*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 tuba1.phase.inp tuba1.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
tuba1.phase.out_freqs : haplotype frequency estimates
tuba1.phase.out_pairs : most likely haplotype pairs for each individual
tuba1.phase.out_recom : estimates of recombination parameters
tuba1.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 95
Number of Loci: 5
Positions of loci: 1856 2107 3180 4129 7254
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file tuba1.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 ACCCC 3.000000
2 AGCAC 2.000000
3 AGCCC 74.000000
4 AGCCT 78.000000
5 AGTAC 4.000000
6 CCCAC 1.000000
7 CCCCC 4.000000
8 CCTAC 23.000000
9 CCTAT 1.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (3,5)
D002: (3,4)
D003: (3,6)
D004: (4,4)
D005: (3,8)
D006: (1,7)
D007: (2,4)
D008: (2,3)
D009: (3,5)
D010: (3,4)
D011: (3,8)
D012: (3,5)
D013: (3,3)
D014: (3,4)
D015: (7,7)
DY01: (3,4)
DY02: (3,3)
DY03: (8,8)
DY04: (3,9)
DY05: (4,8)
DY06: (4,8)
DY07: (3,3)
DY08: (7,8)
DY09: (1,3)
DY10: (3,4)
DY11: (8,8)
DY12: (3,4)
E101: (3,4)
E102: (4,8)
E103: (4,4)
E104: (4,8)
E105: (4,4)
E106: (3,4)
E107: (3,4)
E108: (4,4)
E109: (3,8)
E110: (4,4)
E111: (3,8)
E112: (4,4)
E113: (3,8)
E114: (3,4)
E115: (4,4)
E116: (4,4)
E117: (4,4)
E118: (4,4)
E119: (3,4)
E120: (4,4)
E121: (8,8)
E122: (3,4)
H101: (3,4)
H102: (3,4)
H103: (3,3)
H104: (3,4)
H105: (3,4)
H106: (3,3)
H107: (4,4)
H108: (1,4)
H109: (3,4)
H110: (4,4)
H111: (3,8)
H112: (4,4)
H113: (3,3)
H114: (3,4)
H115: (3,4)
H116: (4,4)
H117: (3,8)
H118: (3,4)
H119: (4,8)
H120: (4,4)
H121: (3,4)
H122: (3,4)
X101: (3,3)
X102: (3,4)
X103: (3,3)
X104: (4,4)
X105: (3,4)
X106: (3,3)
X107: (3,4)
X108: (3,4)
X109: (3,3)
X110: (4,8)
X111: (3,4)
X112: (3,8)
X113: (4,4)
X114: (3,3)
X115: (4,4)
X116: (3,4)
X117: (3,4)
X118: (4,5)
X119: (3,8)
X120: (3,8)
X121: (3,3)
X122: (3,4)
X123: (3,3)
X124: (3,4)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
A G (C) C C
A [G] (T) A C
0 D002
A G C C C
A G C C T
0 D003
A G C (C) C
C C [C] (A) C
0 D004
A G C C T
A G C C T
0 D005
A G C (C) C
C C T (A) C
0 D006
A C C C C
C C C C C
0 D007
A G C (A) C
A G C (C) T
0 D008
A G C A C
A G C C C
0 D009
A [G] (C) C C
A [G] (T) A C
0 D010
A G C C C
A G C C T
0 D011
A G C (C) C
C C T (A) C
0 D012
A G C C C
[A] [G] T A C
0 D013
A G C C C
A G C C C
0 D014
A G C C C
A G C C T
0 D015
C C C C C
C C C C C
0 DY01
A G C C C
A G C C T
0 DY02
A [G] C C C
A G C C C
0 DY03
C C T A C
[C] C T A C
0 DY04
A G (C) (C) (C)
[C] C (T) (A) (T)
0 DY05
A G (C) (C) (T)
C C (T) (A) (C)
0 DY06
A G (C) (C) (T)
C C (T) (A) (C)
0 DY07
A [G] C C C
A G C C C
0 DY08
C C (C) C C
C C (T) A C
0 DY09
A C C C C
A G C C C
0 DY10
A [G] C C C
A G C C T
0 DY11
C C T A C
C C T A C
0 DY12
A G C C C
A G C C T
0 E101
A G C C C
A G C C T
0 E102
A G (C) (C) (T)
C C (T) (A) (C)
0 E103
A G C C T
