Document:

Form of Warrant - Loan and Security Agreement, dated September 21, 2006

 EXHIBIT 4.5 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE
SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR,
IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. 

WARRANT TO PURCHASE STOCK 
  

			
	 Company:
	  	 Complete Genomics, Inc., a Delaware corporation

	 Number of Shares:
	  	 [            ] or such greater amount as set forth in Section 1.7 below

	 Class of Stock:
	  	 Series A Preferred

	 Warrant Price:
	  	 $1.461632 per share

	 Issue Date:
	  	 ____________________

	 Expiration Date:
	  	 The 10th anniversary after the Issue Date

	 Credit Facility:
	  	 This Warrant is issued in connection with the Committed Equipment Line referenced in the Loan and Security Agreement between Company and Silicon Valley Bank dated
September 21, 2006.

 THIS WARRANT CERTIFIES THAT, for good and valuable consideration,
<<LENDER>>, together with any registered holder from time to time of this Warrant or any holder of the shares issuable or issued upon exercise of this Warrant, “Holder”) is entitled to purchase the number of fully paid and
nonassessable shares of the class of securities (the “Shares”) of the Company at the Warrant Price, all as set forth above and as adjusted pursuant to Article 2 of this Warrant, subject to the provisions and upon the terms and conditions
set forth in this Warrant. 
 ARTICLE 1. EXERCISE. 

1.1    Method of Exercise.  Holder may exercise this Warrant by delivering a duly executed
Notice of Exercise in substantially the form attached as Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion right set forth in Article 1.2, Holder shall also deliver to the Company a check, wire transfer
(to an account designated by the Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased. 

1.2    Conversion Right.  In lieu of exercising this Warrant as specified in Article 1.1,
Holder may from time to time convert this Warrant, in whole or in part, into a number of Shares determined by dividing (a) the aggregate fair market value of the Shares or other securities otherwise issuable upon exercise of this Warrant minus
the aggregate Warrant Price of such Shares by (b) the fair market value of one Share. The fair market value of the Shares shall be determined pursuant to Article 1.3. 

 1.3    Fair Market Value.  If the Company’s
common stock is traded in a public market and the Shares are common stock, the fair market value of each Share shall be the closing price of a Share reported for the business day immediately before Holder delivers its Notice of Exercise to the
Company (or in the instance where the Warrant is exercised immediately prior to the effectiveness of the Company’s initial public offering, the “price to public” per share price specified in the final prospectus relating to such
offering). If the Company’s common stock is traded in a public market and the Shares are preferred stock, the fair market value of a Share shall be the closing price of a share of the Company’s common stock reported for the business day
immediately before Holder delivers its Notice of Exercise to the Company (or, in the instance where the Warrant is exercised immediately prior to the effectiveness of the Company’s initial public offering, the initial “price to
public” per share price specified in the final prospectus relating to such offering), in both cases, multiplied by the number of shares of the Company’s common stock into which a Share is convertible. If the Company’s common stock is
not traded in a public market, the Board of Directors of the Company shall determine fair market value in its reasonable good faith judgment. 

1.4    Delivery of Certificate and New Warrant.  Promptly after Holder exercises or converts
this Warrant and, if applicable, the Company receives payment of the aggregate Warrant Price, the Company shall deliver to Holder certificates for the Shares acquired and, if this Warrant has not been fully exercised or converted and has not
expired, a new Warrant representing the Shares not so acquired. 
 1.5    Replacement of
Warrants.  On receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably
satisfactory in form and amount to the Company or, in the case of mutilation on surrender and cancellation of this Warrant, the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor. 

1.6    Treatment of Warrant Upon Acquisition of Company. 

1.6.1    “Acquisition”.  For the purpose of this Warrant, “Acquisition”
means any sale, license, or other disposition of all or substantially all of the assets of the Company, or any reorganization, consolidation, or merger of the Company where the holders of the Company’s securities before the transaction
beneficially own less than 50% of the outstanding voting securities of the surviving entity after the transaction. 

1.6.2    Treatment of Warrant at Acquisition. 

A)        Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that
is not an asset sale and in which the sole consideration is cash, either (a) Holder shall exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such
Acquisition or (b) if Holder elects not to exercise the Warrant, this Warrant will expire upon the consummation of such Acquisition. The Company shall provide Holder with written notice of its request relating to the foregoing (together with
such reasonable information as Holder may request in connection with such contemplated Acquisition giving rise to such notice), which is to be delivered to Holder not less than ten (10) days prior to the closing of the proposed Acquisition.

 B)        Upon the written request of the Company, Holder
agrees that, in the event of an Acquisition that is an “arms length” sale of all or substantially all of the Company’s assets (and only its assets) to a third party that is not an Affiliate (as defined below) of the Company (a
“True Asset Sale”), either (a) Holder shall exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b) if Holder elects
not to exercise the Warrant, this Warrant will continue until the Expiration Date if the Company continues as a going concern following the closing of any such True Asset Sale. The Company shall provide Holder with written notice of its request
relating to the foregoing (together with such reasonable information as Holder may request in connection with such contemplated Acquisition giving rise to such notice), which is to be delivered to Holder not less than ten (10) days prior to the
closing of the proposed Acquisition. 
 C)        Upon the closing of any Acquisition other than
those particularly described in subsections (A) and (B) above, the successor entity shall assume the obligations of this Warrant, and this Warrant shall be exercisable for the same securities, cash, and property as would be payable for the
Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on the record date for the Acquisition and subsequent closing. The Warrant Price and/or number of Shares shall be adjusted accordingly.

