exv10w44



 







Exhibit 10.44




[SOLEXA LETTERHEAD]




May 19, 2006



VIA HAND DELIVERY




Linda M. Rubinstein

Solexa, Inc.

25861 Industrial Boulevard

Hayward, CA 94545





			
	Re:	 	Salary Increase and New Alternative One-Time Bonus Arrangement




Dear Linda:



This letter confirms your recent salary increase and contains the terms and conditions of the new
alternative one-time bonus arrangement that Solexa, Inc. (“Solexa” or the “Company”) is offering
you, subject to the terms and conditions set forth in this letter. This new bonus arrangement will
be a supplemental bonus arrangement and it does not replace or cancel any other current bonus
program of the Company.




A. Salary Increase:



We are pleased to confirm that your annual base salary was increased to $261,700, retroactive to
January 1, 2006.




B. New Bonus Overview:



The two below potential bonuses are alternative one-time bonuses. Accordingly, if the terms and
conditions are met for one of these bonuses at any time, you will not earn or be eligible to
receive any additional such bonus, and you will not earn or be eligible to receive the other
one-time bonus (even if the applicable terms and conditions subsequently are met). In addition,
because the alternative one-time bonuses are intended to incentivize you with respect to your
employment services and your continued employment with the Company, in order to earn and be
eligible to receive either of the below alternative one-time bonuses, you must remain an employee
in good standing of the Company (or a successor entity) as of the date that such bonus is earned.



Additional specific terms and conditions of each alternative one-time bonus are set forth below.




1. One-Time Market Capitalization Bonus:



In the event that the closing price of the Company’s common stock equals or exceeds twenty-seven
dollars and sixty cents ($27.60) per share (as presently constituted) for each of twenty-five (25)
consecutive public trading days (the “Trading Period”), you will be entitled to receive a one-time
bonus of seventy-seven thousand, one hundred fifty-one (77,151) shares of the Company’s common
stock (as adjusted for stock splits, stock dividends or the like) pursuant to the Company’s 2005
Equity Incentive Plan (the “Plan”) (the “Market Capitalization Bonus”). If it is reasonably
determined by the Company that it would be inadvisable or impractical for you to sell or otherwise
dispose of a portion of the common stock constituting the Market Capitalization Bonus for the
purposes of paying applicable taxes, the Company may at its election provide you with cash
compensation in lieu of a portion of the common stock sufficient to pay, valued based on the
average of the per share closing prices during the Trading





 









 








Linda M. Rubinstein

May 19, 2006

Page 2 of 3



Period, the taxes applicable to the Market Capitalization Bonus, with the remaining portion of the
Market Capitalization Bonus to be provided as Company common stock pursuant to the Plan.



If earned, the Market Capitalization Bonus will be provided to you within forty-five (45) days
after the Trading Period. Notwithstanding the preceding sentence, at your written election,
delivery of all or a portion of the Market Capitalization Bonus will be delayed until January 15 of
the tax year following the year in which the bonus is earned, without any interest or additional
consideration being owed to you. The Company shall make all determinations and calculations
regarding whether and when the Market Period Capitalization Bonus has been earned and the amount of
the Market Capitalization Bonus.




2. One-Time Change in Control Bonus:



In the event of a Change in Control (as defined below), you shall be eligible to receive a bonus
equivalent to one quarter of one percent (.25%) of the amount by which the consideration received
by the Company’s stockholders as a direct result of the Change in Control exceeds the sum of One
Hundred Fifty Million Dollars ($150,000,000) plus the aggregate gross proceeds received by the
Company through sales of equity securities occurring after the date of this letter (the “Change in
Control Bonus”).



