*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 trex2.phase.inp trex2.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
trex2.phase.out_freqs : haplotype frequency estimates
trex2.phase.out_pairs : most likely haplotype pairs for each individual
trex2.phase.out_recom : estimates of recombination parameters
trex2.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 95
Number of Loci: 6
Positions of loci: 951 989 1049 3271 4801 5197
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file trex2.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 AIATGC 120.000000
2 AIATAC 2.000000
3 AIACGT 1.000000
4 AIACAC 4.000000
5 AICTGC 27.000000
6 ADATAT 4.000000
7 ADACAC 2.000000
8 ADACAT 14.000000
9 CIATGC 16.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (1,1)
D002: (8,8)
D003: (1,1)
D004: (1,1)
D005: (4,4)
D006: (1,1)
D007: (1,1)
D008: (1,1)
D009: (8,8)
D010: (1,6)
D011: (1,1)
D012: (1,6)
D013: (1,1)
D014: (4,4)
D015: (8,8)
DY01: (1,6)
DY02: (1,1)
DY03: (8,8)
DY04: (1,6)
DY05: (1,1)
DY06: (1,2)
DY07: (1,8)
DY08: (1,3)
DY09: (7,7)
DY10: (8,8)
DY11: (8,8)
DY12: (1,2)
E101: (1,5)
E102: (1,1)
E103: (1,1)
E104: (1,1)
E105: (1,5)
E106: (1,1)
E107: (1,1)
E108: (1,5)
E109: (5,5)
E110: (1,5)
E111: (1,5)
E112: (1,1)
E113: (1,1)
E114: (1,5)
E115: (1,5)
E116: (1,1)
E117: (5,5)
E118: (1,5)
E119: (1,5)
E120: (1,5)
E121: (5,5)
E122: (1,5)
H101: (1,5)
H102: (1,9)
H103: (1,1)
H104: (5,5)
H105: (1,1)
H106: (1,1)
H107: (1,9)
H108: (1,5)
H109: (1,1)
H110: (1,1)
H111: (1,1)
H112: (1,1)
H113: (5,9)
H114: (5,5)
H115: (5,8)
H116: (1,1)
H117: (1,9)
H118: (5,5)
H119: (1,1)
H120: (1,1)
H121: (1,1)
H122: (9,9)
X101: (9,9)
X102: (1,1)
X103: (1,1)
X104: (1,1)
X105: (1,9)
X106: (9,9)
X107: (1,1)
X108: (1,1)
X109: (9,9)
X110: (1,9)
X111: (1,1)
X112: (1,9)
X113: (1,1)
X114: (1,1)
X115: (1,1)
X116: (1,1)
X117: (1,1)
X118: (1,1)
X119: (1,1)
X120: (1,9)
X121: (1,1)
X122: (1,1)
X123: (1,1)
X124: (1,1)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
A I A T G C
A I A T G C
0 D002
A D A C A T
A D A C A T
0 D003
A I A T G C
A I A T G C
0 D004
A I A T G C
A I A T G C
0 D005
A I A C A C
A I A C A C
0 D006
A I A T G C
A I A T G C
0 D007
A I A T G C
A I A T G C
0 D008
A I A T G C
A I A T G C
0 D009
A D A C A T
A D A C A T
0 D010
A I A T G C
A D A T A T
0 D011
A I A T G C
A I A T G C
0 D012
A I A T G C
A D A T A T
0 D013
A I A T G C
A I A T G C
0 D014
A I A C A C
A I A C A C
0 D015
A D A C A T
A D A C A [T]
0 DY01
A I A T G C
A [D] A T A [T]
0 DY02
A I A T G C
A I A T G C
0 DY03
A D A C A T
A D A C A [T]
0 DY04
A I A T G C
A D A T A T
0 DY05
A I A T G C
A I A T G C
0 DY06
A I A T G C
A I A T A C
0 DY07
A I A T G C
A D A C A T
0 DY08
A I A (T) G C
A I A (C) G T
0 DY09
A D A C A C
A D A C A C
0 DY10
A D A C A T
A D A C A [T]
0 DY11
A D A C A T
A D A C A T
0 DY12
A I A T G C
A I A T A C
0 E101
A I A T G C
A I C T G C
0 E102
A I A T G C
A I A T G C
0 E103
A I A T G C
A I A T G C
