=============================================================================
                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C.  20549

                                 SCHEDULE 13D
                Under the Securities and Exchange Act of 1934

                             (Amendment No. 4)1

                                Solexa, Inc.
               ------------------------------------------------
                               (Name of Issuer)

                    Common Stock, Par Value $0.01 per share
                ------------------------------------------------
                        (Title of Class of Securities)

                                  83420X105
                ------------------------------------------------
                               (CUSIP Number)

                           Allison Bennington, Esq.
                              ValueAct Capital
                       435 Pacific Avenue, Fourth Floor
                          San Francisco, CA  94133
                               (415) 362-3700
                ------------------------------------------------
                 (Name, address and telephone number of Person
                 Authorized to Receive Notices and Communications)

                         Christopher G. Karras, Esq.
                                 Dechert LLP
                                  Cira Centre
                                2929 Arch Street
                          Philadelphia, PA 19104-2808
                                (215) 994-4000

                                  May 19, 2006
                ------------------------------------------------
             (Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report
the acquisition that is the subject of this Schedule 13D, and is filing this
schedule because of 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the
following box [ ].

Note:  Schedules filed in paper format shall include a signed original and five
copies of the schedule, including all exhibits. See Rule 240.13d-7 for other
parties to whom copies are to be sent.

1The remainder of this cover page shall be filled out for a reporting person's
initial filing on this form with respect to the subject class of securities, and
for any subsequent amendment containing information which would alter
disclosures provided in a prior cover page.

This information required on the remainder of this cover page shall not be
deemed to be "filed" for the purpose of Section 18 of the Securities Exchange
Act of 1934 ("Act") or otherwise subject to the liabilities of that section of
the Act but shall be subject to all other provisions of the Act (however, see
the Notes).
=============================================================================


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                             Page 2 of 17
-----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   ValueAct Capital Master Fund, L.P.
-----------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
-----------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS (See Instructions)*                                   WC*

-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                         [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION                British Virgin Islands

-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    PN
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                             Page 3 of 17
----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   VA Partners, L.L.C.
-----------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
-----------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                         [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   Delaware
-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    00 (LLC)
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                             Page 4 of 17
----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   ValueAct Capital Management, L.P.
-----------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
-----------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                         [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   Delaware
-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    PN
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                             Page 5 of 17
----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   ValueAct Capital Management, LLC
-----------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
-----------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                         [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   Delaware
-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    00 (LLC)
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                             Page 6 of 17
-----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   Jeffrey W. Ubben
---------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
-----------------------------------------------------------------------------
3. SEC USE ONLY

---------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                         [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   United States
-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    IN
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                              Page 7 of 17
-----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   George F. Hamel, Jr.
---------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
-----------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                        [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   United States
-----------------------------------------------------------------------------
                   7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES          8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH     9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    IN
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                              Page 8 of 17
-----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   Peter H. Kamin
-----------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
---------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                        [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   United States
-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         3,124,040**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        3,124,040**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    3,124,040**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    8.6%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    IN
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5


                                SCHEDULE 13D
--------------------------                          -------------------------
CUSIP NO. 83420X105                                              Page 9 of 17
-----------------------------------------------------------------------------
1. NAME OF REPORTING PERSON/S.S. OR I.R.S. INDENTIFICATION NO. OF ABOVE
   PERSON (entities only)

   G. Mason Morfit
-----------------------------------------------------------------------------
2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*                  (a) [X]
                                                                      (b) [ ]
---------------------------------------------------------------------------
3. SEC USE ONLY

-----------------------------------------------------------------------------
4. SOURCE OF FUNDS*

   00*
-----------------------------------------------------------------------------
5. CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
   PURSUANT TO ITEMS 2(d) or 2(e)                                        [ ]
-----------------------------------------------------------------------------
6. CITIZENSHIP OR PLACE OF ORGANIZATION

   United States
-----------------------------------------------------------------------------
                    7.  SOLE VOTING POWER
                        0
   NUMBER OF       ----------------------------------------------------------
   SHARES           8.  SHARED VOTING POWER
   BENEFICIALLY         2,890**
   OWNED BY EACH   ----------------------------------------------------------
   PERSON WITH      9.  SOLE DISPOSITIVE POWER
                        0
                   ----------------------------------------------------------
                   10.  SHARED DISPOSITIVE POWER
                        2,890**
-----------------------------------------------------------------------------
11. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

