The accompanying notes to the unaudited pro forma condensed combined financial information;

The separate audited consolidated financial statements of Ginkgo as of and for the fiscal year ended December 31, 2021 and the related notes, included in Ginkgo’s Current Report on Form 8-K filed with the SEC on October 4, 2022;

The separate unaudited condensed consolidated financial statements of Ginkgo as of and for the nine months ended September 30, 2022 and the related notes, included in Ginkgo’s Quarterly Report on Form 10-Q for the nine months ended September 30, 2022 filed with the SEC on November 14, 2022;

The separate audited consolidated financial statements of Zymergen as of and for the fiscal year ended December 31, 2021 and the related notes, included in Zymergen’s Annual Report on Form 10-K for the fiscal year ended December 31, 2021 filed with the SEC on March 30, 2022; and

The separate unaudited condensed consolidated financial statements of Zymergen as of and for the nine months ended September 30, 2022 and the related notes, disclosed as Exhibit 99.1 to Ginkgo’s Current Report on Form 8-K filed with the SEC on January 27, 2023.

Each option to purchase Zymergen Common Shares (a “Zymergen Option”) with an exercise price per share that was less than the Merger Consideration Value (as defined below) that was outstanding immediately prior to the Effective Time, whether or not exercisable or vested, was cancelled and converted into the right to receive a number of Ginkgo Class A Shares equal to the Option Consideration Value (as defined below) with respect to such Zymergen Option divided by the Ginkgo Class A Share Price (as defined below), and each Zymergen Option with an exercise price per share that is equal to or greater than the Merger Consideration Value was cancelled for no consideration. “Option Consideration Value” means an amount, without interest, equal to the product of (i) the excess of (A) the Merger Consideration Value over (B) the exercise price per share of such Zymergen Option, and (ii) the total number of Zymergen Common Shares issuable upon exercise in full of such Zymergen Option. “Merger Consideration Value” means an amount (rounded down to the nearest whole cent) equal to the product of (x) the Merger Consideration and (y) the Ginkgo Class A Share Price. “Ginkgo Class A Share Price” means the volume-weighted average price of Ginkgo Class A Shares on the New York Stock Exchange (“NYSE”) for the period of five consecutive trading days ending on and including the second full trading day prior to the Effective Time.

Each vested Zymergen restricted stock unit (each, a “Zymergen RSU”) that was outstanding immediately prior to the Effective Time (including after giving effect to any acceleration of vesting to which such Zymergen RSU was entitled as of immediately prior to the Effective Time as disclosed to Ginkgo) was cancelled and converted into the right to receive the Merger Consideration. The vesting of certain Zymergen RSUs was accelerated immediately prior to the closing of the Merger. Some of the accelerated vesting was outlined in Zymergen’s staged reduction in workforce plans (the “Zymergen RIFs”), which also included certain enhancements to Zymergen’s existing severance plan in the form of cash severance and bonus payments (the “Enhanced Severance”). Further, in connection with the Merger, certain Zymergen employees also received Zymergen RSUs and cash retention bonus payments pursuant to the Zymergen retention plan entered into in 2022 (the “Zymergen New Retention Plan”). Further terminations may be executed under additional Zymergen RIFs following the closing of the Merger, and such terminations will result in the issuance of additional Ginkgo Class A Common Shares and the recognition of additional compensation expense than is presented in this unaudited pro forma condensed combined financial information.

Each unvested Zymergen RSU, not accelerated as outlined above, that was outstanding immediately prior to the Effective Time was cancelled and converted into a Ginkgo restricted stock unit award (“Ginkgo RSU”) with respect to the number of Ginkgo Class A Shares that is equal to the product of (A) the number of Zymergen Common Shares subject to such unvested Zymergen RSU as of immediately prior to the Effective Time and (B) the Merger Consideration, rounded down to the nearest whole share, which such Ginkgo RSU award will be subject to the same vesting terms and conditions applicable to the Zymergen RSU to which it relates as of immediately prior to the Effective Time, including any applicable vesting acceleration provisions in connection with such holder’s termination of employment or service but otherwise will be subject to the terms and conditions of Ginkgo’s 2021 stock incentive award plan.

