*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 ube2a.phase.inp ube2a.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
ube2a.phase.out_freqs : haplotype frequency estimates
ube2a.phase.out_pairs : most likely haplotype pairs for each individual
ube2a.phase.out_recom : estimates of recombination parameters
ube2a.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 95
Number of Loci: 4
Positions of loci: 598 4777 6248 6528
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file ube2a.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 TGTI 2.000000
2 TGTD 3.000000
3 TATI 142.000000
4 TATD 2.000000
5 TACI 5.000000
6 CGTI 1.000000
7 CGTD 2.000000
8 CATI 4.000000
9 CATD 4.000000
10 CACI 25.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (3,3)
D002: (3,3)
D003: (2,2)
D004: (3,3)
D005: (9,9)
D006: (3,3)
D007: (3,3)
D008: (3,3)
D009: (3,3)
D010: (3,3)
D011: (9,9)
D012: (7,7)
D013: (3,3)
D014: (3,3)
D015: (4,4)
DY01: (2,3)
DY02: (3,3)
DY03: (3,3)
DY04: (1,3)
DY05: (3,3)
DY06: (3,3)
DY07: (1,3)
DY08: (3,3)
DY09: (3,3)
DY10: (3,3)
DY11: (3,3)
DY12: (3,8)
E101: (3,3)
E102: (3,3)
E103: (3,3)
E104: (3,3)
E105: (3,3)
E106: (3,3)
E107: (3,3)
E108: (3,3)
E109: (10,10)
E110: (3,3)
E111: (3,3)
E112: (10,10)
E113: (3,3)
E114: (3,10)
E115: (10,10)
E116: (10,10)
E117: (3,3)
E118: (5,6)
E119: (3,3)
E120: (3,5)
E121: (3,3)
E122: (3,3)
H101: (3,3)
H102: (3,3)
H103: (3,3)
H104: (3,3)
H105: (3,5)
H106: (3,3)
H107: (3,3)
H108: (3,5)
H109: (3,3)
H110: (8,10)
H111: (3,3)
H112: (3,10)
H113: (3,3)
H114: (10,10)
H115: (3,5)
H116: (3,3)
H117: (3,3)
H118: (3,3)
H119: (3,3)
H120: (3,3)
H121: (10,10)
H122: (3,3)
X101: (3,10)
X102: (3,3)
X103: (3,3)
X104: (10,10)
X105: (3,3)
X106: (3,3)
X107: (3,10)
X108: (3,3)
X109: (10,10)
X110: (3,3)
X111: (3,3)
X112: (3,3)
X113: (3,3)
X114: (3,3)
X115: (3,3)
X116: (10,10)
X117: (3,3)
X118: (3,8)
X119: (3,3)
X120: (8,10)
X121: (3,3)
X122: (3,3)
X123: (3,3)
X124: (3,10)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
T A T I
T A T I
0 D002
T A T I
T A T I
0 D003
T G T D
T G T D
0 D004
T A T I
T A T I
0 D005
C A T D
C A T D
0 D006
T A T I
T A T I
0 D007
T A T I
T A T I
0 D008
T A T I
T A T I
0 D009
T A T I
T A T I
0 D010
T A T I
T A T I
0 D011
C A T D
C A T D
0 D012
C G T D
C G T D
0 D013
T A T I
T A T I
0 D014
[T] A T I
T A T I
0 D015
T A T D
T A T D
0 DY01
T (G) T D
T (A) T I
0 DY02
T A T I
T A T I
0 DY03
[T] A T I
T A T I
0 DY04
T G T I
T A T I
0 DY05
T A T I
T A T I
0 DY06
[T] A T I
T A T I
0 DY07
T G T I
T A T I
0 DY08
T A T I
T A T I
0 DY09
[T] A T I
T A T I
0 DY10
T A T I
T A T I
0 DY11
[T] A T I
T A T I
0 DY12
T A T I
C A T I
0 E101
T A T I
T A T I
0 E102
T A T I
T A T I
0 E103
T A T I
T A T I
0 E104
T A T I
T A T I
0 E105
T A T I
T A T I
0 E106
T A T I
T A T I
0 E107
T A T I
T A T I
0 E108
T A T I
T A T I
0 E109
C A C I
C A C I
0 E110
T A T I
T A T I
0 E111
T A T I
T A T I
0 E112
C A C I
C A C I
0 E113
[T] A T I
T A T I
0 E114
(T) A T I
(C) A C I
0 E115
C A C I
C A C I
0 E116
C A C I
C A C I
0 E117
T A T I
T A T I
0 E118
(T) (A) (C) I
(C) (G) (T) I
0 E119
T A T I
T A T I
0 E120
T A T I
T A C I
0 E121
T A T I
T A T I
0 E122
T A T I
T A T I
0 H101
T A T I
T A T I
0 H102
T A T I
T A T I
0 H103
T A T I
T A T I
0 H104
T A T I
T A T I
0 H105
T A T I
T A C I
0 H106
T A T I
T A T I
0 H107
T A T I
T A T I
0 H108
T A T I
T A C I
0 H109
T A T I
T A T I
0 H110
C A T I
C A C I
0 H111
T A T I
T A T I
0 H112
(T) A T I
(C) A C I
0 H113
T A T I
T A T I
0 H114
C A C I
C A C I
0 H115
T A T I
T A C I
0 H116
T A T I
T A T I
0 H117
T A T I
T A T I
0 H118
T A T I
T A T I
0 H119
T A T I
T A T I
0 H120
T A T I