    2,890**
-----------------------------------------------------------------------------
12. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
    CERTAIN SHARES                                                        [ ]
-----------------------------------------------------------------------------
13. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

    Less than 1%
-----------------------------------------------------------------------------
14. TYPE OF REPORTING PERSON

    IN
-----------------------------------------------------------------------------
*See Item 3
**See Item 2 and 5



THE PURPOSE OF THIS AMENDMENT NO. 4 TO SCHEDULE 13D IS TO AMEND THE
OWNERSHIP REPORTS OF THE REPORTING PERSONS.  THE INFORMATION BELOW
SUPPLEMENTS THE INFORMATION PREVIOUSLY PROVIDED.

Item 1.     Security and Issuer

      This Schedule 13D relates to the Common Stock, par value $0.01 per
share (the "Common Stock"), of Solexa, Inc., a Delaware corporation
(the "Issuer").  The address of the principal executive offices of the
Issuer is 25861 Industrial Blvd, Hayward, CA 94545.

Item 2.     Identity and Background

      This statement is filed jointly by (a) ValueAct Capital Master Fund,
L.P. ("ValueAct Master Fund"), (b) VA Partners, L.L.C. ("VA Partners"), (c)
ValueAct Capital Management, L.P. ("ValueAct Management L.P. "), (d)
ValueAct Capital Management, LLC ("ValueAct Management LLC"), (e) Jeffrey
W. Ubben, (f) George F. Hamel, Jr., (g) Peter H. Kamin and (h) G. Mason
Morfit (collectively, the "Reporting Persons").

       ValueAct Master Fund is a limited partnership organized under the
laws of the British Virgin Islands. ValueAct Master Fund has a principal
business addres of 435 Pacific Avenue, Fourth Floor, San Francisco, CA
94133.

      VA Partners is a Delaware limited liability company, the principal
business of which is to serve as the General Partner to ValueAct Master
Fund. VA Partners has a principal business address of 435 Pacific Avenue,
Fourth Floor, San Francisco, CA 94133.

      ValueAct Management L.P. is a Delaware limited partnership which
renders management services to ValueAct Master Fund.  ValueAct Management
LLC is a Delaware limited liability company, the principal business of
which is to serve as the General Partner to ValueAct Management L.P.  Each
has a principal business address of 435 Pacific Avenue, Fourth Floor, San
Francisco, CA 94133.

     (a), (b) and (c). Messrs. Ubben, Hamel and Kamin are each managing
members, principal owners and controlling persons of VA Partners and
ValueAct Management LLC, and such activities constitute their principal
occupations.  Such individuals are sometimes collectively referred to
herein as the  "Managing Members" or individually as a "Managing Member".
Messr. Morfit is a Non-Managing Member, sometimes referred to herein as a
"Member" of VA Partners and ValueAct Management LLC. Each Managing Member
and Member is a United States citizen and has a principal business address
of 435 Pacific Avenue, Fourth Floor, San Francisco, CA
94133.

     (d) and (e). None of the entities or persons identified in this Item 2
has during the past five years been convicted of any criminal proceeding
(excluding traffic violations or similar misdemeanors), nor been a party to
a civil proceeding of a judicial or administrative body of competent
judgment, decree or final order enjoining future violations of, or
prohibiting or mandating activities subject to, federal or state securities
laws or finding any violation with respect to such laws.

                              Page 10 of 17



ITEM 3.  SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.

         The source of funds used for the purchase of the Issuer's
securities was disclosed in Item 3 of Schedule 13D filed by the Reporting
Persons with the Securities and Exchange Commission on January 30, 2006.

Item 4.     Purpose of Transaction

      The Reporting Persons have acquired the Issuer's Common Stock for
investment purposes, and such purchases have been made in the Reporting
Persons' ordinary course of business.

