
Debt instrument, convertible, conversion price (in dollars per share)		$ 3.50							$ 5.00
Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	1,363,636
Debt conversion, converted instrument (in shares)		2,836,364	2,742,160
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500
Exercise price per share (in dollars per share)								$ 5.02								$ 2.87
Class of warrant or right, outstanding (in shares)																960,225
Return of pre-delivery shares previously issued in connection with debt agreement (in shares)	2,600,000
Senior convertible notes | Convertible notes payable | One Holder
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	700,000
Second Amendment to New Notes and the W&F Agreements | Convertible notes payable
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	700,000
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500
2014 Rule 144A Convertible Note
Class of Warrant or Right [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)										$ 2.87	$ 56.16
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 2.87
Fair value adjustment of warrants				$ 1,300	$ 200
Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)		$ 2.87	$ 3.25						$ 3.25
Class of warrant or right, outstanding (in shares)		2,000,000
Class of warrant or right, number of securities called by warrants or rights (in shares)			3,000,000
Rights Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		431,378	2,484,321

XML

Stockholders' Deficit - Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws (Details) - Preferred Stock - June 2020 PIPE - USD ($) $ / shares in Units, $ in Millions	Jun. 05, 2020	Jun. 04, 2020	Jun. 01, 2020
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)	$ 1,000
Convertible preferred stock, shares issued upon conversion (in shares)	333.33
Debt instrument, convertible, threshold percentage of stock price trigger	19.99%
Debt instrument, convertible, beneficial conversion feature	$ 67.2
Stock price (in dollars per share)		$ 4.88	$ 5.35
Debt instrument, convertible, conversion price (in dollars per share)	$ 3.00

XML

Stockholders' Deficit - Warrant Activity (Details) - $ / shares			9 Months Ended
	Jan. 31, 2020	Jan. 13, 2020	Sep. 30, 2020	Mar. 11, 2020
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			65,755,629
Additional warrants issued (in shares)			21,649,961
Exercises (in shares)	(25,326,095)	(4,877,386)	(30,694,457)
Expiration (in shares)			(7,219,778)
Number outstanding, ending balance (in shares)			49,491,355
Exercise price per share (in dollars per share)	$ 2.87	$ 2.87		$ 2.87
High Trail/Silverback warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			0
Additional warrants issued (in shares)			3,000,000
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,000,000
Exercise price per share (in dollars per share)			$ 2.87
High trail/Silverback warrants due January 14,2022
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 3.25
2020 PIPE right shares
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			0
Additional warrants issued (in shares)			8,710,802
Exercises (in shares)			(5,226,481)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			3,484,321
Exercise price per share (in dollars per share)			$ 2.87
January 2020 warrant exercise right shares
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			0
Additional warrants issued (in shares)			9,939,159
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			9,939,159
Exercise price per share (in dollars per share)			$ 2.87
Foris LSA warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,438,829
Additional warrants issued (in shares)			0
Exercises (in shares)			(3,438,829)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
November 2019 Foris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,000,000
Additional warrants issued (in shares)			0
Exercises (in shares)			(1,000,000)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
August 2019 Foris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			4,871,795
Additional warrants issued (in shares)			0
Exercises (in shares)			(4,871,795)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
April 2019 PIPE warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			8,084,770
Additional warrants issued (in shares)			0
Exercises (in shares)			(4,712,781)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			3,371,989
April 2019 PIPE warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 4.76
April 2019 PIPE warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 5.02
April 2019 Foris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			5,424,804
Additional warrants issued (in shares)			0
Exercises (in shares)			(5,424,804)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
September and November 2019 Investor Credit Agreement warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			5,233,551
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			5,233,551
Exercise price per share (in dollars per share)			$ 2.87
Naxyris LSA warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			2,000,000
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			2,000,000
Exercise price per share (in dollars per share)			$ 2.87
October 2019 Naxyris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			2,000,000
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			2,000,000
Exercise price per share (in dollars per share)			$ 3.87
May-June 2019 6% Note Exchange warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			2,181,818
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			2,181,818
May-June 2019 6% Note Exchange warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 2.87
May-June 2019 6% Note Exchange warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			5.12
April 2019 PIPE warrants due April 29, 2021 [Member]
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 4.76
May 2019 6.50% Note Exchange warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,744,241
Additional warrants issued (in shares)			0
Exercises (in shares)			(784,016)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			960,225
Exercise price per share (in dollars per share)			$ 2.87
July 2019 Wolverine warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,080,000
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			1,080,000
Exercise price per share (in dollars per share)			$ 2.87
August 2018 warrant exercise agreements
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			12,097,164
Additional warrants issued (in shares)			0
Exercises (in shares)			(4,877,386)
Expiration (in shares)			(7,219,778)
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
May 2017 cash warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			6,078,156
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			6,078,156
Exercise price per share (in dollars per share)			$ 2.87
August 2017 cash warrants
Class of Warrant or Right [Line Items]
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 warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,968,116
Exercise price per share (in dollars per share)			$ 2.87
May 2017 dilution warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,085,893
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,085,893
Exercise price per share (in dollars per share)			$ 0
August 2017 dilution warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,028,983
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,028,983
Exercise price per share (in dollars per share)			$ 0
February 2016 related party private placement
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			171,429
Additional warrants issued (in shares)			0
Exercises (in shares)			(152,381)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0.15
Number outstanding, ending balance (in shares)			19,048
Exercise price per share (in dollars per share)			$ 0.15
July 2015 related party debt exchange
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			133,334
Additional warrants issued (in shares)			0
Exercises (in shares)			(133,334)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0.15
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
July 2015 private placement
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			72,650
Additional warrants issued (in shares)			0
Exercises (in shares)			(72,650)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0.15
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
July 2015 related party debt exchange
Class of Warrant or Right [Line Items]
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 warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			58,690
Exercise price per share (in dollars per share)			$ 0.15
Other
Class of Warrant or Right [Line Items]
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 warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			1,406
Exercise price per share (in dollars per share)			$ 160.05