 As used herein “Affiliate” shall mean any person or entity that owns or controls directly or indirectly ten
(10) percent or more of the stock of Company, any person or entity that controls or is controlled by or is under common control with such persons or entities, and each of such person’s or entity’s officers, directors, joint venturers
or partners, as applicable. 
 1.7    Number of Shares.  The initial aggregate number
of shares of Series A Preferred Stock issuable under this Warrant shall be [            ] provided, however, at such time as Holder makes any Equipment Advance to Company pursuant to
the Loan Agreement, the additional number of shares of Series A Preferred Stock issuable hereunder shall equal to two percent (2.0%) of each Equipment Advance divided by the price per share of Series A Preferred Stock in effect as of the date
of such Equipment Advance. 
 ARTICLE 2. ADJUSTMENTS TO THE SHARES. 

2.1    Stock Dividends, Splits, Etc.  If the Company declares or pays a dividend on the Shares
payable in common stock, or other securities, then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total number and kind of securities to which Holder would have been entitled had Holder
owned the Shares of record as of the date the dividend occurred. If the Company subdivides the Shares by reclassification or otherwise into a greater number of shares or takes any other action which increase the amount of stock into which the Shares
are convertible, the number of shares purchasable hereunder shall be proportionately increased and the Warrant Price shall be proportionately decreased. If the outstanding shares are combined or consolidated, by reclassification or otherwise, into a
lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares shall be proportionately decreased. 

 2.2    Reclassification, Exchange, Combinations or
Substitution.  Upon any reclassification, exchange, substitution, or other event that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this Warrant, Holder shall be entitled to
receive, upon exercise or conversion of this Warrant, the number and kind of securities and property that Holder would have received for the Shares if this Warrant had been exercised immediately before such reclassification, exchange, substitution,
or other event. Such an event shall include any automatic conversion of the outstanding or issuable securities of the Company of the same class or series as the Shares to common stock pursuant to the terms of the Company’s Articles or
Certificate (as applicable) of Incorporation upon the closing of a registered public offering of the Company’s common stock. The Company or its successor shall promptly issue to Holder an amendment to this Warrant setting forth the number and
kind of such new securities or other property issuable upon exercise or conversion of this Warrant as a result of such reclassification, exchange, substitution or other event that results in a change of the number and/or class of securities issuable
upon exercise or conversion of this Warrant. The amendment to this Warrant shall provide for adjustments which shall be as nearly equivalent as may be practicable to the adjustments provided for in this Article 2 including, without limitation,
adjustments to the Warrant Price and to the number of securities or property issuable upon exercise of the new Warrant. The provisions of this Article 2.2 shall similarly apply to successive reclassifications, exchanges, substitutions, or other
events. 
 2.3    Adjustments for Diluting Issuances.  The Warrant Price and the
number of Shares issuable upon exercise of this Warrant or, if the Shares are preferred stock, the number of shares of common stock issuable upon conversion of the Shares, shall be subject to adjustment, from time to time in the manner set forth in
the Company’s Articles or Certificate of Incorporation as if the Shares were issued and outstanding on and as of the date of any such required adjustment. The provisions set forth for the Shares in the Company’s Articles or Certificate (as
applicable) of Incorporation relating to the above in effect as of the Issue Date may not be amended, modified or waived, without the prior written consent of Holder unless such amendment, modification or waiver affects the rights associated with
the Shares in the same manner as such amendment, modification or waiver affects the rights associated with all other shares of the same series and class as the Shares granted to Holder. 

2.4    No Impairment.  The Company shall not, by amendment of its Articles or Certificate (as
applicable) of Incorporation or through a reorganization, transfer of assets, consolidation, merger, dissolution, issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms to
be observed or performed under this Warrant by the Company, but shall at all times in good faith assist in carrying out of all the provisions of this Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s
rights under this Article against impairment. 
 2.5    Fractional Shares.  No
fractional Shares shall be issuable upon exercise or conversion of this Warrant and the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the
Warrant, the Company shall eliminate such fractional share interest by paying Holder the amount computed by multiplying the fractional interest by the fair market value of a full Share. 

 2.6    Certificate as to Adjustments.  Upon each
adjustment of the Warrant Price, the Company shall promptly notify Holder in writing, and, at the Company’s expense, promptly compute such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth such
adjustment and the facts upon which such adjustment is based. The Company shall, upon written request, furnish Holder a certificate setting forth the Warrant Price in effect upon the date thereof and the series of adjustments leading to such Warrant
Price. 
 ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY. 

3.1    Representations and Warranties.  The Company represents and warrants to Holder as
follows: 
 (a)      The initial Warrant Price referenced on the first page of this Warrant
is not greater than (i) the price per share at which the Shares were last issued in an arms-length transaction in which at least $500,000 of the Shares were sold and (ii) the fair market value of the Shares as of the date of this Warrant.

 (b)      All Shares which may be issued upon the exercise of the purchase right
represented by this Warrant, and all securities, if any, issuable upon conversion of the Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except for restrictions
on transfer provided for herein or under applicable federal and state securities laws. 

