*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 birc2.phase.inp birc2.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
birc2.phase.out_freqs : haplotype frequency estimates
birc2.phase.out_pairs : most likely haplotype pairs for each individual
birc2.phase.out_recom : estimates of recombination parameters
birc2.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 95
Number of Loci: 6
Positions of loci: 1788 6810 15907 19512 20569 31914
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file birc2.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 ACCIAC 20.000000
2 AGCIAC 84.000000
3 AGCIGC 10.000000
4 AGTIAC 47.000000
5 AGTDAC 14.000000
6 GCCIAC 2.000000
7 GCCIAT 11.000000
8 GCTIAT 2.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (1,7)
D002: (1,2)
D003: (1,2)
D004: (2,6)
D005: (4,8)
D006: (1,8)
D007: (1,2)
D008: (4,7)
D009: (2,6)
D010: (2,7)
D011: (2,4)
D012: (2,2)
D013: (1,7)
D014: (1,1)
D015: (1,1)
DY01: (1,2)
DY02: (1,2)
DY03: (1,2)
DY04: (1,7)
DY05: (2,2)
DY06: (2,2)
DY07: (2,4)
DY08: (2,4)
DY09: (1,2)
DY10: (2,2)
DY11: (2,7)
DY12: (1,2)
E101: (4,4)
E102: (1,4)
E103: (2,2)
E104: (2,4)
E105: (3,7)
E106: (2,4)
E107: (1,4)
E108: (3,7)
E109: (2,4)
E110: (2,2)
E111: (2,4)
E112: (2,4)
E113: (2,2)
E114: (2,2)
E115: (1,2)
E116: (2,4)
E117: (1,2)
E118: (7,7)
E119: (4,4)
E120: (2,2)
E121: (2,4)
E122: (4,7)
H101: (2,2)
H102: (5,5)
H103: (3,4)
H104: (3,5)
H105: (3,5)
H106: (2,2)
H107: (4,5)
H108: (3,3)
H109: (5,5)
H110: (3,4)
H111: (2,4)
H112: (2,5)
H113: (3,4)
H114: (2,2)
H115: (2,5)
H116: (2,4)
H117: (2,3)
H118: (2,5)
H119: (2,4)
H120: (2,4)
H121: (2,2)
H122: (2,2)
X101: (2,2)
X102: (2,4)
X103: (2,5)
X104: (2,5)
X105: (2,4)
X106: (4,4)
X107: (2,4)
X108: (2,4)
X109: (2,4)
X110: (2,5)
X111: (2,4)
X112: (2,2)
X113: (2,4)
X114: (2,4)
X115: (4,4)
X116: (2,2)
X117: (4,4)
X118: (2,4)
X119: (2,4)
X120: (4,4)
X121: (2,4)
X122: (2,5)
X123: (2,4)
X124: (2,2)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
A C C I A C
G C C I A T
0 D002
A C C I A C
A G C I A C
0 D003
A C C I A C
A G C I A C
0 D004
(A) G C I A C
(G) C C I A C
0 D005
A G T I A C
G C T I A T
0 D006
A C C I A C
G C T I A T
0 D007
A C C I A C
A G C I A C
0 D008
A G (T) I A C
G C (C) I A T
0 D009
(A) G C I A C
(G) C C I A C
0 D010
A G C I A C
G C C I A T
0 D011
A G C I A C
A G T I A C
0 D012
A G C I A C
A G C I A C
0 D013
A C C I A C
G C C I A T
0 D014
A C C I A C
A C C I A C
0 D015
A C C I A C
A C C I A C
0 DY01
A C C I A C
A G C I A C
0 DY02
A C C I A C
A G C I A C
0 DY03
A C C I A C
A G C I A C
0 DY04
A C C I A C
G C C I A T
0 DY05
A G C I A C
A G C I A C
0 DY06
A G C I A C
A G C I A C
0 DY07
A G C I A C
A G [T] I A C
0 DY08
A G C I A C
A G T I A C
0 DY09
A C C I A C
A G [C] I A C
0 DY10
A G C I A C
A G C I A C
0 DY11
A [G] C I A C
G C C I A T
0 DY12
A C C I A C
A G C I A C
0 E101
A G T I A C
A G T I A C
0 E102
A C C I A C
A G T I A C
0 E103
A G C I A C
A G C I A C
0 E104
A G C I A C
A G T I A C
0 E105
A G C I G C
G C C I A T
0 E106
A G C I A C
A G T I A C
0 E107
A C C I A C
A G T I A C
0 E108
A G C I G C
G C C I A T
0 E109
A G C I A C
A G T I A C
0 E110
A G C I A C
A G C I A C
0 E111
A G C I A C
A G T I A C
0 E112
A G C I A C
A G T I A C
0 E113
A G C I A C
A G C I A C
0 E114
A G C I A C
A G C I A C
0 E115
A C C I A C
A G C I A C
0 E116
A G C I A C
A G T I A C
0 E117
A C C I A C
A G C I A C
0 E118
G C C I A T
G C C I A T
0 E119
A G T I A C
A G T I A C
0 E120
A G C I A C
A G C I A C
0 E121
A G C I A C
A G T I A C