The Zymergen Employee Stock Purchase Plan (the “ESPP”) terminated immediately prior to the completion of the Merger and any Zymergen ESPP participants in the current offering period were allowed to purchase Zymergen Common Shares on the day immediately preceding the completion of the Merger.

Each Zymergen Common Share that was (i) held by Zymergen as treasury stock; (ii) owned by Ginkgo or Merger Subsidiary; or (iii) owned by any direct or indirect wholly owned subsidiary of Ginkgo or Merger Subsidiary as of immediately prior to the Effective Time was automatically cancelled and extinguished without any conversion thereof or consideration paid therefor.

Assets

Current assets:

Cash and cash equivalents

Accounts receivable, net

Accounts receivable – related parties

Inventory, net

Prepaid expenses and other current assets ($6,177 from related party)

Total current assets

Property and equipment, net

Investments

Equity method investments

Intangible assets, net

Goodwill

Other non-current assets

Total assets

Liabilities and Stockholders’ Equity

Current liabilities:

Accounts payable

Deferred revenue (includes $11,461 from related parties)

Accrued expenses and other current liabilities

Total current liabilities

Non-current liabilities:

Deferred rent, net of current

Deferred revenue, net of current portion (includes $127,586 from related parties)

Lease financing obligation

Warrant liabilities

Other non-current liabilities

Total liabilities

Commitments and contingencies

Stockholders’ equity:

Preferred stock

Common stock

Additional paid-in capital

Accumulated deficit

Accumulated other comprehensive loss

Total Ginkgo Bioworks Holdings, Inc. stockholders’ equity

Non-controlling interest

Total stockholders’ equity

Total liabilities and stockholders’ equity

Foundry revenue

Biosecurity revenue:

Product

Service

Collaborations, grants and other

Total revenue

Costs and operating expenses:

Cost of Biosecurity product revenue

Cost of Biosecurity service revenue

Research and development

General and administrative

Goodwill impairment charge

Restructuring charges (benefit)

Total operating expenses

Loss from operations

Other (expense) income:

Interest income (expense), net

Loss on equity method investments

Loss on investments

Change in fair value of warrant liabilities

Gain on deconsolidation of subsidiary

Other income (expense), net

Total other (expense) income, net

Loss before income taxes

Income tax benefit

Net loss

Net loss attributable to non-controlling interest

Net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders

Net loss per share attributable to Ginkgo Bioworks Holdings, Inc. common stockholders, basic and diluted

Weighted average common shares outstanding, basic and diluted

Foundry revenue

Biosecurity revenue:

Product

Service

Collaborations, grants and other

Total revenue

Costs and operating expenses:

Cost of Biosecurity product revenue

Cost of Biosecurity service revenue

Research and development

General and administrative

Restructuring charges (benefit)

Total operating expenses

Loss from operations

Other income (expense):

Interest income

Interest expense

Loss on equity method investments

Loss on investments

Change in fair value of warrant liabilities

Gain on settlement of partnership agreement

Other income (expense), net

Total other income (expense), net

Loss before income taxes

Income tax (benefit) provision

Net loss

Net loss attributable to non-controlling interest

Net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders

Net loss per share attributable to Ginkgo Bioworks Holdings, Inc. common stockholders:

Basic

Diluted

Weighted average common shares outstanding:

Basic

Diluted

Refer to the table below for a summary of reclassification adjustments made to conform Zymergen’s historical balance sheet presentation as of September 30, 2022 with that of Ginkgo’s:

(in thousands)

Ginkgo Historical
Condensed Consolidated
Balance Sheet Line Items

Zymergen Historical
Condensed Consolidated
Balance Sheet Line Items

Reclassification of $0.2 million of accounts receivable, unbilled to accounts receivable, net.

Reclassification of $2.8 million of restricted cash, current to prepaid expenses and other current assets.

Reclassification of $1.2 million of other current assets to prepaid expenses and other current assets.

Reclassification of $10.0 million of non-current restricted cash to other non-current assets.

Reclassification of $127.9 million of operating lease right-of-use assets to other non-current assets.

Reclassification of $7.8 million of short-term operating lease liabilities to accrued expenses and other current liabilities.

Reclassification of $176.2 million of long-term operating lease liabilities to other non-current liabilities.