(c)      The Company’s capitalization table attached hereto as Schedule 1 is true and
complete as of the Issue Date. 
 3.2    Notice of Certain Events.  If the Company
proposes at any time (a) to declare any dividend or distribution upon any of its stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; (b) to offer for sale any shares of the
Company’s capital stock (or other securities convertible into such capital stock), other than (i) pursuant to the Company’s stock option or other compensatory plans, (ii) in connection with commercial credit arrangements or
equipment financings, or (iii) in connection with strategic transactions for purposes other than capital raising; (c) to effect any reclassification or recapitalization of any of its stock; (d) to merge or consolidate with or into any
other corporation, or sell, lease, license, or convey all or substantially all of its assets, or to liquidate, dissolve or wind up; or (e) offer holders of registration rights the opportunity to participate in an underwritten public offering of
the Company’s securities for cash, then, in connection with each such event, the Company shall give Holder: (1) at least 10 days prior written notice of the date on which a record will be taken for such dividend, distribution, or
subscription rights (and specifying the date on which the holders of common stock will be entitled thereto) or for determining rights to vote, if any, in respect of the matters referred to in (a) and (b) above; (2) in the case of the
matters referred to in (c) and (d) above at least 10 days prior written notice of the date when the same will take place (and specifying the date on which the holders of common stock will be entitled to exchange their common stock for
securities or other property deliverable upon the occurrence of such event); and (3) in the case of the matter referred to in (e) above, the same notice as is given to the holders of such registration rights. Company will also provide
information requested by Holder reasonably necessary to enable Holder to comply with Holder’s accounting or reporting requirements. 

 3.3    Registration Under Securities Act of 1933, as
amended.  The Company agrees that the Shares or, if the Shares are convertible into common stock of the Company, such common stock, shall have certain “piggyback,” registration rights pursuant to and as set forth in the
Company’s Investor Rights Agreement or similar agreement. The provisions set forth in the Company’s Investors’ Right Agreement or similar agreement relating to the above in effect as of the Issue Date may not be amended, modified or
waived without the prior written consent of Holder unless such amendment, modification or waiver affects the rights associated with the Shares in the same manner as such amendment, modification, or waiver affects the rights associated with all other
shares of the same series and class as the Shares granted to Holder. 
 3.4    No Shareholder
Rights.  Except as provided in this Warrant, Holder will not have any rights as a shareholder of the Company until the exercise of this Warrant. 

ARTICLE 4. REPRESENTATIONS, WARRANTIES OF HOLDER. Holder represents and warrants to the Company as follows: 

4.1    Purchase for Own Account.  This Warrant and the securities to be acquired upon exercise
of this Warrant by Holder will be acquired for investment for Holder’s account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Act. Holder also represents that Holder has not been
formed for the specific purpose of acquiring this Warrant or the Shares. 
 4.2    Disclosure of
Information.  Holder has received or has had full access to all the information it considers necessary or appropriate to make an informed investment decision with respect to the acquisition of this Warrant and its underlying
securities. Holder further has had an opportunity to ask questions and receive answers from the Company regarding the terms and conditions of the offering of this Warrant and its underlying securities and to obtain additional information (to the
extent the Company possessed such information or could acquire it without unreasonable effort or expense) necessary to verify any information furnished to Holder or to which Holder has access. 

4.3    Investment Experience.  Holder understands that the purchase of this Warrant and its
underlying securities involves substantial risk. Holder has experience as an investor in securities of companies in the development stage and acknowledges that Holder can bear the economic risk of such Holder’s investment in this Warrant and
its underlying securities and has such knowledge and experience in financial or business matters that Holder is capable of evaluating the merits and risks of its investment in this Warrant and its underlying securities and/or has a preexisting
personal or business relationship with the Company and certain of its officers, directors or controlling persons of a nature and duration that enables Holder to be aware of the character, business acumen and financial circumstances of such persons.

 4.4    Accredited Investor Status.  Holder is an “accredited investor”
within the meaning of Regulation D promulgated under the Act. 
 4.5    The
Act.  Holder understands that this Warrant and the Shares issuable upon exercise or conversion hereof have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among

 
other things, the bona fide nature of Holder’s investment intent as expressed herein. Holder understands that this Warrant and the Shares issued upon any exercise or conversion hereof must
be held indefinitely unless subsequently registered under the Act and qualified under applicable state securities laws, or unless exemption from such registration and qualification are otherwise available. 

ARTICLE 5. MISCELLANEOUS. 

5.1    Term.  This Warrant is exercisable in whole or in part at any time and from time to
time on or before the Expiration Date. 
 5.2    Legends.  This Warrant and the
Shares (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form: 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
“ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE
STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. 

5.3    Compliance with Securities Laws on Transfer.  This Warrant and the Shares issuable upon
exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and state securities laws by the
transferor and the transferee (including, without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). The Company shall not require Silicon
Valley Bank (“Bank”) to provide an opinion of counsel if the transfer is to Bank’s parent company, SVB Financial Group (formerly Silicon Valley Bancshares), or any other affiliate of Bank. Additionally, the Company shall also not
require an opinion of counsel if there is no material question as to the availability of current information as referenced in Rule 144(c), Holder represents that it has complied with Rule 144(d) and (e) in reasonable detail, the selling broker
represents that it has complied with Rule 144(f), and the Company is provided with a copy of Holder’s notice of proposed sale. 