      In pursuing such investment purposes, the Reporting Persons may
further purchase, hold, vote, trade, dispose or otherwise deal in the
Common Stock at times, and in such manner, as they deem advisable to
benefit from changes in market prices of such Common Stock, changes in the
Issuer's operations, business strategy or prospects, or from sale or merger
of the Issuer.  To evaluate such alternatives, the Reporting Persons will
routinely monitor the Issuer's operations, prospects, business development,
management, competitive and strategic matters, capital structure, and
prevailing market conditions, as well as alternative investment
opportunities, liquidity requirements of the Reporting Persons and other
investment considerations.  Consistent with its investment research methods
and evaluation criteria, the Reporting Persons may discuss such matters
with management or directors of the Issuer, other shareholders, industry
analysts, existing or potential strategic partners or competitors,
investment and financing professionals, sources of credit and other
investors.  Such factors and discussions may materially affect, and result
in, the Reporting Persons' modifying their ownership of Common Stock,
exchanging information with the Issuer pursuant to appropriate
confidentiality or similar agreements, proposing changes in the Issuer's
operations, governance or capitalization, or in proposing one or more of
the other actions described in subsections (a) through (j) of Item 4 of
Schedule 13D.

               In a Securities Purchase Agreement dated as of November 18,
2005 (the "Purchase Agreement") by and among the Issuer, ValueAct Master Fund
and various other investors (the "Investors") for a private placement of
common stock and warrants to purchase common stock. Pursuant to the Purchase
Agreement, the Issuer sold approximately 3,851,840 shares of common stock and
warrants to purchase up to approximately 1,348,145 shares of common stock on
November 23, 2005 in a first closing (the "First Closing"). And an additional
6,148,160 shares of common stock and warrants to purchase up to approximately
3,151,855 shares of common stock in a second closing (the "Second Closing").
At the First Closing, which occurred on November 23, 2005, ValueAct Master
Fund purchased 0 of the Issuer's common stock and warrants to purchase 0
shares of the Issuer's common stock.  At the Second Closing, which occurred
on January 19, 2006, ValueAct Master Fund purchased 230,770 of the Issuer's
common stock at a price of $6.50 and warrants to purchase 80,770 shares of
the Issuer's common stock with an exercise price of $7.50 per share.

         The foregoing description of certain provisions of the Purchase
Agreement is qualified in its entirety by reference to the Purchase
Agreement, which is attached to the 13D, filed January 30, 2006, as
Exhibit B and the terms of which are incorporated therein by reference.


                              Page 11 of 17


      The Reporting Persons reserve the right to formulate other plans
and/or make other proposals, and take such actions with respect to their
investment in the Issuer, including any or all of the actions set forth in
paragraphs (a) through (j) of Item 4 of Schedule 13D, or acquire additional
Common Stock or dispose of all the Common Stock beneficially owned by them,
in the public market or privately negotiated transactions.  The Reporting
Persons may at any time reconsider and change their plans or proposals
relating to the foregoing.

Item 5.     Interest in Securities of the Issuer

(a) and (b).  Set forth below is the beneficial ownership of shares
of Common Stock of the Issuer for each person named in Item 2.  Shares
reported as beneficially owned by ValueAct Master Fund are also reported as
beneficially owned by (i) VA Partners, as General Partner of each such
investment partnership,(ii) ValueAct Management L.P. as the manager of each
such investment partnership, (iii) ValueAct Management LLC, as General
Partner of ValueAct Management L.P. and (iv) the Managing Members as
controlling persons of VA Partners and ValueAct Management LLC.  VA
Partners, ValueAct Management LLC and the Managing Members also, directly
or indirectly, may own interests in one or more than one of the
partnerships from time to time.  Unless otherwise indicated below, by
reason of such relationships each of the ValueAct Master Fund is reported
as having shared power to vote or to direct the vote, and shared power to
dispose or direct the disposition of, such shares of Common Stock, with VA
Partners, ValueAct Management L.P., ValueAct Management LLC and the
Managing Members.

     As of the date hereof, ValueAct Master Fund is the beneficial owner of
3,124,040 shares of Common Stock (which includes warrants to purchase
80,770 shares of common stock which are exercisable within 60 days of
the date hereof), representing approximately 8.6% of the Issuer's
outstanding Common Stock.  VA Partners, ValueAct Management L.P.,
ValueAct Management LLC and the Managing Members may each be deemed the
beneficial owner of an aggregate of 3,124,040 shares of Common Stock
(which includes warrants to purchase 80,770 shares of common stock which
are exercisable within 60 days of the date hereof), representing
approximately 8.6% of the Issuer's outstanding Common Stock.  Mr. Morfit
is the beneficial owner of 2,890 shares of Common Stock, acquired as
director of the Issuer and under an agreement with ValueAct Master Fund,
Messr. Morfit is deemed to hold the stock for the benefit of ValueAct
Master Fund, and indirectly for VA Partners, LLC as general partner of
ValueAct Master Fund, representing less than 1% of the Issuer's
outstanding Common Stock. All percentages set forth in this Schedule 13D
are based upon the Issuer's reported 36,488,011 outstanding shares of
Common Stock reported as of March 31, 2006.