0 E122
A G (T) I A C
G C (C) I A T
0 H101
A G C I A C
A G C I A C
0 H102
A G T D A C
A G T D A C
0 H103
A G C I G C
A G T I A C
0 H104
A G C I G C
A G T D A C
0 H105
A G C I G C
A G T D A C
0 H106
A G C I A C
A G C I A C
0 H107
A G T I A C
A G T D A C
0 H108
A G C I G C
A G C I G C
0 H109
A G T D A C
A G T D A C
0 H110
A G C I G C
A G T I A C
0 H111
A G C I A C
A G T I A C
0 H112
A G C I A C
A G T D A C
0 H113
A G C I G C
A G T I A C
0 H114
A G C I A C
A G C I A C
0 H115
A G C I A C
A G T D A C
0 H116
A G C I A C
A G T I A C
0 H117
A G C I A C
A G C I G C
0 H118
A G C I A C
A G T D A C
0 H119
A G C I A C
A G T I A C
0 H120
A G C I A C
A G [T] I A C
0 H121
A G C I A C
A G C I A C
0 H122
A G C I A C
A G C I A C
0 X101
A G C I A C
A G C I A C
0 X102
A G C I A C
A G [T] I A C
0 X103
A G C I A C
A G T D A C
0 X104
A G C I A C
A G T D A C
0 X105
A G C I A C
A G T I A C
0 X106
A G T I A C
A G T I A C
0 X107
A G C I A C
A G [T] I A C
0 X108
A G C I A C
A G [T] I A C
0 X109
A G C I A C
A G [T] I A C
0 X110
A G C I A C
A G T D A C
0 X111
A G C I A C
A G T I A C
0 X112
A G C I A C
A G C I A C
0 X113
A G C I A C
A G T I A C
0 X114
A G C I A C
A G [T] I A C
0 X115
A G T I A C
A G T I A C
0 X116
A G C I A C
A G C I A C
0 X117
A G T I A C
A G T I A C
0 X118
A G C I A C
A G T I A C
0 X119
A G C I A C
A G T I A C
0 X120
A G T I A C
A G T I A C
0 X121
A G C I A C
A G T I A C
0 X122
A G [C] I A C
A G T D A C
0 X123
A G C I A C
A G [T] I A C
0 X124
A G C I A C
A G C I A 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
A = ? = = C
G = ? = = T
0 D002
= C = = ? =
= G = = ? =
0 D003
= C = = ? =
= G = = ? =
0 D004
(A) G = = = =
(G) C = = = =
0 D005
A G = = ? C
G C = = ? T
0 D006
A = C = = C
G = T = = T
0 D007
= C = = = =
= G = = = =
0 D008
A G (T) = = C
G C (C) = = T
0 D009
(A) G = = = =
(G) C = = = =
0 D010
A G = = = C
G C = = = T
0 D011
= = C = = =
= = T = = =
0 D012
= = = = = =
= = = = = =
0 D013
A = = = = C
G = = = = T
0 D014
= = = = = =
= = = = = =
0 D015
= = ? = = =
= = ? = = =
0 DY01
= C = = = =
= G = = = =
0 DY02
= C = = = =
= G = = = =
0 DY03
= C = = ? =
= G = = ? =
0 DY04
A = = = ? C
G = = = ? T
0 DY05
= = = = = =
= = = = = =
0 DY06
= = = = = =
= = = = = =
0 DY07
= = ? = = =
= = ? = = =
0 DY08
= = C = = =
= = T = = =
0 DY09
= C ? = ? =
= G ? = ? =
0 DY10
= = = = = =
= = = = = =
0 DY11
A ? = = = C
G ? = = = T
0 DY12
= C = = ? =
= G = = ? =
0 E101
= = = = = =
= = = = = =
0 E102
= C C = = =
= G T = = =
0 E103
= = = = = =
= = = = = =
0 E104
= = C = = =
= = T = = =
0 E105
A G = = G C
G C = = A T
0 E106
= = C = = =
= = T = = =
0 E107
= C C = = =
= G T = = =
0 E108
A G = = G C
G C = = A T
0 E109
= = C = = =
= = T = = =
0 E110
= = = = = =
= = = = = =
0 E111
= = C = = =
= = T = = =
0 E112
= = C = = =
= = T = = =
0 E113
= = = = = =
= = = = = =
0 E114
= = = = = =
= = = = = =
0 E115
= C = = = =
= G = = = =
0 E116
= = C = = =
= = T = = =
0 E117
= C = = = =
= G = = = =
0 E118
= = = = = =
= = = = = =
0 E119
= = = = = =
= = = = = =
0 E120
= = = = = =
= = = = = =
0 E121
= = C = = =
= = T = = =
0 E122
A G (T) = = C
G C (C) = = T
0 H101
= = = = = =
= = = = = =
0 H102
= = = = = =
= = = = = =
0 H103
= = C = G =
= = T = A =
0 H104
= = C I G =
= = T D A =
0 H105
= = C I G =
= = T D A =
0 H106
= = = = = =
= = = = = =
0 H107
= = = I = =
= = = D = =
0 H108
= = = = = =
= = = = = =
0 H109
= = = = = =
= = = = = =
0 H110
= = C = G =
= = T = A =
0 H111
= = C = = =
= = T = = =
0 H112
= = C I = =
= = T D = =
0 H113
= = C = G ?