5.4    Transfer Procedure.  After receipt by Bank of the executed Warrant, Bank will transfer
all of this Warrant to SVB Financial Group by execution of an Assignment substantially in the form of Appendix 2. Subject to the provisions of Article 5.3 and upon providing the Company with written notice, SVB Financial Group and any subsequent
Holder may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or the Shares issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee, provided, however, in connection with any
such transfer, SVB Financial Group or any subsequent Holder will give the Company notice of the portion of the Warrant being transferred with the name, address and taxpayer 

 
identification number of the transferee and Holder will surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable). The Company may refuse to transfer
this Warrant or the Shares to any person who directly competes with the Company, unless, in either case, the stock of the Company is publicly traded. 

5.5    Notices.  All notices and other communications from the Company to Holder, or vice
versa, shall be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, at such address as may have been furnished to the Company or Holder, as the case may (or on the first
business day after transmission by facsimile) be, in writing by the Company or such Holder from time to time. Effective upon receipt of the fully executed Warrant and the initial transfer described in Article 5.4 above, all notices to Holder shall
be addressed as follows until the Company receives notice of a change of address in connection with a transfer or otherwise: 

<< LENDER >> 

Notice to the Company shall be addressed as follows until Holder receives notice of a change in address: 

Complete Genomics, Inc. 

Attn: Chief Financial Officer 

750 North Pastoria Avenue 

Sunnyvale, CA 94085 

Telephone: (408) 730-5700 

Facsimile:
                                 

5.6    Waiver.  This Warrant and any term hereof may be changed, waived, discharged or
terminated only by an instrument in writing signed by the party against which enforcement of such change, waiver, discharge or termination is sought. 

5.7    Attorneys’ Fees.  In the event of any dispute between the parties concerning the
terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees. 

5.8    Automatic Conversion upon Expiration.  In the event that, upon the Expiration Date, the
fair market value of one Share (or other security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above is greater than the Warrant Price in effect on such date, then this Warrant shall automatically be deemed on
and as of such date to be converted pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised or converted, and the Company shall promptly deliver a certificate representing
the Shares (or such other securities) issued upon such conversion to Holder. 

 5.9    Counterparts.  This Warrant may be
executed in counterparts, all of which together shall constitute one and the same agreement. 

5.10  Governing Law.  This Warrant shall be governed by and construed in accordance with the laws of the
State of California, without giving effect to its principles regarding conflicts of law. 
 [Signature page follows.] 

													
	 “COMPANY”
	 	 Date:
	 	  

				
	 Complete Genomics, Inc.
	 		 		 	
					
	 By:
	 	  
	 		 	 By:
	 	  

					
	 Name:
	 	  
	 		 	 Name:
	 	  

		 		 	 (Print)
	 		 		 		 	 (Print)

	 Title:
	 	 Chairman of the Board, President or Vice President
	 		 	 Title:
	 		 	 Chief Financial Officer, Secretary, Assistant Treasurer or Assistant Secretary

				
	 “HOLDER”
	 		 		 	
				
	 << LENDER >>
	 		 		 	
						
	 By:
	 	  
	 		 		 		 	
						
	 Name:
	 	  
	 		 		 		 	
		 		 	 (Print)
	 		 		 		 	
	 Title:
	 	  
	 		 		 		 	

 SCHEDULE 1 

CAPITALIZATION TABLE 

[See attached.] 

 APPENDIX 1 

NOTICE OF EXERCISE 

1.        Holder elects to purchase
                     shares of the Common/Series              Preferred
[strike one] Stock of                                     
pursuant to the terms of the attached Warrant, and tenders payment of the purchase price of the shares in full. 

  [or] 

1.        Holder elects to convert the attached Warrant into Shares/cash [strike one] in
the manner specified in the Warrant. This conversion is exercised for
                                        
of the Shares covered by the Warrant. 
 [Strike paragraph that does not apply.] 

2.        Please issue a certificate or certificates representing the shares in the name
specified below: 
  

					
		 	  
	 	
		 	 Holders Name
	 	
		 		 	
		 	  
	 	
		 		 	
		 	  
	 	
		 	 (Address)
	 	

 3.        By its execution below and for the benefit of
the Company, Holder hereby restates each of the representations and warranties in Article 4 of the Warrant as the date hereof. 
  

					
	 HOLDER:
	 	
		 		 	
	  
	 	
		
	 By:
	 	  

		
	 Name:
	 	  

		
	 Title:
	 	  

		
	 (Date):
	 	  

 APPENDIX 2 

ASSIGNMENT 

For value received, << LENDER >> hereby sells, assigns and transfers unto 

 

					
		 	 Name:
	    	
		 	 Address:
	    	
			
		 	 Tax ID:
	    	

 that certain Warrant to Purchase Stock issued by
                                         
            (the “Company”), on                     ,
2             (the “Warrant”) together with all rights, title and interest therein. 

 

			
	 << LENDER >>

		
	 By:
	 	  

		
	 Name:
	 	  

		
	 Title:
	 	  

Date:                       
                  
 By its execution below, and
for the benefit of the Company, [                    ] makes each of the representations and warranties set forth in Article 4 of the Warrant
and agrees to all other provisions of the Warrant as of the date hereof. 
  

			
		
	 By:
	 	  

		
	 Name:
	 	  

		
	 Title:Form of Warrant - 2007 convertible bridge loan financing transaction

 EXHIBIT 4.6 

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE BEEN ACQUIRED FOR INVESTMENT AND HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
1933, AS AMENDED. THIS WARRANT AND THE UNDERLYING SECURITIES MAY NOT BE SOLD OR TRANSFERRED WITHOUT (I) AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (II) AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH
REGISTRATION IS NOT REQUIRED UNDER THE ACT OR (III) RECEIPT OF A NO ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION. COPIES OF THE AGREEMENT COVERING THE ACQUISITION OF THIS WARRANT AND RESTRICTING ITS TRANSFER MAY BE OBTAINED AT NO COST
BY WRITTEN REQUEST MADE BY THE HOLDER OF RECORD OF THIS WARRANT TO THE SECRETARY OF THE COMPANY AT THE PRINCIPAL EXECUTIVE OFFICES OF THE COMPANY. 