Reclassification of $3.5 million of non-current deferred revenue within other long-term liabilities to deferred revenue, net of current portion.

Refer to the table below for a summary of adjustments made to conform Zymergen’s historical statements of operations and comprehensive loss presentation for the nine months ended September 30, 2022 with that of Ginkgo’s:

(in thousands)

Ginkgo Historical
Condensed Consolidated

Statements of Operations

and Comprehensive Loss

Line Items

Zymergen Historical

Condensed Consolidated

Statements of Operations

and Comprehensive Loss

Line Items

Reclassification of $6.2 million of revenues from research and development service agreements to foundry revenue.

Reclassification of $0.5 million of automation revenue to foundry revenue.

Reclassification of $0.9 million of grant revenue to collaboration and other revenue.

Reclassification of $1.6 million of cost of automation revenue to research and development.

Reclassification of $29.0 million of cost of service revenue to research and development.

Reclassification of $12.0 million of sales and marketing to general and administrative.

Reclassification of $0.1 million of interest income to interest expense, net.

Refer to the table below for a summary of adjustments made to conform Zymergen’s historical statements of operations and comprehensive loss presentation for the year ended December 31, 2021 with that of Ginkgo’s:

(in thousands)

Ginkgo Historical

Consolidated Statements

of Operations and

Comprehensive Loss

Line Items

Zymergen Historical
Consolidated Statements of
Operations and
Comprehensive Loss

Line Items

Reclassification of $12.4 million of revenues from research and development service agreements to foundry revenue.

Reclassification of $69.7 million of cost of service revenue to research and development.

Reclassification of $23.6 million of sales and marketing to general and administrative.

(in thousands)

Estimated fair value of Ginkgo Class A Common Shares issued to Zymergen shareholders (i)

Estimated fair value of replacement Ginkgo RSUs and Ginkgo Class A Common Shares issued under Zymergen RIFs attributable to pre-combination services (ii)

Less: Estimated Enhanced Severance and Zymergen New Retention Plan cash bonuses incurred for the benefit of the combined company (iii)

Total estimated consideration transferred

As consideration for the Merger, the Company delivered to Zymergen common stockholders approximately 99,422,907 of its Class A Common Shares, of which approximately 96,859,594 of its Class A Common Shares represent estimated consideration transferred for the Merger under ASC 805. The fair value of the Company’s Class A Common Shares issued as consideration transferred was determined based on a per share price of $2.44, which was the closing price of Company’s Class A Common Shares on October 19, 2022. An immaterial amount related to the incremental fair value attributable to Zymergen stock options, calculated as the difference between the fair value of the options immediately before the Merger and the Option Consideration Value the option holders received upon closing of the Merger, was excluded from total estimated consideration transferred and will be recognized in Ginkgo’s unaudited pro forma condensed combined financial information as stock-based compensation expense in the period subsequent to the Merger.

Represents the estimated fair value of the replacement Ginkgo RSUs and the Ginkgo Class A Common Shares issued under the Zymergen RIFs attributable to pre-combination services. The remaining portion of the fair value is associated with future service and will be recognized in the post-combination financial statements over the remaining service period.

Represents estimated cash bonuses payable to Zymergen employees in accordance with the Enhanced Severance and the Zymergen New Retention Plan. These payments were determined to be for the benefit of the combined company, and a portion of the fair value recognized as estimated consideration transferred will be allocated to compensation expense in Ginkgo’s unaudited pro forma condensed combined financial information in the period subsequent to the Merger.

(in thousands)

Cash and cash equivalents

Accounts receivable

Inventory

Prepaid expenses and other current assets

Property and equipment (i)

Intangible assets (ii)

Goodwill

Other non-current assets

Accounts payable

Deferred revenue (iii)

Accrued expenses and other current liabilities

Deferred revenue, net of current portion (iii)

Other non-current liabilities

Estimated preliminary purchase consideration

Preliminary property and equipment in the unaudited pro forma condensed combined financial information consists of the following:

Leasehold improvements

Laboratory equipment

Furniture and fixtures

Computer equipment

Software

General equipment

Construction-in-progress

Total property and equipment acquired

Preliminary identifiable intangible assets in the unaudited pro forma condensed combined financial information consist of the following:

Software design tools

Software workflow tools

Strain engineering tools

Codebase assets

Automation core technology

Total intangible assets acquired

The unaudited pro forma condensed combined financial information presented reflects the early adoption of Accounting Standards Update (“ASU”) 2021-08, Accounting for Contract Assets and Contract Liabilities from Contracts with Customers. Under this new standard, deferred revenue acquired in a business combination is measured pursuant to ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”), rather than at its assumed acquisition date fair value. Ginkgo early adopted the requirements of ASU 2021-08 and is required to apply the amendments prospectively to all business combinations that occurred on or after April 1, 2022. The

(in thousands)

Pro forma transaction accounting adjustments:

Eliminate Zymergen’s historical prepaid rent (i)

Eliminate Zymergen’s historical prepaid directors and officers insurance policies (ii)

Net pro forma transaction accounting adjustment to prepaid expenses and other current assets

Eliminate Zymergen’s prepaid rent in accordance with ASC 805.

Eliminate Zymergen’s existing prepaid directors and officers insurance policies that were terminated upon the closing of the Merger.

(in thousands)

Pro forma transaction accounting adjustments:

Eliminate Zymergen’s historical net book value of property and equipment

Record the preliminary fair value of acquired property and equipment

Net pro forma transaction accounting adjustment to property and equipment, net

(in thousands)

Pro forma transaction accounting adjustments:

Eliminate Zymergen’s historical net book value of intangible assets

Record the preliminary fair value of acquired intangible assets

Net pro forma transaction accounting adjustment to intangible assets, net

(in thousands)

Pro forma transaction accounting adjustments:

Reclassify Ginkgo’s deferred equity issuance costs from other non-current assets to additional paid-in capital upon Merger close (i)

Remove Zymergen’s historical right-of-use asset to align with Ginkgo’s ASC 840 accounting policy (ii)

Net pro forma transaction accounting adjustment to other non-current assets

Record an adjustment to reclassify deferred equity issuance costs incurred by Ginkgo as of September 30, 2022 related to the issuance of Ginkgo Class A Common Shares in connection with the Merger from other non-current assets to additional paid-in capital.

Record an accounting policy conformity adjustment to derecognize Zymergen’s right-of-use asset resulting from the alignment of Zymergen’s accounting for leases pursuant to ASC 842 to Ginkgo’s accounting for leases pursuant to ASC 840.

(in thousands)

Pro forma transaction accounting adjustments:

Record incurred transaction costs (i)

Record liability related to new Zymergen directors and officers and other insurance policies (ii)

Net pro forma transaction accounting adjustment to accounts payable

Record transaction costs of $1.5 million incurred since September 30, 2022 by Ginkgo and $4.5 million incurred since September 30, 2022 by Zymergen in connection with the Merger. As of September 30, 2022, Ginkgo had not recorded any transaction costs incurred in connection with the Merger in accounts payable in its historical financial information. As of September 30, 2022, Zymergen had recorded less than $0.1 million of transaction costs incurred in connection with the Merger in accounts payable in its respective historical financial information.

Record accounts payable of $7.2 million related to insurance premiums payable by Zymergen required to be entered into upon the closing of the Merger. These policies primarily relate to claims against directors and officers for actions that occurred prior to the Merger.

(in thousands)

Pro forma transaction accounting adjustments:

Record liability related to Zymergen Enhanced Severance (i)

Record incremental liability related to Zymergen New Retention Plan cash bonuses (ii)

Record incremental liability related to existing Zymergen cash bonus program (iii)

Remove liability related to Zymergen ESPP (iv)

Record incurred transaction costs (v)

Record Ginkgo’s incurred equity issuance costs (vi)

Remove Zymergen’s historical short-term operating lease liability to align with Ginkgo’s ASC 840 accounting policy (vii)

Net pro forma transaction accounting adjustment to accrued expenses and other current liabilities

Record a liability for the cash bonuses payable pursuant to Zymergen’s Enhanced Severance triggered upon termination and the occurrence of a change in control within twelve months of termination (see “Description of the Merger” for further detail regarding the Enhanced Severance).

