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

BEGIN COMMAND_LINE 
/usr/local/genome/lib/phase/PHASE2 -d1 c1qbp.phase.inp c1qbp.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
c1qbp.phase.out_freqs : haplotype frequency estimates
c1qbp.phase.out_pairs : most likely haplotype pairs for each individual
c1qbp.phase.out_recom : estimates of recombination parameters
c1qbp.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 13
Positions of loci: 1163 2573 2602 2698 3634 3643 6132 7310 7656 7853 8238 8260 8390 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file c1qbp.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1 CAGCACICCGATC    3.000000
         2 CAGCGCDGAGGCT    2.000000
         3 CAGTACICCGATC   58.000000
         4 CAGTACICCTATC    8.000000
         5 CAGTACDGAGGCT    3.000000
         6 CAGTGGICCGATC    1.000000
         7 CATCACICCGATC    2.000000
         8 CATCGCDGAGGCT    3.000000
         9 CGGCACICCGATC    9.000000
        10 TAGTGGICCGATC    5.000000
END LIST_SUMMARY


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

BEGIN BESTPAIRS_SUMMARY
DY01: (1,3)
DY02: (3,4)
DY03: (3,5)
DY04: (3,7)
DY05: (3,4)
DY06: (3,5)
DY07: (3,6)
DY08: (3,4)
DY09: (4,9)
DY10: (3,4)
DY11: (3,9)
DY12: (3,9)
DY13: (3,3)
DY14: (3,10)
DY15: (3,5)
DY16: (4,9)
DY17: (3,7)
DY18: (3,3)
DY19: (9,10)
DY20: (4,9)
DY21: (3,10)
DY22: (1,3)
DY23: (3,3)
DY24: (3,4)
E101: (3,3)
E102: (3,9)
E103: (3,3)
E104: (3,3)
E105: (3,3)
E106: (3,3)
E107: (3,8)
E108: (2,3)
E109: (3,10)
E110: (3,3)
E111: (3,10)
E112: (3,8)
E113: (2,3)
E114: (3,3)
E115: (3,9)
E116: (3,8)
E117: (3,3)
E118: (3,3)
E119: (3,3)
E120: (3,3)
E121: (1,3)
E122: (3,3)
E123: (3,9)
END BESTPAIRS_SUMMARY


