*************************************************************
****                                                     ****
****            Output from PHASE v2.0                   ****
****  Code by M Stephens, with contributions from N Li   ****
****                                                     ****
*************************************************************

BEGIN COMMAND_LINE 
/usr/local/genome/lib/phase/PHASE2 -d1 cxcr4.phase.inp cxcr4.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
cxcr4.phase.out_freqs : haplotype frequency estimates
cxcr4.phase.out_pairs : most likely haplotype pairs for each individual
cxcr4.phase.out_recom : estimates of recombination parameters
cxcr4.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 10
Positions of loci: 517 602 720 877 2782 2996 3570 3684 4139 6474 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file cxcr4.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1  TTCCCACCTT   10.000000
         2  TTCCCACTTT   28.000000
         3  TTCCCACTAT   22.000000
         4  TTCCCATCTT    3.000000
         5  TTCCCCCTTT    4.000000
         6  TTCCTACCAT   11.000000
         7  TTCACACTTT    7.000000
         8  TTGCCATCTC    3.000000
         9  TTGCCATCTT    1.000000
        10  CTCCCACCTT    1.000000
        11  CGCCCACCTT    4.000000
END LIST_SUMMARY


Summary of best reconstruction
(numbers refer to the list of haplotypes given above)

BEGIN BESTPAIRS_SUMMARY
D001: (2,8)
D002: (1,7)
D003: (7,7)
D004: (1,11)
D005: (1,4)
D006: (7,10)
D007: (3,6)
D008: (2,2)
D009: (2,11)
D010: (1,7)
D011: (7,8)
D012: (1,2)
D013: (2,9)
D014: (2,4)
D015: (1,1)
D016: (2,2)
D033: (2,2)
D034: (1,8)
D035: (1,2)
D036: (3,6)
D037: (2,4)
D038: (6,7)
D039: (2,3)
D040: (11,11)
E001: (2,5)
E002: (3,3)
E003: (2,6)
E004: (5,6)
E005: (2,3)
E006: (5,6)
E007: (2,3)
E008: (2,3)
E009: (2,3)
E010: (3,6)
E011: (3,6)
E012: (3,6)
E013: (2,2)
E014: (3,6)
E015: (3,5)
E016: (2,2)
E017: (3,3)
E018: (3,3)
E019: (2,3)
E020: (2,3)
E021: (2,3)
E022: (1,3)
E023: (2,6)
END BESTPAIRS_SUMMARY


Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:

BEGIN BESTPAIRS1
0 D001
T T C C C A C T T T 
T T G C C A T C T C 
0 D002
T T C C C A C C T T 
T T C A C A C T T T 
0 D003
T T C A C A C T T T 
T T C A C A C T T T 
0 D004
T T C C C A C C T T 
C G C C C A C C T T 
0 D005
T T C C C A C C T T 
T T C C C A T C T T 
0 D006
(T) T C A C A C T T T 
(C) T C C C A C C T T 
0 D007
T T C C C A C T A T 
T T C C T A C C A T 
0 D008
T T C C C A C [T] T T 
T T C C C A C [T] T T 
0 D009
T T C C C A C T T T 
C G C C C A C C T T 
0 D010
T T C C C A C C T T 
T T C A C A C T T T 
0 D011
T T C A C A C T T T 
T T G C C A T C T C 
0 D012
T T C C C A C C T T 
T T C C C A C T T T 
0 D013
T T C C C A C T T T 
T T G C C A T C T T 
0 D014
T T C C C A C T T T 
T T C C C A T C T T 
0 D015
T T C C C A C C T T 
T T C C C A C C T T 
0 D016
T T C C C A C T T T 
T T C C C A C T T T 
0 D033
T T C C C A C [T] T T 
T T C C C A C [T] T T 
0 D034
T T C C C A C C T T 
T T G C C A T C T C 
0 D035
T T C C C A C C T T 
T T C C C A C T T T 
0 D036
T T C C C A C T A T 
T T C C T A C C A T 
0 D037
T T C C C A C T T T 
T T C C C A T C T T 
0 D038
T T C C T A C C A T 
T T C A C A C T T T 
0 D039
T T C C C A C T T T 
T T C C C A C T A T 
0 D040
C G C C C A C C T T 
C G C C C A C C T T 
0 E001
T T C C C A C T T T 
T T C C C C C T T T 
0 E002
T T C C C A C T A T 
T T C C C A C T A T 
0 E003
T T C C C A C T T T 
T T C C T A C C A T 
0 E004
T T C C C C C T T T 
T T C C T A C C A T 
0 E005
T T C C C A C T T T 
T T C C C A C T A T 
0 E006
T T C C C C C T T T 
T T C C T A C C A T 
0 E007
T T C C C A C T  T  T 
T T C C C A C T [A] T 
0 E008
T T C C C A C [T] T T 
T T C C C A C  T  A T 
0 E009
T T C C C A C T T T 
T T C C C A C T A T 
0 E010
T T C C C A C T A T 
T T C C T A C C A T 
0 E011
T T C C C A C T A T 
T T C C T A C C A T 
0 E012
T T C C C A C T A T 
T T C C T A C C A T 
0 E013
T T C C C A C T T T 
T T C C C A C T T T 
0 E014
T T C C C A C T A T 
T T C C T A C C A T 
0 E015
T T C C C A C T A T 
T T C C C C C T T T 
0 E016
T T C C C A C T T T 
T T C C C A C T T T 
0 E017
T T C C C A C T A T 
T T C C C A C T A T 
0 E018
T T C C C A C T A T 
T T C C C A C T A T 
0 E019
T T C C C A C T T T 
T T C C C A C T A T 
0 E020
T T C C C A C T T T 
T T C C C A C T A T 
0 E021
T T C C C A C T T T 
T T C C C A C T A T 
0 E022
T T C C C A C C T T 
T T C C C A C T A T 
0 E023
T T C C C A C T T T 
T T C C T A C C A T 
END BESTPAIRS1


Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []
with phase known positions indicated by =

BEGIN BESTPAIRS2
0 D001
= = C = = = C T = T 
= = G = = = T C = C 
0 D002
= = = C = = = C = = 
= = = A = = = T = = 
0 D003
= = = = = = = = = = 
= = = = = = = = = = 
0 D004
T T = = = = = = = = 
C G = = = = = = = = 
0 D005
= = = = = = C = = = 
= = = = = = T = = = 
0 D006
(T) = = A = = = T = = 
(C) = = C = = = C = = 
0 D007
= = = = C = = T = = 
= = = = T = = C = = 
0 D008
= = = = = = ? ? = = 
= = = = = = ? ? = = 
0 D009
T T = = = = = T = = 
C G = = = = = C = = 
0 D010
= = = C = = = C = = 
= = = A = = = T = = 
0 D011
= = C A = = C T = T 
= = G C = = T C = C 
0 D012
= = = = = = = C = = 
= = = = = = = T = = 
0 D013
= = C = = = C T = = 
= = G = = = T C = = 
0 D014
= = = = = = C T = = 
= = = = = = T C = = 
0 D015
= = = = = = = = = = 
= = = = = = = = = = 
0 D016
= = = = = = = = = = 
= = = = = = = = = = 
0 D033
= = = = = = ? ? = = 
= = = = = = ? ? = = 
0 D034
= = C = = = C = = T 
= = G = = = T = = C 
0 D035
= = = = = = = C = = 
= = = = = = = T = = 
0 D036
= = = = C = = T = = 
= = = = T = = C = = 
0 D037
= = = = = = C T = = 
= = = = = = T C = = 
0 D038
= = = C T = = C A = 
= = = A C = = T T = 
0 D039
= = = = = = = = T = 
= = = = = = = = A = 
0 D040
= = = = = = = = = = 
= = = = = = = = = = 
0 E001
= = = = = A = = = = 
= = = = = C = = = = 
0 E002
= = = = = = = = = = 
= = = = = = = = = = 
0 E003
= = = = C = = T T = 
= = = = T = = C A = 
0 E004
= = = = C C = T T = 
= = = = T A = C A = 
0 E005
= = = = = = = = T = 
= = = = = = = = A = 
0 E006
= = = ? C C = T T = 
= = = ? T A = C A = 
0 E007
= = = = ? ? = = ? = 
= = = = ? ? = = ? = 
0 E008
= = = = = = ? ? T = 
= = = = = = ? ? A = 
0 E009
= = = = = = = = T = 
= = = = = = = = A = 
0 E010
= = = = C = = T = = 
= = = = T = = C = = 
0 E011
= = = = C = = T = = 
= = = = T = = C = = 
0 E012
= = = = C = = T = = 
= = = = T = = C = = 
0 E013
= = = = = = = = = = 
= = = = = = = = = = 
0 E014
= = = = C = = T = = 
= = = = T = = C = = 
0 E015
= = = = = A = = A = 
= = = = = C = = T = 
0 E016
= = = = = = ? = = = 
= = = = = = ? = = = 
0 E017
= = = = = = = = = = 
= = = = = = = = = = 
0 E018
= = = = = = = = = = 
= = = = = = = = = = 
0 E019
= = = = = = = = T = 
= = = = = = = = A = 
0 E020
= = = = = ? = = T = 
= = = = = ? = = A = 
0 E021
= = = = = = = = T = 
= = = = = = = = A = 
0 E022
= = = = = = = C T = 
= = = = = = = T A = 
0 E023
= = = = C = = T T = 
= = = = T = = C A = 
END BESTPAIRS2


Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?

BEGIN PHASEPROBS
= = 1.00 = = = 1.00 1.00 = 1.00 
= = = 0.94 = = = 1.00 = = 
= = = = = = = = = = 
1.00 1.00 = = = = = = = = 
= = = = = = 1.00 = = = 
0.60 = = 0.96 = = = 0.97 = = 
= = = = 1.00 = = 1.00 = = 
= = = = = = ? ? = = 
1.00 1.00 = = = = = 1.00 = = 
= = = 0.95 = = = 1.00 = = 
= = 1.00 1.00 = = 1.00 1.00 = 1.00 
= = = = = = = 1.00 = = 
= = 1.00 = = = 1.00 0.99 = = 
= = = = = = 0.98 1.00 = = 
= = = = = = = = = = 
= = = = = = = = = = 
= = = = = = ? ? = = 
= = 1.00 = = = 1.00 = = 1.00 
= = = = = = = 1.00 = = 
= = = = 1.00 = = 1.00 = = 
= = = = = = 0.99 1.00 = = 
= = = 0.99 1.00 = = 1.00 1.00 = 
= = = = = = = = 1.00 = 
= = = = = = = = = = 
= = = = = 1.00 = = = = 
= = = = = = = = = = 
= = = = 1.00 = = 1.00 0.99 = 
= = = = 1.00 0.97 = 1.00 0.99 = 
= = = = = = = = 1.00 = 
= = = ? 1.00 0.97 = 1.00 1.00 = 
= = = = ? ? = = ? = 
= = = = = = ? ? 1.00 = 
= = = = = = = = 1.00 = 
= = = = 1.00 = = 1.00 = = 
= = = = 1.00 = = 1.00 = = 
= = = = 1.00 = = 1.00 = = 
= = = = = = = = = = 
= = = = 1.00 = = 1.00 = = 
= = = = = 0.95 = = 1.00 = 
= = = = = = ? = = = 
= = = = = = = = = = 
= = = = = = = = = = 
= = = = = = = = 1.00 = 
= = = = = ? = = 1.00 = 
= = = = = = = = 1.00 = 
= = = = = = = 0.98 1.00 = 
= = = = 1.00 = = 1.00 0.99 = 
END PHASEPROBS