The Change in Control Bonus will be provided to you in the same form as the consideration received
by the Company’s stockholders as a direct result of the Change in Control. For example, if cash is
the consideration provided to the Company’s stockholders as a direct result of the Change in
Control, you will be provided a cash Change in Control Bonus; and if the consideration provided to
the Company’s stockholders as a direct result of the Change in Control consists of securities or
other non-cash consideration, your Change in Control Bonus (if earned) will be paid in such form
and determined based on the value thereof established in the Change in Control, provided that,
notwithstanding the preceding, the Company may in its sole discretion elect to substitute cash for
all or any portion of the securities or other non-cash consideration that would otherwise be
payable based on the value thereof established in the Change in Control. The Company shall make
all determinations and calculations regarding whether the Change in Control Bonus has been earned
and the amount of the Change in Control Bonus.



For purposes of the Change in Control Bonus, a “Change of Control” means the happening of any of
the following events: (a) a dissolution or liquidation of Solexa; (b) a sale, lease, exchange or
other transfer (in one transaction or a series of related transactions) of all or substantially all
of the assets of Solexa; (c) a consolidation or merger of Solexa in which Solexa is not the
continuing or surviving corporation or pursuant to which the stock of Solexa would be converted
into cash, securities or other property, other than a merger or consolidation of Solexa in which
the holders of such entity’s stock immediately prior to the merger or consolidation hold more than
fifty percent (50%) of the stock or other forms of equity of the surviving corporation immediately
after the merger in substantially the same proportions of ownership of shares of Solexa
immediately prior to the merger or consolidation; or (d) a sale or exchange by the shareholders of
Solexa, in a single transaction or series of related transactions, of more than fifty percent (50%)
of the voting stock of such entity, after which the shareholders of such entity immediately before
such transaction do not retain immediately after such transaction, in substantially the same
proportions of their ownership of shares of Solexa immediately before the transaction, direct or
indirect beneficial ownership of more than fifty percent (50%) of the combined voting power of such
entity.




C. Miscellaneous:



Nothing in this letter is intended to alter the at-will nature of your employment with the Company.
In addition, this letter does not alter any existing agreement between you and the Company
(including but not limited to your offer letter agreement dated March 23, 2005), except to the
extent such other existing





 









 








Linda M. Rubinstein

May 19, 2006

Page 3 of 3



agreement contains any terms inconsistent with this letter, which inconsistent terms are hereby
superseded. This letter constitutes the complete, final and exclusive embodiment of the entire
agreement between the Company and you with regard to this subject matter. It is entered into
without reliance on any promise or representation, written or oral, other than those expressly
contained herein, and it supersedes any other such promises, warranties or representations. This
letter agreement may not be modified or amended except in a writing signed by you and a duly
authorized officer of the Company. This letter agreement will bind the heirs, personal
representatives, successors and assigns of both you and the Company, and inure to the benefit of
both you and the Company, their heirs, successors and assigns. If any provision of this letter
agreement is determined to be invalid or unenforceable, in whole or in part, this determination
shall not affect any other provision of this letter agreement and the provision in question shall
be modified so as to be rendered enforceable in a manner consistent with the intent of the parties
insofar as possible under applicable law. This letter agreement shall be construed and enforced in
accordance with the laws of the State of California without regard to conflicts of law principles.
Any ambiguity in this letter agreement shall not be construed against either party as the drafter.
Any waiver of a breach of this letter agreement, or rights hereunder, shall be in writing and shall
not be deemed to be a waiver of any successive breach or rights hereunder. This letter agreement
may be executed in counterparts which shall be deemed to be part of one original, and facsimile
signatures shall be equivalent to original signatures.



To indicate your understanding and acceptance of your salary increase and new bonus arrangement,
please sign and date this letter below, and return this letter to me within five (5) business days.
You may retain the enclosed additional copy of this letter for your files.



We are very pleased to offer these new employment terms, and look forward to a continued productive
employment relationship.




	 	 	 
	Sincerely,

Solexa, Inc.
	 	 
	 
	 	 
	/s/ John West
	 	 
	 

John West

	 	 
	Chief Executive Officer
	 	 
	 
	 	 
	UNDERSTOOD AND AGREED:
	 	 
	 
	 	 
	/s/ Linda M. Rubsinstein
	 	 
	 

Linda M. Rubinstein

	 	 
	 
	 	 
	5/19/06 

	 	 
	Date