0 E104
A I A T G C
A I A T G C
0 E105
A I A T G C
A I C T G C
0 E106
A I A T G C
A I A T G C
0 E107
A I A T G C
A I A T G C
0 E108
A I A T G C
A I C T G C
0 E109
A I C T G C
A I C T G C
0 E110
A I A T G C
A I C T G C
0 E111
A I A T G C
A I C T G C
0 E112
A I A T G C
A I A T G C
0 E113
A I A T G C
A I A T G C
0 E114
A I A T G C
A I C T G C
0 E115
A I A T G C
A I C T G C
0 E116
A I A T G C
A I A T G C
0 E117
A I C T G C
A I C T G C
0 E118
A I A T G C
A I C T G C
0 E119
A I A T G C
A I C T G C
0 E120
A I A T G C
A I C T G C
0 E121
A I C T G C
A I C T G C
0 E122
A I A T G C
A I C T G C
0 H101
A I A T G C
A I C T G C
0 H102
A I A T G C
C I A T G C
0 H103
A I A T G C
A I A T G C
0 H104
A I C T G C
A I C T G C
0 H105
A I A T G C
A I A T G C
0 H106
A I A T G C
A I A T G C
0 H107
A I A T G C
C I A T G C
0 H108
A I A T G C
A I C T G C
0 H109
A I A T G C
A I A T G C
0 H110
A I A T G C
A I A T G C
0 H111
A I A T G C
A I A T G C
0 H112
A I A T G C
A I A T G C
0 H113
A I C T G C
C I A T G C
0 H114
A I C T G C
A I C T G C
0 H115
A I C T G C
A D A C A [T]
0 H116
A I A T G C
A I A T G C
0 H117
A I A T G C
C I A T G C
0 H118
A I C T G C
A I C T G C
0 H119
A I A T G C
A I A T G C
0 H120
A I A T G C
A I A T G C
0 H121
A I A T G C
A I A T G C
0 H122
C I A T G C
C I A T G C
0 X101
C I A T G C
C I A T G C
0 X102
A I A T G C
A I A T G C
0 X103
A I A T G C
A I A T G C
0 X104
A I A T G C
A I A T G C
0 X105
A I A T G C
C I A T G C
0 X106
C I A T G C
C I A T G C
0 X107
A I A T G C
A I A T G C
0 X108
A I A T G C
A I A T G C
0 X109
C I A T G C
C I A T G C
0 X110
A I A T G C
C I A T G C
0 X111
A I A T G C
A I A T G C
0 X112
A I A T G C
C I A T G C
0 X113
A I A T G C
A I A T G C
0 X114
A I A T G C
A I A T G C
0 X115
A I A T G C
A I A T G C
0 X116
A I A T G C
A I A T G C
0 X117
A I A T G C
A I A T G C
0 X118
A I A T G C
A I A T G C
0 X119
A I A T G C
A I A T G C
0 X120
A I A T G C
C I A T G C
0 X121
A I A T G C
A I A T G C
0 X122
A I A T G C
A I A T G C
0 X123
A I A T G C
A I A T G C
0 X124
A I A T G C
A I A T G 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 D001
= = = = = =
= = = = = =
0 D002
= = = = = =
= = = = = =
0 D003
= = = = = =
= = = = = =
0 D004
= = = = = =
= = = = = =
0 D005
= = = = = =
= = = = = =
0 D006
= = = = = =
= = = = = =
0 D007
= = = = = =
= = = = = =
0 D008
= = = = = =
= = = = = =
0 D009
= = = = = =
= = = = = =
0 D010
= I = = G ?
= D = = A ?
0 D011
= = = = = =
= = = = = =
0 D012
= I = = G C
= D = = A T
0 D013
= = = = = =
= = = = = =
0 D014
= = = = = =
= = = = = =
0 D015
= = = = = ?
= = = = = ?
0 DY01
? ? = = G ?
? ? = = A ?
0 DY02
= = = = = ?
= = = = = ?
0 DY03
= = = = = ?
= = = = = ?
0 DY04
= I = = G C
= D = = A T
0 DY05
= = = = = ?
= = = = = ?
0 DY06
= = = = G =
= = = = A =
0 DY07
= I = T G C
= D = C A T
0 DY08
= = = (T) = C
= = = (C) = T
0 DY09
= = = = = =
= = = = = =
0 DY10
= = = = = ?
= = = = = ?
0 DY11
= = = = = =
= = = = = =
0 DY12
= = = = G ?