XML

Loss Per Share - Calculation of Basic and Diluted Net Loss Per Share of Common Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Earnings Per Share, Basic and Diluted [Abstract]
Net loss	$ (23,156)	$ (59,562)	$ (221,422)	$ (163,893)
Deemed Dividend related to Preferred Shareholder on Issuance and Modifications of Common Stock Warrants	0	0	0	(34,964)
Less: deemed dividend to preferred stockholders upon conversion of Series E preferred stock	(67,151)	0	(67,151)	0
Add: losses allocated to participating securities	6,832	1,655	15,369	6,233
Net loss attributable to Amyris, Inc. common stockholders, basic	(83,475)	(57,907)	(273,204)	(192,624)
Adjustment to earnings allocated to participating securities	744	0	120	0
Interest on convertible debt	1,081	0	317	0
Gain from change in fair value of debt	(17,221)	0	(5,945)	0
Net loss attributable to Amyris, Inc. common stockholders, diluted	$ (98,871)	$ (57,907)	$ (278,712)	$ (192,624)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic (in shares)	227,267,553	103,449,612	189,192,973	91,344,150
Loss per share attributable to common stockholders, basic and diluted (in dollars per share)	$ (0.37)	$ (0.56)	$ (1.44)	$ (2.11)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted (in shares)	242,732,234	103,449,612	191,506,499	91,344,150
Effect of dilutive convertible debt (in shares)	15,464,681	0	2,313,526	0
Diluted loss per share (in dollars per share)	$ (0.41)	$ (0.56)	$ (1.46)	$ (2.11)

XML

Loss Per Share - Antidilutive Securities Excluded From Computation of Earnings Per Share (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	59,536,735,000	79,769,300,000	68,111,134,000	79,769,300,000
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted (in shares)	242,732,234	103,449,612	191,506,499	91,344,150
Period-end common stock warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	43,298,741,000	52,612,330,000	43,298,741,000	52,612,330,000
Convertible promissory notes
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	0	14,259,214,000	8,574,399,000	14,259,214,000
Period-end stock options to purchase common stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	6,571,703,000	5,398,834,000	6,571,703,000	5,398,834,000
Period-end restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	7,722,630,000	4,543,190,000	7,722,630,000	4,543,190,000
Period-end Preferred Shares
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	1,943,661,000	2,955,732,000	1,943,661,000	2,955,732,000

