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

BEGIN COMMAND_LINE 
/usr/local/genome/lib/phase/PHASE2 -d1 adr2b.phase.inp adr2b.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
adr2b.phase.out_freqs : haplotype frequency estimates
adr2b.phase.out_pairs : most likely haplotype pairs for each individual
adr2b.phase.out_recom : estimates of recombination parameters
adr2b.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 11
Positions of loci: 931 3879 4870 5158 5753 8331 8536 8708 10411 10895 11090 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file adr2b.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1 CGICCIACTCC   63.000000
         2 CGICCIACCCC    9.000000
         3 CGIAADGCTCC    3.000000
         4 ACDACDGATGA    2.000000
         5 ACDAADGATGA   17.000000
END LIST_SUMMARY


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

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


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

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