Void after [Five Years from Date of Issuance] 

COMPLETE GENOMICS, INC. 

STOCK PURCHASE WARRANT 

No. B-«Warrant_No» 

THIS CERTIFIES THAT, for value received, «LENDER» , or its registered assigns
(hereinafter called the “Holder”) is entitled to purchase from COMPLETE GENOMICS, INC., a Delaware corporation, with its principal place of business at 658 North Pastoria Ave.,
Sunnyvale, CA 94085 (the “Company”), at any time after the date specified in Section 1 hereof and ending at 5:00 p.m. Pacific Standard Time on the Expiration Date, as such term is defined in Section 1 hereof, up to that number of
shares of the Company’s Series B Preferred Stock as calculated in the paragraph below. Upon the initial closing of the Next Financing (as defined below), the Company and the Holder shall execute an acknowledgement in the form attached hereto as
Attachment A, which shall confirm the number of shares (as calculated in the paragraph below) of the Company’s Series B Preferred Stock that Holder is entitled to purchased upon exercise of this Warrant. 

This Warrant (the “Warrant”) is being issued pursuant to the terms of that certain Bridge Loan
Agreement, dated as of February 21, 2007 by and among the Holder, the Company and certain other investors set forth therein (the “Loan Agreement”). This Warrant may be exercised in whole or in part, at the option of the Holder.
Unless otherwise defined herein, defined terms in this Warrant shall have the meanings ascribed to them in the Loan Agreement. Unless indicated otherwise, the number of shares of Series B Preferred Stock that Holder may purchase by exercising this
Warrant is as follows: the quotient of numerator (A) the product of (x) 0.05, (y) the applicable Loan Amount loaned by such Investor at such Closing and (z) the number of months as measured by the number of complete months and the percentage of a
complete month comprised by any less-than-complete month, between the date of the applicable Closing and the date of the closing of the Next Financing (as defined below) and denominator (B) the per share price of the New Preferred Stock issued and
sold in the Next Financing. 

 1. Definitions. As used herein, the following terms shall have the
following respective meanings. Any capitalized terms not defined herein shall have the meaning given to them in the Loan Agreement. 

(a) Subject to Section 5.1, “Exercise Date” shall mean the period ending on the earlier of (i) [Five
Years from Date of Issuance] or (ii) the closing of the initial public offering of the Company’s Common Stock, unless terminated earlier as provided below. 

(b) “Exercise Price” shall mean the per share price of the Series B Preferred Stock sold in the Next
Financing, subject to adjustments pursuant to Section 5 below. 
 (c) “Warrant Shares” shall
mean the shares of the Company’s Series B Preferred Stock issuable upon exercise of this Warrant, subject to adjustments pursuant to the terms herein, including but not limited to adjustment pursuant to Section 5 below. 

2. Term and Vesting Schedule. This Warrant shall be exercisable through the Expiration Date according to the
following schedule: 
 3. Method of Exercise; Payment; Issuance of New Warrant. Subject to Section 1
hereof, the purchase right represented by this Warrant may be exercised by the Holder, in whole or in part, by: 

3.1. the surrender of this Warrant (with an executed notice of exercise in the form attached hereto as
Attachment B and an duly executed Investment Representation Statement in the form attached hereto as Attachment C) by delivery to the Company at its address set forth above (or such other address as it may designate by notice in
writing to the Holder); and 
 3.2. the payment to the Company, by check, wire transfer, forgiveness of
indebtedness, or any combination of the foregoing, of an amount equal to the then applicable Warrant Price per share multiplied by the number of Warrant Shares then being purchased. 

If this Warrant should be exercised in part only, the Company shall, upon surrender of this Warrant, execute and deliver
a new Warrant evidencing the rights of the Holder thereof to purchase the balance of the Warrant Shares purchasable hereunder. Upon receipt by the Company of this Warrant and such notice of exercise, together with, if applicable, the aggregate
Warrant Price, at such office, or by the stock transfer agent or warrant agent of the Company at its office, the Holder shall be deemed to be the holder of record of the applicable Warrant Shares, notwithstanding that the stock transfer books of the
Company shall then be closed or that certificates representing such Warrant Shares shall not then be actually delivered to the Holder. The Company shall pay any and all documentary stamp or similar issue or transfer taxes payable in respect of the
issue or delivery of the Warrant Shares. 
 3.3. Net Exercise. 

(a) In addition to and without limiting the rights of the Holder under the terms of this Warrant, the Holder may elect
to convert this Warrant or any portion thereof (the “Conversion Right”) into Warrant Shares, the aggregate value of which Warrant Shares 

 
shall be equal to the value of this Warrant or the portion thereof being converted. The Conversion Right may be exercised by the Holder by surrender of this Warrant at the principal office of the
Company together with notice of the Holder’s intention to exercise the Conversion Right, in which event the Company shall issue to the Holder a number of Warrant Shares computed using the following formula: 

 

							
		 	 X=
	 	 Y(A-B)
	  	
		 		 	A	  	

 Where: 

X - The number of Warrant Shares to be issued to the Holder upon exercise of the Conversion Right.