XML

Revenue Recognition and Contract Assets and Liabilities - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Disaggregation of Revenue [Line Items]
Revenue	$ 34,258	$ 34,953	$ 93,393	$ 112,021
United States
Disaggregation of Revenue [Line Items]
Revenue	21,022	19,041	49,831	38,821
Europe
Disaggregation of Revenue [Line Items]
Revenue	8,234	6,268	25,887	57,132
Asia
Disaggregation of Revenue [Line Items]
Revenue	3,478	7,187	14,625	13,053
Brazil
Disaggregation of Revenue [Line Items]
Revenue	1,298	2,300	2,546	2,821
Other
Disaggregation of Revenue [Line Items]
Revenue	226	157	504	194
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	27,577	17,363	70,619	41,367
Renewable Products | United States
Disaggregation of Revenue [Line Items]
Revenue	20,759	9,927	49,568	22,806
Renewable Products | Europe
Disaggregation of Revenue [Line Items]
Revenue	3,752	2,609	10,100	7,565
Renewable Products | Asia
Disaggregation of Revenue [Line Items]
Revenue	1,542	2,398	7,901	8,015
Renewable Products | Brazil
Disaggregation of Revenue [Line Items]
Revenue	1,298	2,272	2,546	2,787
Renewable Products | Other
Disaggregation of Revenue [Line Items]
Revenue	226	157	504	194
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	3,563	2,305	9,714	43,387
Licenses and Royalties | United States
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Licenses and Royalties | Europe
Disaggregation of Revenue [Line Items]
Revenue	3,563	2,305	9,714	43,387
Licenses and Royalties | Asia
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Licenses and Royalties | Brazil
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Licenses and Royalties | Other
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	3,118	15,285	13,060	27,267
Grants and Collaborations | United States
Disaggregation of Revenue [Line Items]
Revenue	263	9,114	263	16,015
Grants and Collaborations | Europe
Disaggregation of Revenue [Line Items]
Revenue	919	1,354	6,073	6,180
Grants and Collaborations | Asia
Disaggregation of Revenue [Line Items]
Revenue	1,936	4,789	6,724	5,038
Grants and Collaborations | Brazil
Disaggregation of Revenue [Line Items]
Revenue	0	28	0	34
Grants and Collaborations | Other
Disaggregation of Revenue [Line Items]
Revenue	$ 0	$ 0	$ 0	$ 0

XML

Revenue Recognition and Contact Assets and Liabilities - Narrative (Details) - USD ($) $ in Thousands		3 Months Ended			9 Months Ended		12 Months Ended
	May 02, 2019	Sep. 30, 2020	Mar. 31, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Dec. 31, 2019	Apr. 30, 2019	Mar. 18, 2019
Disaggregation of Revenue [Line Items]
Revenue		$ 34,258		$ 34,953	$ 93,393	$ 112,021
Contract assets		2,082			2,082		$ 8,485
Cost of products sold		25,822		20,654	60,710	53,482
Interest expense		6,627		16,857	41,747	44,608
Revenue, remaining performance obligation, constrained variable consideration		302,100			302,100
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue		3,563		2,305	9,714	43,387
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue		3,118		$ 15,285	13,060	$ 27,267
DSM International B.V.
Disaggregation of Revenue [Line Items]
Contract with customer, liability		12,500			12,500			$ 12,500
Contract with customer, liability, cumulative catch-up adjustment to revenue, modification of contract			$ 3,800		37,100		$ 8,800
Yifan
Disaggregation of Revenue [Line Items]
Estimated total unconstrained transaction price		21,000			21,000
Yifan | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue		1,900			6,700
Contract assets		1,800			1,800
Revenue from contract with customer, cumulative to date					12,800
The Cannabinoid Agreement
Disaggregation of Revenue [Line Items]
Contract assets		8,300			8,300
The Cannabinoid Agreement | Lavvan
Disaggregation of Revenue [Line Items]
Agreement amount									$ 300,000
Estimated total unconstrained transaction price	$ 145,000
Revenue	$ 18,300
Variable consideration related to milestones		282,000			282,000
Contract assets		8,300			8,300
Collaborative Arrangement | DSM International B.V.
Disaggregation of Revenue [Line Items]
Estimated total unconstrained transaction price		14,100			14,100
Revenue from contract with customer, cumulative to date		$ 9,900			$ 9,900