= = T = A ?
0 H114
= = = = = =
= = = = = =
0 H115
= = C I = =
= = T D = =
0 H116
= = C = = =
= = T = = =
0 H117
= = = = A =
= = = = G =
0 H118
= = C I = =
= = T D = =
0 H119
= = C = = =
= = T = = =
0 H120
= = ? = = =
= = ? = = =
0 H121
= = = = = =
= = = = = =
0 H122
= = = = = =
= = = = = =
0 X101
= = = = = =
= = = = = =
0 X102
= = ? = = =
= = ? = = =
0 X103
= = C I = =
= = T D = =
0 X104
= = C I = =
= = T D = =
0 X105
= = C = = =
= = T = = =
0 X106
= = = = = =
= = = = = =
0 X107
= = ? = = =
= = ? = = =
0 X108
= = ? = = =
= = ? = = =
0 X109
= = ? = = =
= = ? = = =
0 X110
= = C I = =
= = T D = =
0 X111
= = C = = =
= = T = = =
0 X112
= = = = = =
= = = = = =
0 X113
= = C = = =
= = T = = =
0 X114
= = ? = = =
= = ? = = =
0 X115
= = = = = =
= = = = = =
0 X116
= = = = ? =
= = = = ? =
0 X117
= = = = = =
= = = = = =
0 X118
= = C = = =
= = T = = =
0 X119
= = C = = =
= = T = = =
0 X120
= = = = = =
= = = = = =
0 X121
= = C = = =
= = T = = =
0 X122
= = ? I = =
= = ? D = =
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 = = ? =
0.84 1.00 = = = =
1.00 1.00 = = ? 1.00
1.00 = 0.97 = = 1.00
= 1.00 = = = =
1.00 1.00 0.68 = = 1.00
0.83 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 = = ? =
= = = = = =
= 0.99 1.00 = = =
= = = = = =
= = 1.00 = = =
1.00 1.00 = = 0.96 1.00
= = 1.00 = = =
= 0.98 1.00 = = =
1.00 1.00 = = 0.96 1.00
= = 1.00 = = =
= = = = = =
= = 1.00 = = =
= = 1.00 = = =
= = = = = =
= = = = = =
= 1.00 = = = =
= = 1.00 = = =
= 1.00 = = = =
= = = = = =
= = = = = =
= = = = = =
= = 1.00 = = =
1.00 1.00 0.67 = = 1.00
= = = = = =
= = = = = =
= = 0.98 = 1.00 =
= = 1.00 1.00 0.98 =
= = 1.00 1.00 0.98 =
= = = = = =
= = = 1.00 = =
= = = = = =
= = = = = =
= = 0.98 = 1.00 =
= = 1.00 = = =
= = 0.99 1.00 = =
= = 0.98 = 1.00 ?
= = = = = =
= = 0.99 1.00 = =
= = 1.00 = = =
= = = = 1.00 =
= = 1.00 1.00 = =
= = 1.00 = = =
= = ? = = =
= = = = = =
= = = = = =
= = = = = =
= = ? = = =
= = 0.99 1.00 = =
= = 1.00 1.00 = =
= = 1.00 = = =
= = = = = =
= = ? = = =
= = ? = = =
= = ? = = =
= = 0.99 1.00 = =
= = 1.00 = = =
= = = = = =
= = 1.00 = = =
= = ? = = =
= = = = = =
= = = = ? =
= = = = = =
= = 1.00 = = =
= = 1.00 = = =
= = = = = =
= = 1.00 = = =
= = ? 1.00 = =
= = ? = = =
= = = = = =
END PHASEPROBS