 Y- The number of Warrant Shares issuable upon exercise of this Warrant (or such lesser number
as are being exercised). 
 A - The fair market value of one Warrant Share, as determined
pursuant to Section 3.3(b) hereof, as of the time the Conversion Right is exercised pursuant to this Section 3. 

B- Exercise Price for one Warrant Share under this Warrant (as adjusted to the date of such
calculations). 
 Notwithstanding the foregoing, this Warrant shall be deemed to have converted into Warrant Shares pursuant to
this Section 3.3(a) upon the Expiration Date if not previously exercised or converted before such date. 

(b) Fair Market Value. For purposes of Section 3.3, “fair market value of one Warrant
Share” shall mean, as of any date: 
 (i) the last closing price per share of the Company’s
Common Stock on the principal national securities exchange on which the Common Stock is listed or admitted to trading; 

(ii) the last reported sales price per share of the Company’s Common Stock on the NASDAQ Global Market or the
NASDAQ Capital Market (collectively, “Nasdaq”) if the Company’s Common Stock is not listed or traded on any such exchange; 

(iii) the average of the bid and asked price per share as reported in the “pink sheets” published by the
National Quotation Bureau, Inc. (the “pink sheets”) if the Company’s Common Stock is not listed or traded on any exchange or Nasdaq; or 

(iv) if such quotations are not available, the fair market value per share of the New Preferred Stock issued in the Next
Financing on the date such notice was 

 
received by the Company, as determined in good faith by the Board of Directors of the Company. 

4. Stock Fully Paid; Reservation of Warrant Shares. All shares of stock which may be issued upon the exercise of
the rights represented by this Warrant will, upon issuance, be fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issue thereof. During the period within which the rights represented by this Warrant may be
exercised, the Company will at all times have authorized and reserved for the purpose of issue upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its stock to provide for the exercise of the rights
represented by this Warrant. In the event that there is an insufficient number of Warrant Shares reserved for issuance pursuant to the exercise of this Warrant, the Company will take appropriate action to authorize an increase in its capital stock
to allow for such issuance or similar issuance acceptable to the Holder. 
 5. Adjustment of Warrant Price
and Number of Warrant Shares. The number and kind of Warrant Shares purchasable upon the exercise of this Warrant and the Warrant Price shall be subject to adjustment from time to time upon the occurrence of certain events, as follows:

 5.1. Reclassification; Merger. In case of any reclassification or change of outstanding securities of
the class issuable upon exercise of this Warrant (other than a change in par value, or from par value to no par value, or from no par value to par value, or as a result of a subdivision or combination), or in case of any consolidation or merger of
the Company with or into another corporation (other than a merger with another corporation in which the Company is a continuing corporation and which does not result in any reclassification or change of outstanding securities issuable upon exercise
of this Warrant), or any other corporate reorganization in which the Company shall not be the continuing or surviving entity of such consolidation, merger or reorganization, or any transaction in which in excess of 50% of the Company’s voting
power is transferred, or any sale of all or substantially all of the stock or assets of the Company, the Company shall provide to Holder ten (10) days advance written notice of such reorganization, reclassification, consolidation, merger or sale or
other disposition of the Company’s assets, and this Warrant shall terminate unless exercised prior to the date such reorganization, reclassification, consolidation, merger or sale or other disposition of the Company’s assets. 

5.2. Subdivision or Combination of Warrant Shares. If the Company at any time while this Warrant remains
outstanding and unexpired shall subdivide or combine its stock, the Warrant Price shall be proportionately decreased in the case of a subdivision or increased in the case of a combination. 

5.3. Stock Dividends. If the Company at any time while this Warrant is outstanding and unexpired shall pay a
dividend with respect to stock payable in, or make any other distribution with respect to stock (except any distribution specifically provided for in the foregoing Sections 5.1 and 5.2) of, stock, then the Warrant Price shall be adjusted, from and
after the date of determination of stockholders entitled to receive such dividend or distribution, to that price determined by multiplying the Warrant Price in effect immediately prior to such date of determination by a fraction (i) the numerator of
which shall be the total number of shares of stock outstanding immediately prior to such dividend or distribution, and (ii) the denominator of 

 
which shall be the total number of shares of stock outstanding immediately after such dividend or distribution. 

5.4. Adjustment of Number of Warrant Shares. Upon each adjustment in the Warrant Price, the number of shares of
stock purchasable hereunder shall be adjusted, to the nearest whole share, to the product obtained by multiplying the number of Warrant Shares purchasable immediately prior to such adjustment in the Warrant Price by a fraction, the numerator of
which shall be the Warrant Price immediately prior to such adjustment and the denominator of which shall be the Warrant Price immediately thereafter. 

6. Fractional Warrant Shares. No fractional Warrant Shares will be issued in connection with any exercise
hereunder, but in lieu of such fractional shares the Company shall make a cash payment therefor upon the basis of the Warrant Price then in effect. 