T A T I
0 H121
C A C I
C A C I
0 H122
T A T I
T A T I
0 X101
(T) A T I
(C) A C I
0 X102
T A T I
T A T I
0 X103
T A T I
T A T I
0 X104
C A C I
C A C I
0 X105
T A T I
T A T I
0 X106
T A T I
T A T I
0 X107
(T) A T I
(C) A C I
0 X108
T A T I
T A T I
0 X109
C A C I
C A C I
0 X110
T A T I
T A T I
0 X111
T A T I
T A T I
0 X112
T A T I
T A T I
0 X113
T A T I
T A T I
0 X114
T A T I
T A T I
0 X115
T A T I
T A T I
0 X116
C A C I
C A C I
0 X117
T A T I
T A T I
0 X118
T A T I
C A T I
0 X119
T A T I
T A T I
0 X120
C A T I
C A C I
0 X121
T A T I
T A T I
0 X122
T A T I
T A T I
0 X123
T A T I
T A T I
0 X124
(T) A T I
(C) A C I
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
= ? = =
= ? = =
0 D011
= ? = =
= ? = =
0 D012
= = = =
= = = =
0 D013
= = = =
= = = =
0 D014
? = = =
? = = =
0 D015
= ? = =
= ? = =
0 DY01
? (G) = D
? (A) = I
0 DY02
= ? = =
= ? = =
0 DY03
? ? = =
? ? = =
0 DY04
? G = =
? A = =
0 DY05
= = = =
= = = =
0 DY06
? ? = =
? ? = =
0 DY07
= G = =
= A = =
0 DY08
= ? = =
= ? = =
0 DY09
? = = =
? = = =
0 DY10
= = = =
= = = =
0 DY11
? ? = =
? ? = =
0 DY12
T ? = =
C ? = =
0 E101
= ? = =
= ? = =
0 E102
= = = =
= = = =
0 E103
= = = =
= = = =
0 E104
= = = =
= = = =
0 E105
= ? = =
= ? = =
0 E106
= = = =
= = = =
0 E107
= = = =
= = = =
0 E108
= = = =
= = = =
0 E109
= = = =
= = = =
0 E110
= = = =
= = = =
0 E111
= = = =
= = = =
0 E112
= = = =
= = = =
0 E113
? ? = =
? ? = =
0 E114
(T) = T =
(C) = C =
0 E115
= = = =
= = = =
0 E116
= ? = =
= ? = =
0 E117
= = = =
= = = =
0 E118
(T) (A) (C) =
(C) (G) (T) =
0 E119
= ? = =
= ? = =
0 E120
= = T =
= = C =
0 E121
= ? = =
= ? = =
0 E122
= = = =
= = = =
0 H101
= = = =
= = = =
0 H102
= = = =
= = = =
0 H103
= = = =
= = = =
0 H104
= = = =
= = = =
0 H105
= = T =
= = C =
0 H106
= = = =
= = = =
0 H107
= = = =
= = = =
0 H108
= ? T =
= ? C =
0 H109
= = = =
= = = =
0 H110
= = T =
= = C =
0 H111
= = = =
= = = =
0 H112
(T) = T =
(C) = C =
0 H113
= = = =
= = = =
0 H114
= = = =
= = = =
0 H115
? = T =
? = C =
0 H116
= = = =
= = = =
0 H117
= = = =
= = = =
0 H118
= = = =
= = = =
0 H119
= = = =
= = = =
0 H120
= = = =
= = = =
0 H121
= = = =
= = = =
0 H122
= = = =
= = = =
0 X101
(T) = T =
(C) = C =
0 X102
= ? = =
= ? = =
0 X103
= = = =
= = = =
0 X104
= = = =
= = = =
0 X105
= = = =
= = = =
0 X106
= = = =
= = = =
0 X107
(T) ? T =
(C) ? C =
0 X108
= = = =
= = = =
0 X109
= ? = =
= ? = =
0 X110
= = = =
= = = =
0 X111
= ? = =
= ? = =
0 X112
= ? = =
= ? = =
0 X113
= = = =
= = = =
0 X114
= ? = =
= ? = =
0 X115
= = = =
= = = =
0 X116
= = = =
= = = =
0 X117
= = = =
= = = =
0 X118
T ? ? =
C ? ? =
0 X119
= = = =
= = = =
0 X120
= ? T =
= ? C =
0 X121
= = = =
= = = =
0 X122
= = = =
= = = =
0 X123
= ? = =
= ? = =
0 X124
(T) = T =
(C) = C =
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
= ? = =
= ? = =
= = = =
= = = =
= ? = =
= = = =
= = = =
= = = =
= ? = =
= ? = =
= ? = =
= = = =
= = = =
? = = =
= ? = =
? 0.59 = 1.00
= ? = =
? ? = =
? 1.00 = =
= = = =
? ? = =
= 1.00 = =
= ? = =
? = = =
= = = =
? ? = =
1.00 ? = =
= ? = =
= = = =
= = = =
= = = =
= ? = =
= = = =
= = = =
= = = =
= = = =
= = = =
= = = =
= = = =
? ? = =
0.50 = 1.00 =
= = = =
= ? = =
= = = =
0.75 0.75 0.75 =
= ? = =
= = 1.00 =
= ? = =
= = = =
= = = =
= = = =
= = = =
= = = =
= = 1.00 =
= = = =
= = = =
= ? 1.00 =
= = = =
= = 1.00 =
= = = =
0.50 = 1.00 =
= = = =
= = = =
? = 1.00 =
= = = =
= = = =
= = = =
= = = =
= = = =
= = = =
= = = =
0.50 = 1.00 =
= ? = =
= = = =
= = = =
= = = =
= = = =
0.50 ? 1.00 =
= = = =
= ? = =
= = = =
= ? = =
= ? = =
= = = =
= ? = =
= = = =
= = = =
= = = =
1.00 ? ? =
= = = =
= ? 1.00 =
= = = =
= = = =
= ? = =
0.50 = 1.00 =
END PHASEPROBS