XML

Revenue Recognition and Contract Assets and Liabilities - Revenue in Connection With Significant Revenue Agreement (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Disaggregation of Revenue [Line Items]
Revenue	$ 34,258	$ 34,953	$ 93,393	$ 112,021
Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	15,060	22,280	38,405	79,365
DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	838	844	8,962	44,190
Sephora | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	3,501	2,625	10,389	6,369
Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	8,662	7,261	13,726	10,937
Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,059	3,312	5,328	6,127
Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	19,198	12,673	54,988	32,656
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	27,577	17,363	70,619	41,367
Renewable Products | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	10,747	10,493	23,218	18,937
Renewable Products | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	88	0	193	2
Renewable Products | Sephora | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	3,501	2,625	10,389	6,369
Renewable Products | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	5,099	4,556	7,308	6,439
Renewable Products | Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,059	3,312	5,328	6,127
Renewable Products | Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	16,830	6,870	47,401	22,430
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	3,563	2,305	9,714	43,387
Licenses and Royalties | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	3,563	2,305	9,714	43,387
Licenses and Royalties | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	0	3,750	40,302
Licenses and Royalties | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	3,563	2,305	5,964	3,085
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	3,118	15,285	13,060	27,267
Grants and Collaborations | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	750	9,482	5,473	17,041
Grants and Collaborations | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	750	844	5,019	3,886
Grants and Collaborations | Sephora | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Grants and Collaborations | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	400	454	1,413
Grants and Collaborations | Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue		0		0
Grants and Collaborations | Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	$ 2,368	$ 5,803	$ 7,587	$ 10,226

XML

Revenue Recognition and Contract Assets and Liabilities - Contract Balances (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Revenue from Contract with Customer [Abstract]
Accounts receivable, net	$ 27,365	$ 16,322
Accounts receivable - related party, net	419	3,868
Contract assets	2,082	8,485
Contract assets - related party	1,203	0
Contract assets, noncurrent - related party	0	1,203
Contract liabilities	4,430	1,353
Contract liability, net of current portion	$ 111	$ 1,449

XML

Revenue Recognition and Contract Assets and Liabilities - Remaining Performance Obligations (Details) $ in Thousands	Sep. 30, 2020 USD ($)
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 9,181
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-10-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 1,928
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period	3 months
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	$ 5,052
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, 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	$ 1,630
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, 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	$ 571
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period

XML

Related Party Transactions - Related Party Debt (Details) - USD ($)	Sep. 30, 2020	Jan. 31, 2020	Dec. 31, 2019
Related Party Transaction [Line Items]
Principal	$ 175,296,000		$ 297,462,000
Change in Fair Value	25,349,000		24,392,000
Net	174,406,000	$ 60,000,000.0	261,772,000
Foris $5 Million Note | Foris notes
Related Party Transaction [Line Items]
Debt instrument, face amount	5,000,000
Related Party Debt
Related Party Transaction [Line Items]
Principal	111,955,000		182,966,000
Unaccreted Debt Discount	(3,582,000)		(14,959,000)
Change in Fair Value	8,426,000		0
Net	116,799,000		168,007,000
Foris notes | Related Party Debt | Foris notes
Related Party Transaction [Line Items]
Principal	55,041,000		115,351,000
Unaccreted Debt Discount	0		(9,516,000)
Change in Fair Value	8,426,000		0
Net	63,467,000		105,835,000
DSM International B.V. | Related Party Debt | DSM notes
Related Party Transaction [Line Items]
Principal	33,000,000		33,000,000
Unaccreted Debt Discount	(3,007,000)		(4,621,000)
Change in Fair Value	0		0
Net	29,993,000		28,379,000
Naxyris note | Related Party Debt | Naxyris note
Related Party Transaction [Line Items]
Principal	23,914,000		24,437,000
Unaccreted Debt Discount	(575,000)		(822,000)
Change in Fair Value	0		0
Net	23,339,000		23,615,000
Total | Related Party Debt | 2014 Rule 144A convertible notes
Related Party Transaction [Line Items]
Principal	0		10,178,000
Unaccreted Debt Discount	0		0
Change in Fair Value	0		0
Net	$ 0		$ 10,178,000

XML

Related Party Transactions - Additional Information (Details) - shares			1 Months Ended
	Aug. 17, 2020	Jun. 05, 2020	Aug. 31, 2020	Jun. 30, 2020	Jan. 31, 2020
Series E Convertible Preferred Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)	34,052,084	102,156
Foris notes
Related Party Transaction [Line Items]
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)					5,226,481
Foris notes | Series E Convertible Preferred Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)			9,999,999	30,000
Vivo Capital LLC | Series E Convertible Preferred Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)				8,932.32
Vivo Capital LLC | Series E Convertible Common Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)			2,977,442	3,689,225

XML

Related Party Transactions - Related Party Accounts Receivable (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Related Party Transaction [Line Items]
Due to related parties, current	$ 0	$ 18,492
DSM International B.V. | Accounts receivable - related party
Related Party Transaction [Line Items]
Accounts receivable, unbilled, related party	419	3,868
DSM International B.V. | Contract assets - related party
Related Party Transaction [Line Items]
Accounts receivable, unbilled, related party	1,203	0
DSM International B.V. | Contract assets, noncurrent - related party
Related Party Transaction [Line Items]
Accounts receivable, unbilled, related party	0	1,203
DSM International B.V. | Accounts payable
Related Party Transaction [Line Items]
Due to related parties, current	$ 5,789	$ 13,957