Record the incremental liability for cash bonuses payable pursuant to the Zymergen New Retention Plan triggered upon a change in control (see “Description of the Merger” for further detail regarding the Zymergen New Retention Plan).

Record the incremental liability for cash bonuses payable pursuant to Zymergen’s existing bonus program triggered upon a change in control.

Derecognize the liability related to Zymergen’s ESPP that was terminated immediately prior to the completion of the Merger in exchange for the right to receive Merger Consideration.

Record transaction costs of $5.9 million incurred since September 30, 2022 by Ginkgo in connection with the Merger. As of September 30, 2022, Ginkgo had accrued for $4.3 million and Zymergen had accrued for $5.2 million of transaction costs incurred in connection with the Merger in their respective historical financial information.

Record equity issuance costs incurred since September 30, 2022 related to the issuance of Ginkgo Class A Common Shares in conjunction with the Merger.

Record an accounting policy conformity adjustment to derecognize the short-term portion of Zymergen’s operating lease liability from accrued expenses and other current liabilities resulting from the alignment of Zymergen’s accounting for leases pursuant to ASC 842 to Ginkgo’s accounting for leases pursuant to ASC 840.

(in thousands)

Pro forma transaction accounting adjustments:

Eliminate Zymergen’s historical Common Stock

Record par value of Ginkgo Class A Common Shares issued to acquire Zymergen

Net pro forma transaction accounting adjustment to common stock

(in thousands)

Pro forma transaction accounting adjustments:

Eliminate Zymergen’s historical additional paid-in capital (i)

Record purchase consideration in excess of the par value of Ginkgo Class A Common Shares issued to acquire Zymergen (ii)

Record stock-based compensation expense for accelerated Zymergen options and the accelerated Zymergen RSUs under the Zymergen RIFs and the Zymergen New Retention Plan (iii)

Record Ginkgo’s incurred equity issuance costs (iv)

Net pro forma transaction accounting adjustment to additional paid-in capital

Eliminate Zymergen’s historical additional paid-in capital.

Record the estimated purchase consideration in excess of the par value of Ginkgo Class A Common Shares issued to acquire Zymergen.

Record adjustments related to (a) the incremental fair value attributable to Zymergen stock options exchanged for Ginkgo Class A Common Shares upon a change in control, calculated as the difference between the fair value of the options immediately before the Merger and the Option Consideration Value the option holders received upon closing of the Merger, and (b) accelerated vesting related to Zymergen RSUs under the Zymergen RIFs and the Zymergen New Retention Plan deemed to be for the benefit of the combined company. The corresponding expense was recognized by Ginkgo as a one-time stock-based compensation charge upon the closing of the Merger as these awards required no further service by Zymergen employees.

Record equity issuance costs incurred by Ginkgo as of and since September 30, 2022 related to the issuance of Ginkgo Class A Common Shares in connection with the Merger as a reduction to additional paid-in capital.

(in thousands)

Pro forma transaction accounting adjustments:

Eliminate Zymergen’s accumulated deficit (i)

Record estimated Enhanced Severance and Zymergen New Retention Plan cash bonuses incurred for the benefit of the combined company (ii)

Record stock-based compensation expense for accelerated Zymergen options and the accelerated Zymergen RSUs under the Zymergen RIFs and the Zymergen New Retention Plan (iii)

Record incurred transaction costs (iv)

Net pro forma transaction accounting adjustment to accumulated deficit

Eliminate Zymergen’s historical accumulated deficit.

Represents an adjustment for estimated cash bonuses payable to Zymergen employees in accordance with the Enhanced Severance and the Zymergen New Retention Plan. These payments were determined to be for the benefit of the combined company, and a portion of the fair value otherwise recognized as estimated consideration transferred will be allocated to compensation expense in Ginkgo’s unaudited pro forma condensed combined financial information in the period subsequent to the Merger.

Record a one-time stock-based compensation charge related (a) the incremental fair value attributable to Zymergen stock options exchanged for Ginkgo Class A Common Shares upon a change in control, calculated as the difference between the fair value of the options immediately before the Merger and the Option Consideration Value the option holders received upon closing of the Merger, and (b) and accelerated vesting related to Zymergen RSUs under the Zymergen RIFs and the Zymergen New Retention Plan deemed to be for the benefit of the combined company. The corresponding expense was recognized by Ginkgo as a one-time stock-based compensation charge upon the closing of the Merger as these awards required no further service by Zymergen employees.