(c) The  following  transactions  in the  Issuer's  Common  Stock were
effected by the Reporting  Persons.

Reporting Person          Trade Date     Warrants     Price/Share
----------   	        ---------      -------     -----------
ValueAct Master Fund      01/19/2006      80,770        $7.50


 (d) and (e)  Not applicable.

                              Page 12 of 17


Item 6.     Contracts, Arrangements, Understandings or Relationships with
Respect to Securities of the Issuer

       Other than as described elsewhere in this Report and as previously
reported, the Reporting Persons have no understandings, arrangements,
relationships or contracts relating to the Issuer's Common Stock which are
required to be described hereunder.

Item 7.		Material to Be Filed as Exhibits

(1) Joint Filing Agreement



                              Page 13 of 17


                                  SIGNATURE
              After reasonable inquiry and to the best of his knowledge and
belief, the undersigned certifies that the information set forth in this
statement is true, complete and correct.

                               POWER OF ATTORNEY
KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears
below on this Schedule 13D hereby constitutes and appoints Jeffrey W. Ubben,
George F. Hamel, Jr. and Peter H. Kamin, and each of them, with full power to
act without the other, his or its true and lawful attorney-in-fact and agent,
with full power of substitution and resubstitution, for him or it and in his
or its name, place and stead, in any and all capacities (until revoked in
writing) to sign any and all amendments to this Schedule 13D, and to file the
same, with all exhibits thereto and other documents in connection therewith,
with the Securities and Exchange Commission, granting unto said attorneys-in
fact and agents, and each of them, full power and authority to do and perform
each and every act and thing requisite and necessary fully to all intents and
purposes as he or it might or could do in person, thereby ratifying and
confirming all that said attorneys-in-fact and agents or any of them, or
their or his substitute or substitutes, may lawfully do or cause to be done
by virtue hereof.

                              ValueAct Capital Master Fund L.P., by
                              VA Partners, L.L.C., its General Partner

                              By:     /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member

                              VA Partners, L.L.C.

                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member


                               ValueAct Capital Management, L.P., by
                               ValueAct Capital Management, LLC its
                               General Partner

                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member


                               ValueAct Capital Management, LLC

                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member


                              Page 14 of 17



                              By:    /s/  Jeffrey W. Ubben
                                --------------------------------------
Dated:  May 19, 2006            Jeffrey W. Ubben, Managing Member


                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member


                              By:    /s/  Peter H. Kamin
                                --------------------------------------
Dated:  May 19, 2006            Peter H. Kamin, Managing Member


                              By:    /s/  G. Mason Morfit
                                --------------------------------------
Dated:  May 19, 2006            G. Mason Morfit, Member


                              Page 15 of 17

  
                                 Exhibit 1
JOINT FILING UNDERTAKING
The undersigned parties hereby agree that the Schedule 13D filed herewith
(and any amendments thereto) relating to the Common Stock of Solexa, Inc. is
being filed jointly on behalf of each of them with the Securities and
Exchange Commission pursuant to Section 13(d) of the Securities Exchange Act
of 1934, as amended.

                           ValueAct Capital Master Fund L.P., by
                              VA Partners, L.L.C., its General Partner

                              By:     /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member



                              VA Partners, L.L.C.

                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member



                               ValueAct Capital Management, L.P.,
                               by, ValueAct Capital Management, LLC
                               its General Partner

                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member



                               ValueAct Capital Management, LLC

                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member


                              Page 16 of 17



                              By:    /s/  Jeffrey W. Ubben
                                --------------------------------------
Dated:  May 19, 2006            Jeffrey W. Ubben, Managing Member


                              By:    /s/  George F. Hamel, Jr.
                                --------------------------------------
Dated:  May 19, 2006            George F. Hamel, Jr., Managing Member


                              By:    /s/  Peter H. Kamin
                                --------------------------------------
Dated:  May 19, 2006            Peter H. Kamin, Managing Member


                              By:    /s/  G. Mason Morfit
                                --------------------------------------
Dated:  May 19, 2006            G. Mason Morfit, Member

                              Page 17 of 17