XML

Stock-based Compensation - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2020	Dec. 31, 2019
Share-based Payment Arrangement [Abstract]
Outstanding, beginning balance (in shares)	5,620,419
Outstanding, weighted average exercise price (in dollars per share)	$ 10.27
Outstanding, weighted average remaining contractual life	7 years 9 months 18 days	7 years 9 months 18 days
Outstanding, aggregate intrinsic value, in thousands	$ 50	$ 24
Granted (in shares)	1,258,298
Granted, weighted average grant-date fair value (in dollars per share)	$ 3.76
Exercised (in shares)	(5,227)
Exercised, weighted average grant-date fair value (in dollars per share)	$ 2.99
Forfeited or expired (in shares)	(301,787)
Forfeited or expired, weighted average grant-date fair value (in dollars per share)	$ 39.38
Outstanding, ending balance (in shares)	6,571,703	5,620,419
Outstanding, weighted average exercise price (in dollars per share)	$ 7.69	$ 10.27
Vested or expected to vest (in shares)	6,024,158
Vested or expected to vest, weighted average grant-date fair value (in dollars per share)	$ 7.96
Vested or expected to vest, weighted average remaining contractual life	7 years 9 months 18 days
Vested or expected to vest, aggregate intrinsic value, in thousands	$ 46
Exercisable (in shares)	1,440,934
Exercisable, weighted average grant-date fair value (in dollars per share)	$ 18.26
Exercisable, weighted average remaining contractual life	6 years 3 months 18 days
Exercisable, aggregate intrinsic value, in thousands	$ 4

XML

Stock-based Compensation - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity (Details) - Restricted Stock Units (RSUs) - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2020	Dec. 31, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding, RSUs (in shares)	5,782,651
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 4.77
Outstanding, weighted average remaining contractual life	1 year 7 months 6 days	1 year 8 months 12 days
Awarded, RSUs (in shares)	4,333,999
Awarded, weighted average grant-date fair value (in dollars per share)	$ 3.74
RSUs released (in shares)	(1,830,077)
RSUs released, weighted average grant-date fair value (in dollars per share)	$ 4.88
RSUs forfeited (in shares)	(563,943)
RSUs forfeited, weighted average grant-date fair value (in dollars per share)	$ 4.35
Outstanding, RSUs (in shares)	7,722,630	5,782,651
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 4.19	$ 4.77
Vested or expected to vest (in shares)	7,060,040
Vested or expected to vest, weighted average grant-date fair value (in dollars per share)	$ 4.21
Vested or expected to vest, weighted average remaining contractual life	1 year 7 months 6 days

XML

Stock-based Compensation - Employee Service Share-based Compensation, Allocation of Recognized Period Costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	$ 3,420	$ 3,234	$ 9,855	$ 10,060
Research and development
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	928	663	2,774	2,002
Sales, general and administrative
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	$ 2,492	$ 2,571	$ 7,081	$ 8,058

XML

Stock-based Compensation - Additional Information (Details) - USD ($) $ in Millions	9 Months Ended
	Sep. 30, 2020	May 31, 2020	Dec. 31, 2019	Jan. 01, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding balance (in shares)			117,742,677
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation expense related to stock options and RSUs	$ 33.6
Weighted-average period	2 years 7 months 6 days
Equity Incentive Plan, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Automatic annual increase available for grant and issuance (in shares)				5,887,133
Automatic annual increase in shares available for grant and issuance, percentage of outstanding stock			0.50%	5.00%
Automatic annual increase reserved for issuance (in shares)				588,713
2020 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant (in shares)		9,896,751

XML

Subsequent Events (Details) - Second Amendment to Ginkgo Note and Partnership Agreement - USD ($) $ in Millions	Aug. 10, 2020	Aug. 09, 2020
Subsequent Event [Line Items]
Debt instrument, interest rate, stated percentage	9.00%	12.00%
Debt Instrument, Redemption, Period One
Subsequent Event [Line Items]
Debt instrument, periodic payment	$ 2.1
Debt Instrument, Redemption, Period Two
Subsequent Event [Line Items]
Debt instrument, periodic payment	9.8
Debt Instrument, Redemption, Period Three
Subsequent Event [Line Items]
Debt instrument, face amount	12.0
Debt instrument, periodic payment	$ 10.4