7. Compliance with Securities Act; Non-transferability of Warrant; Disposition of Shares of Stock. 

7.1. Compliance with Securities Act. The Holder, by acceptance hereof, agrees that this Warrant and the Warrant
Shares are being acquired for investment and that he, she or it will not offer, sell or otherwise dispose of this Warrant or any Warrant Shares except under circumstances which will not result in a violation of the Securities Act of 1933, as amended
(the “Act”). Upon exercise of this Warrant, the Holder hereof shall confirm in writing, in a form attached hereto as Attachment C, that the Warrant Shares so purchased are being acquired for investment and not with a view
toward distribution or resale. In addition, the Holder shall provide such additional information regarding such Holder’s financial and investment background, as the Company may reasonably request, as is relevant for purposes of determining the
Holder’s suitability with respect to a purchase of the Warrant Shares. All Warrant Shares (unless registered under the Act) shall be stamped or imprinted with a legend in substantially the following form (in addition to any legend required
under applicable state securities laws): 
 THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
1933, AS AMENDED. THIS SECURITY MAY NOT BE SOLD OR TRANSFERRED WITHOUT (I) AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (II) AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE
ACT OR (III) RECEIPT OF A NO ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION. COPIES OF THE WARRANT AGREEMENT COVERING THE ACQUISITION OF THIS SECURITY AND RESTRICTING ITS TRANSFER MAY BE OBTAINED AT NO COST BY WRITTEN REQUEST MADE BY THE
HOLDER OF RECORD OF THIS SECURITY TO THE SECRETARY OF THE COMPANY AT THE PRINCIPAL EXECUTIVE OFFICES OF THE COMPANY. 

7.2. Transferability of Warrant. This Warrant may not be transferred or assigned in whole or in part without (i)
an effective registration statement related thereto, (ii) an opinion of counsel for the Holder, satisfactory to the Company, that such registration is not 

 
required under the Act or (iii) receipt of a no action letter from the Securities and Exchange Commission (together, “Securities Law Compliance Guarantees”); provided,
however, that the Warrant may be transferred in whole or in part without Securities Law Compliance Guarantees upon any of the following provided that the transferee agrees in writing to be subject to the terms hereof to the same extent as if
he/she were an original Holder hereunder: 
 (a) A transfer of the Warrant by a Holder who is a natural person
during such Holder’s lifetime or on death by will or intestacy to such Holder’s immediate family or to any custodian or trustee for the account of such Holder or such Holder’s immediate family. “Immediate family” as
used herein shall mean spouse, lineal descendant, father, mother, brother, or sister of the Holder; 
 (b) A
transfer of the Warrant to the Company; 
 (c) A transfer of the Warrant to a parent, subsidiary or affiliate
of a Holder; or 
 (d) A transfer of the Warrant by a Holder which is a limited or general partnership to any
of its partners or former partners (with, a, b and c, a “Permitted Transfer”). 
 7.3.
Disposition of Warrant Shares. Upon exercise of the Warrant Shares, the Holder will be entitled to any registration rights granted to all holders of the New Preferred Stock issued in the Next Financing. With respect to any offer, sale or
other disposition of any Warrant Shares prior to registration of such shares, the Holder and each subsequent Holder of this Warrant agrees to give written notice to the Company prior thereto, describing briefly the manner thereof, together with a
written opinion of such Holder’s counsel, if requested by the Company, to the effect that such offer, sale or other disposition may be effected without registration or qualification (under the Act as then in effect or any federal or state law
then in effect) of such Warrant Shares and indicating whether or not under the Act certificates for such shares to be sold or otherwise disposed of require any restrictive legend as to applicable restrictions on transferability in order to ensure
compliance with the Act; provided, however, that no such opinion of counsel or no-action letter shall be necessary for a Permitted Transfer if the transferee agrees in writing to be subject to the terms hereof to the same extent as if he/she were an
original Holder hereunder. 
 8. Rights of Stockholders. No Holder of this Warrant shall be entitled to
vote or receive dividends or be deemed the holder of stock or any other securities of the Company which may at any time be issuable on the exercise hereof for any purpose, nor shall anything contained herein be construed to confer upon the Holder of
this Warrant, as such, any of the rights of a stockholder of the Company or any right to vote for the election of directors or upon any matter submitted to stockholders at any meeting thereof, or to give or withhold consent to any corporate action
(whether upon any recapitalization, issuance of stock, reclassification of stock, change of par value or change of stock to no par value, consolidation, merger, conveyance, or otherwise) or to receive notice of meetings, or to receive dividends or
subscription rights or otherwise until this Warrant has been exercised and the Warrant Shares shall have become deliverable, as provided herein. 

 9. Governing Law. The terms and conditions of this Warrant shall be
governed by and construed in accordance with California law, without giving effect to conflict of law principles. 

10. Miscellaneous. The headings in this Warrant are for purposes of convenience and reference only, and shall not
be deemed to constitute a part hereof. All notices and other communications shall be delivered by hand or mailed by first-class registered or certified mail, postage prepaid, to the respective addresses provided in the Loan Agreement, or to such
other address as the Company or Holder may designate to the other parties hereto. 
 11. Loan Agreement.
This Warrant is a Warrant referred to in the Loan Agreement and is entitled to all the benefits provided therein. 

12. Loss, Theft or Destruction of Warrant. Upon receipt by the Company of evidence reasonably satisfactory to it
of the loss, theft or destruction of this Warrant and of indemnity or security reasonably satisfactory to it, the Company will make and deliver an affidavit of lost warrant which shall carry the same rights carried by this Warrant, stating that such
affidavit of lost warrant is issued in replacement of this Warrant, making reference to the original date of issuance of this Warrant (and any successors hereto) and dated as of such cancellation, in lieu of this Warrant. 

13. Amendment and Waiver. Any provision of this Warrant may be waived or amended (either generally or in a
particular instance, either retroactively or prospectively, and either for a specified period of time or indefinitely), pursuant to Section 4.1 of the Loan Agreement. 