Record transaction costs that were incurred since September 30, 2022 by Ginkgo in connection with the Merger. See adjustments (g) and (h) above for further detail.

(in thousands)

Pro forma transaction accounting adjustments:

Remove historical Zymergen depreciation of property and equipment (i)

Record depreciation of fair value of Zymergen’s property and equipment (ii)

Remove historical Zymergen amortization of intangible assets (iii)

Record amortization of fair value of Zymergen’s intangible assets (iv)

Record compensation expense for Enhanced Severance and Zymergen RSUs granted, and cash retention bonuses paid under the Zymergen New Retention Plan (v)

Adjust the expense for Zymergen’s consumables inventory (vi)

Record incremental rent expense for Zymergen’s operating leases (vii)

Net pro forma transaction accounting adjustment to research and development expense

Remove historical Zymergen depreciation of property and equipment.

Record depreciation of the estimated fair value of property and equipment.

Remove historical Zymergen amortization of intangible assets.

Record amortization of the estimated fair value of intangible assets.

Record preliminary compensation expense for (a) cash bonuses payable under the Enhanced Severance upon termination and a change in control and (b) Zymergen RSUs issued and incremental cash retention bonuses payable under the Zymergen New Retention Plan. Under the Enhanced Severance, certain Zymergen employees were eligible to receive cash severance and bonus payments upon termination of employment and occurrence of a change in control within twelve months of termination. Under the Zymergen New Retention Plan, certain Zymergen employees were granted modifications to their RSUs, which accelerated a portion of the vesting upon a change in control and required future service for the remainder of the vesting term. In addition, certain Zymergen employees were granted cash retention bonuses, a portion of which became

Adjust the expense related to the alignment of Zymergen’s consumables inventory to Ginkgo’s accounting policy for inventory.

Record incremental rent expense resulting from recalculating straight-line rent expense as of the pro forma acquisition date and from aligning accounting policies to report Zymergen’s leases under ASC 840.

(in thousands)

Pro forma transaction accounting adjustments:

Remove historical Zymergen depreciation of property and equipment (i)

Record depreciation of fair value of Zymergen’s property and equipment (ii)

Remove historical Zymergen amortization of intangible assets (iii)

Record incurred transaction costs (iv)

Record compensation expense for Enhanced Severance as well as Zymergen RSUs granted and cash retention bonuses paid under the Zymergen New Retention Plan (v)

Record incremental rent expense for Zymergen’s operating leases (vi)

Net pro forma transaction accounting adjustment to general and administrative expense

Remove historical Zymergen depreciation of property and equipment.

Record depreciation of the estimated fair value of property and equipment.

Remove historical Zymergen amortization of intangible assets.

Record transaction costs related to the Merger incurred by Ginkgo since September 30, 2022 that are nonrecurring and are not anticipated to affect the unaudited pro forma condensed combined statements of operations beyond twelve months after the closing of the Merger.

Record preliminary compensation expense for (a) cash bonuses payable under the Enhanced Severance upon termination and a change in control and (b) Zymergen RSUs issued and incremental cash retention bonuses payable under the Zymergen New Retention Plan. Under the Enhanced Severance, certain Zymergen employees were eligible to receive cash severance and bonus payments upon termination of employment and occurrence of a change in control within twelve months of termination. Under the Zymergen New Retention Plan, certain Zymergen employees were granted modifications to their RSUs, which accelerated a portion of the vesting upon a change in control and required future service for the remainder of the vesting term. In addition, certain Zymergen employees were granted cash retention bonuses, a portion of which became payable upon a change in control, with the remainder payable within six months following the closing of the Merger. Of the total compensation expense of $4.1 million recognized through this adjustment to the unaudited pro forma condensed combined statement of operations for the year ended December 31, 2021, $2.7 million represents a one-time charge.

Record incremental rent expense resulting from recalculating straight-line rent expense as of the pro forma acquisition date and from aligning accounting policies to report Zymergen’s leases under ASC 840.