= = = = A ?
0 E101
= = A = = =
= = C = = =
0 E102
= = = = = =
= = = = = =
0 E103
= = = = = =
= = = = = =
0 E104
= = = = = =
= = = = = =
0 E105
= = A = = =
= = C = = =
0 E106
= = = = = ?
= = = = = ?
0 E107
= = = = = ?
= = = = = ?
0 E108
= = A = = ?
= = C = = ?
0 E109
= = = = = =
= = = = = =
0 E110
= = A = = =
= = C = = =
0 E111
= = A = = =
= = C = = =
0 E112
= = = = = ?
= = = = = ?
0 E113
= = = = = ?
= = = = = ?
0 E114
= = A = = =
= = C = = =
0 E115
= = A = = =
= = C = = =
0 E116
= = = = ? ?
= = = = ? ?
0 E117
= = = = = ?
= = = = = ?
0 E118
= = A = = ?
= = C = = ?
0 E119
= = A = = =
= = C = = =
0 E120
= = A = = =
= = C = = =
0 E121
= = = = = ?
= = = = = ?
0 E122
= = A = = =
= = C = = =
0 H101
= = A = = =
= = C = = =
0 H102
A = = = ? ?
C = = = ? ?
0 H103
= = = = = ?
= = = = = ?
0 H104
= = = = = =
= = = = = =
0 H105
= = = = ? ?
= = = = ? ?
0 H106
= = = = = =
= = = = = =
0 H107
A = = = = =
C = = = = =
0 H108
= = A = = =
= = C = = =
0 H109
= = = = = =
= = = = = =
0 H110
= = = = = =
= = = = = =
0 H111
= = = = = =
= = = = = =
0 H112
= = = = = ?
= = = = = ?
0 H113
A = C = = =
C = A = = =
0 H114
= = = = = =
= = = = = =
0 H115
= I C T G ?
= D A C A ?
0 H116
= = = = = =
= = = = = =
0 H117
A = = = = =
C = = = = =
0 H118
= = = = = =
= = = = = =
0 H119
= = = = = =
= = = = = =
0 H120
= = = = = ?
= = = = = ?
0 H121
= = = = = =
= = = = = =
0 H122
= = = = = =
= = = = = =
0 X101
= = = = = =
= = = = = =
0 X102
= = = = = =
= = = = = =
0 X103
= = = = = ?
= = = = = ?
0 X104
= = = = = =
= = = = = =
0 X105
A = = = = ?
C = = = = ?
0 X106
= = = = = ?
= = = = = ?
0 X107
= = = = = ?
= = = = = ?
0 X108
= = = = = ?
= = = = = ?
0 X109
= = = = = ?
= = = = = ?
0 X110
A = = = = ?
C = = = = ?
0 X111
= = = = ? ?
= = = = ? ?
0 X112
A = = = = ?
C = = = = ?
0 X113
= = = = ? ?
= = = = ? ?
0 X114
= = = = = ?
= = = = = ?
0 X115
= = = = = ?
= = = = = ?
0 X116
= = = = = ?
= = = = = ?
0 X117
= = = = ? ?
= = = = ? ?
0 X118
= = = = = =
= = = = = =
0 X119
= = = = = ?
= = = = = ?
0 X120
A = = = = =
C = = = = =
0 X121
= = = = = =
= = = = = =
0 X122
= = = = = =
= = = = = =
0 X123
= = = = = ?
= = = = = ?
0 X124
= = = = = =
= = = = = =
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
= = = 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 = = = = =
= = 1.00 = = =
= = = = = =
= = = = = =
= = = = = =
= = = = = ?
0.98 = 1.00 = = =
= = = = = =
= 1.00 1.00 1.00 1.00 ?
= = = = = =
1.00 = = = = =
= = = = = =
= = = = = =
= = = = = ?
= = = = = =
= = = = = =
= = = = = =
= = = = = =
= = = = = ?
= = = = = =
1.00 = = = = ?
= = = = = ?
= = = = = ?
= = = = = ?
= = = = = ?
1.00 = = = = ?
= = = = ? ?
1.00 = = = = ?
= = = = ? ?
= = = = = ?
= = = = = ?
= = = = = ?
= = = = ? ?
= = = = = =
= = = = = ?
1.00 = = = = =
= = = = = =
= = = = = =
= = = = = ?
= = = = = =
END PHASEPROBS