(Remainder of Page Intentionally Left Blank) 

 IN WITNESS WHEREOF, the Company has caused this Warrant to be duly executed
by its officers, thereunto duly authorized this      day of February, 2007. 
  

					
	 COMPLETE GENOMICS, INC.

		
	 By:
	 	  

	 Name:
	 	 Clifford A. Reid

	 Title:
	 	 President and Chief Executive Officer

 ATTACHMENT A TO WARRANT NO. B-«Warrant_No» 

ACKNOWLEDGEMENT 

The undersigned hereby acknowledge as follows: 
  

	 	 1.
	 «LENDER». (“Holder”) is the record holder of Stock Purchase Warrant No.
B-«Warrant_No», dated February 21, 2007 (the “Warrant”). 

  

	 	 2.
	 Holder may, by exercising the Warrant, purchase up to that number of shares of Series B Preferred Stock of Complete Genomics, Inc. (the
“Company”) as calculated pursuant to the terms of the Warrant. 

  

	 	 3.
	 The applicable Loan Amount loaned by Holder at the February 21, 2007 Closing is         .

  

	 	 4.
	 The date of closing of the Next Financing is March 19, 2007. 

 

	 	 5.
	 The per share price of the New Preferred Stock issued and sold in the Next Financing is $2.30. 

 

	 	 6.
	 The maximum aggregate number of shares of the Company’s Series B Preferred Stock that Holder may purchase upon exercise of the Warrant,
calculated in accordance with the applicable provisions of the Warrant, is         . 

  

	 	 7.
	 Unless otherwise defined in this Acknowledgement, capitalized terms shall have the meanings ascribed to them in the Warrant.

  

					
	 COMPLETE GENOMICS, INC.

		
	 By:
	 	  

	 Name:
	 	 Clifford A. Reid

	 Title:
	 	 President and Chief Executive Officer

 

			
	 «LENDER»

	 By:
	 	  

	 Name:
	 	  

	 Title:
	 	  

 ATTACHMENT B TO WARRANT NO. B-«Warrant_No» 

NOTICE OF EXERCISE 
  

	 TO:
	 Complete Genomics, Inc. 

1. The undersigned hereby elects to purchase
                     shares of New Preferred Stock of COMPLETE GENOMICS, INC. as defined
in that certain Bridge Loan Agreement, dated February         , 2007 and pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full,
together with all applicable transfer taxes, if any. 
 2. The undersigned hereby elects to convert the attached
Warrant into Warrant Shares in the manner specified in Section 3.3 of the Warrant. This conversion is exercised with respect to
                                         of the
Shares covered by the Warrant. 
 [Strike paragraph above that does not apply.] 

2. Please issue a certificate or certificates representing said shares of stock in the name of the undersigned or in such
other name as is specified below: 
  

									
		 	 Name:
	  	  
	 		 	
		 	 Address:
	  	  
	 		 	
		 		  	  
	 		 	
		 		  	  
	 		 	

 3. The undersigned represents that the aforesaid shares of stock are being acquired
for the account of the undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares. In support thereof, the
undersigned has executed an Investment Representation Statement attached hereto as Attachment C. 
  

									
		 	 «LENDER»
	 		 		 	
		 	 By:
	 	  
	 		 	
		 	 Name:
	 	  
	 		 	
		 	 Title:
	 	  
	 		 	

Date:                    

 ATTACHMENT C TO WARRANT NO. «Warrant_No» 

INVESTMENT REPRESENTATION STATEMENT 
  

					
	 PURCHASER
	 	 :
	    	
	 COMPANY
	 	 :
	    	 Complete Genomics, Inc.

	 SECURITY
	 	 :
	    	
	 AMOUNT
	 	 :
	    	
	 DATE
	 	 :
	    	

 In connection with the purchase of the above-listed securities and underlying stock
(the “Securities”), the undersigned represents to the Company the following: 
 (a) I/We am
purchasing these Securities for my/our own account for investment purposes only and not with a view to, or for the resale in connection with, any “distribution” thereof for purposes of the Securities Act of 1933, as amended (the
“Act”). 
 (b) I/We understand that the Securities have not been registered under the Act in
reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of my/our investment intent as expressed herein. In this connection, I/we understand that, in the view of the Securities and
Exchange Commission (the “SEC”), the statutory basis for such exemption may be unavailable if my/our representation was predicated solely upon a present intention to hold these Securities for the minimum capital gains period
specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the Securities, or for a period of one year or any other fixed period in the future. 

(c) I/We further understand that the Securities must be held indefinitely unless subsequently registered under the Act or
unless an exemption from registration is otherwise available. Moreover, I/we understand that the Company is under no obligation to register the Securities. In addition, I/we understand that the certificate evidencing the Securities will be imprinted
with a legend which prohibits the transfer of the Securities unless they are registered or such registration is not required in the opinion of counsel for the Company. 

(d) I/We am/are aware of the provisions of Rule 144, promulgated under the Act, which, in substance, permits limited
public resale of “restricted securities” acquired, directly or indirectly, from the issuer thereof (or from an affiliate of such issuer), in a non-public offering subject to the satisfaction of certain conditions. 

(e) I/We further understand that at the time I/we wish to sell the Securities there may be no public market upon which to
make such a sale. 
  

			
	 «LENDER»

		
	 By:
	 	  

	 Name:
	 	  

	 Title:

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