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

BEGIN BESTPAIRS1
0 DY01
C A G C A C I C C G A T C 
C A G T A C I C C G A T C 
0 DY02
C A G T A C I C C G A T C 
C A G T A C I C C T A T C 
0 DY03
C A G T A C I C C G A T C 
C A G T A C D G A G G C T 
0 DY04
C A G T A C I C C G A T C 
C A T C A C I C C G A T C 
0 DY05
C A G T A C I C C G A T C 
C A G T A C I C C T A T C 
0 DY06
C A G T A C I C C G A T C 
C A G T A C D G A G G C T 
0 DY07
C A G T A C I C C G A T C 
C A G T G G I C C G A T C 
0 DY08
C A G T A C I C C G A T C 
C A G T A C I C C T A T C 
0 DY09
C A G T A C I C C (T) A T C 
C G G C A C I C C (G) A T C 
0 DY10
C A G T A C I C C G A T C 
C A G T A C I C C T A T C 
0 DY11
C A G T A C I C C G A T C 
C G G C A C I C C G A T C 
0 DY12
C A G T A C I C C G A T C 
C G G C A C I C C G A T C 
0 DY13
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 DY14
C A G T A C I C C G A T C 
T A G T G G I C C G A T C 
0 DY15
C A G T A C I C C G A T C 
C A G T A C D G A G G C T 
0 DY16
C A G T A C I C C (T) A T C 
C G G C A C I C C (G) A T C 
0 DY17
C A G T A C I C C G A T C 
C A T C A C I C C G A T C 
0 DY18
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 DY19
C G G C A C I C C G A T C 
T A G T G G I C C G A T C 
0 DY20
C A G T A C I C C (T) A T C 
C G G C A C I C C (G) A T C 
0 DY21
C A G T A C I C C G A T C 
T A G T G G I C C G A T C 
0 DY22
C A G C A C I C C G A T C 
C A G T A C I C C G A T C 
0 DY23
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 DY24
C A G T A C I C C G A T C 
C A G T A C I C C T A T C 
0 E101
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E102
C A G T A C I C C G A T C 
C G G C A C I C C G A T C 
0 E103
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E104
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E105
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E106
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E107
C A G T A C I C C G A T C 
C A T C G C D G A G G C T 
0 E108
C A G C G C D G A G G C T 
C A G T A C I C C G A T C 
0 E109
C A G T A C I C C G A T C 
T A G T G G I C C G A T C 
0 E110
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E111
C A G T A C I C C G A T C 
T A G T G G I C C G A T C 
0 E112
C A G T A C I C C G A T C 
C A T C G C D G A G G C T 
0 E113
C A G C G C D G A G G C T 
C A G T A C I C C G A T C 
0 E114
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E115
C A G T A C I C C G A T C 
C G G C A C I C C G A T C 
0 E116
C A G T A C I C C G A T C 
C A T C G C D G A G G C T 
0 E117
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E118
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E119
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E120
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E121
C A G C A C I C C G A T C 
C A G T A C I C C G A T C 
0 E122
C A G T A C I C C G A T C 
C A G T A C I C C G A T C 
0 E123
C A G T A C I C C G A T C 
C G G C A C I C C G A T C 
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 DY01
= = = C = = = = = = = = = 
= = = T = = = = = = = = = 
0 DY02
= = = = = = = = = G = = = 
= = = = = = = = = T = = = 
0 DY03
= = = = = = I C C = A T C 
= = = = = = D G A = G C T 
0 DY04
= = G T = = = = = = = = = 
= = T C = = = = = = = = = 
0 DY05
= = = = = = = = = G = = = 
= = = = = = = = = T = = = 
0 DY06
= = = = = = I C C = A T C 
= = = = = = D G A = G C T 
0 DY07
= = = = A C = = = = = = = 
= = = = G G = = = = = = = 
0 DY08
= = = = = = = = = G = = = 
= = = = = = = = = T = = = 
0 DY09
= A = T = = = = = (T) = = = 
= G = C = = = = = (G) = = = 
0 DY10
= = = = = = = = = G = = = 
= = = = = = = = = T = = = 
0 DY11
= A = T = = = = = = = = = 
= G = C = = = = = = = = = 
0 DY12
= A = T = = ? = = = = = = 
= G = C = = ? = = = = = = 
0 DY13
= = = = ? ? = = = = = = = 
= = = = ? ? = = = = = = = 
0 DY14
C = = = A C ? = = = = = = 
T = = = G G ? = = = = = = 
0 DY15
= = = = = = I C C = A T C 
= = = = = = D G A = G C T 
0 DY16
= A = T = = = = = (T) = = = 
= G = C = = = = = (G) = = = 
0 DY17
= = G T = = = = = = = = = 
= = T C = = = = = = = = = 
0 DY18
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 DY19
C G = C A C = = = = = = = 
T A = T G G = = = = = = = 
0 DY20
= A = T = = = = = (T) = = = 
= G = C = = = = = (G) = = = 
0 DY21
C = = = A C = = = = = = = 
T = = = G G = = = = = = = 
0 DY22
= = = C = = = = = = = = = 
= = = T = = = = = = = = = 
0 DY23
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 DY24
= = = = = = ? = = G = = = 
= = = = = = ? = = T = = = 
0 E101
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E102
= A = T = = = = = = = = = 
= G = C = = = = = = = = = 
0 E103
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E104
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E105
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E106
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E107
= = G T A = I C C = A T C 
= = T C G = D G A = G C T 
0 E108
= = = C G = D G A = G C T 
= = = T A = I C C = A T C 
0 E109
C = = = A C = = = = = = = 
T = = = G G = = = = = = = 
0 E110
= = = = = = = ? = = = = = 
= = = = = = = ? = = = = = 
0 E111
C = ? = A C = ? = = = = = 
T = ? = G G = ? = = = = = 
0 E112
? = G T A = ? C C = A T C 
? = T C G = ? G A = G C T 
0 E113
= = = C G = D ? A = G C T 
= = = T A = I ? C = A T C 
0 E114
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E115
? A = T = = = = = = = = = 
? G = C = = = = = = = = = 
0 E116
= = G T A = I C C = A T C 
= = T C G = D G A = G C T 
0 E117
= = = = = = ? = = = = = = 
= = = = = = ? = = = = = = 
0 E118
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E119
= = = = = = ? = = = = = = 
= = = = = = ? = = = = = = 
0 E120
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E121
= = = C = = = = = = = = = 
= = = T = = = = = = = = = 
0 E122
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
0 E123
= A = T = = = = = = = = = 
= G = C = = = = = = = = = 
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 1.00 = 1.00 1.00 1.00 
= = 0.98 1.00 = = = = = = = = = 
= = = = = = = = = 1.00 = = = 
= = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 
= = = = 1.00 1.00 = = = = = = = 
= = = = = = = = = 1.00 = = = 
= 1.00 = 1.00 = = = = = 0.62 = = = 
= = = = = = = = = 1.00 = = = 
= 1.00 = 1.00 = = = = = = = = = 
= 1.00 = 1.00 = = ? = = = = = = 
= = = = ? ? = = = = = = = 
1.00 = = = 1.00 1.00 ? = = = = = = 
= = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 
= 1.00 = 1.00 = = = = = 0.65 = = = 
= = 0.98 1.00 = = = = = = = = = 
= = = = = = = = = = = = = 
1.00 1.00 = 1.00 1.00 1.00 = = = = = = = 
= 1.00 = 1.00 = = = = = 0.65 = = = 
1.00 = = = 1.00 1.00 = = = = = = = 
= = = 1.00 = = = = = = = = = 
= = = = = = = = = = = = = 
= = = = = = ? = = 1.00 = = = 
= = = = = = = = = = = = = 
= 1.00 = 1.00 = = = = = = = = = 
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
= = = = = = = = = = = = = 
= = 0.99 0.99 1.00 = 1.00 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 1.00 = = = = = = = 
= = = = = = = ? = = = = = 
1.00 = ? = 1.00 1.00 = ? = = = = = 
? = 0.99 0.99 1.00 = ? 1.00 1.00 = 1.00 1.00 1.00 
= = = 0.94 1.00 = 1.00 ? 1.00 = 1.00 1.00 1.00 
= = = = = = = = = = = = = 
? 1.00 = 1.00 = = = = = = = = = 
= = 0.99 0.99 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 
= = = = = = ? = = = = = = 
= = = = = = = = = = = = = 
= = = = = = ? = = = = = = 
= = = = = = = = = = = = = 
= = = 1.00 = = = = = = = = = 
= = = = = = = = = = = = = 
= 1.00 = 1.00 = = = = = = = = = 
END PHASEPROBS