A G C C T
0 E104
A G (C) (C) (T)
C C (T) (A) (C)
0 E105
A G C C T
A G C C T
0 E106
A [G] C C C
A G C C T
0 E107
A G C C C
A G C C T
0 E108
A G C C T
A G C C T
0 E109
A G C (C) C
C C T (A) C
0 E110
A G C C T
A G C C T
0 E111
A G C (C) C
[C] C T (A) C
0 E112
A G C C T
A G C C T
0 E113
A G C (C) C
C C T (A) C
0 E114
A G C C C
A G C C T
0 E115
A G C C T
A G C C T
0 E116
A G C C T
A G C C T
0 E117
A G C C T
A G C C T
0 E118
A G C C T
A G C C T
0 E119
A G C C C
A G C C T
0 E120
A G C C T
A G C C T
0 E121
C C T A C
C C T A C
0 E122
A G C C C
A G C C T
0 H101
A G C C C
A G C C T
0 H102
A G C C C
A G C C T
0 H103
A G C C C
A G C C C
0 H104
A G C C C
A G C C T
0 H105
A G C C C
A G C C T
0 H106
A G C C C
A G C C C
0 H107
A G C C T
A G C C T
0 H108
A (C) C C C
A (G) C C T
0 H109
A G C C C
A G C C T
0 H110
A G C C T
A G C C T
0 H111
A G (C) (C) C
[C] C (T) (A) C
0 H112
A G C C T
A G C C T
0 H113
A G C C C
A G C C C
0 H114
A G C C C
A G C C T
0 H115
A G C C C
A G C C T
0 H116
A G C C T
A G C C T
0 H117
A G C (C) C
C C T (A) C
0 H118
A G C C C
A G C C T
0 H119
A G (C) (C) (T)
C C (T) (A) (C)
0 H120
A G C C T
A G C C T
0 H121
A G C C C
A G C C T
0 H122
A G C C C
A G C C T
0 X101
A G C C C
A G C C C
0 X102
A G C C C
A G C C T
0 X103
A G C C C
A G C C C
0 X104
A G C C T
A G C C T
0 X105
A G C C C
A G C C T
0 X106
A G C C C
A G C C C
0 X107
A G C C C
A G C C T
0 X108
A G C C C
A G C C T
0 X109
A G C C C
A G C C C
0 X110
A G C (C) (T)
C C T (A) (C)
0 X111
A G C C C
A G C C T
0 X112
A G C (C) C
C C T (A) C
0 X113
A G C C T
A G C C T
0 X114
A G C C C
A G C C C
0 X115
A G C C T
A G C C T
0 X116
A G C C C
A G C C T
0 X117
A G C C C
A G C C T
0 X118
A [G] (C) (C) (T)
[A] [G] (T) (A) (C)
0 X119
A G C (C) C
C C T (A) C
0 X120
A G C (C) C
C C T (A) C
0 X121
A G C C C
A G C C C
0 X122
A G C C C
A G C C T
0 X123
A G C C C
A G C C C
0 X124
A G C C C
A G C C T
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
? ? (C) C =
? ? (T) A =
0 D002
? ? ? = C
? ? ? = T
0 D003
A G ? (C) =
C C ? (A) =
0 D004
= = = = =
= = = = =
0 D005
A G C (C) =
C C T (A) =
0 D006
A = = = =
C = = = =
0 D007
? ? ? (A) C
? ? ? (C) T
0 D008
? ? ? A =
? ? ? C =
0 D009
? ? (C) C =
? ? (T) A =
0 D010
= = = = C
= = = = T
0 D011
A G C (C) =
C C T (A) =
0 D012
? ? C C =
? ? T A =
0 D013
= ? = = =
= ? = = =
0 D014
? ? = = C
? ? = = T
0 D015
= = = = =
= = = = =
0 DY01
= = = = C
= = = = T
0 DY02
? ? = = =
? ? = = =
0 DY03
? = = = =
? = = = =
0 DY04
? G (C) (C) (C)
? C (T) (A) (T)
0 DY05
A G (C) (C) (T)
C C (T) (A) (C)
0 DY06
A G (C) (C) (T)
C C (T) (A) (C)
0 DY07
? ? = = =
? ? = = =
0 DY08
= = (C) C =
= = (T) A =
0 DY09
= C = = =
= G = = =
0 DY10
? ? = = C
? ? = = T
0 DY11
= = = = =
= = = = =
0 DY12
= = = = C
= = = = T
0 E101
? = = = C
? = = = T
0 E102
A G (C) (C) (T)
C C (T) (A) (C)
0 E103
? = = = =
? = = = =
0 E104
A G (C) (C) (T)
C C (T) (A) (C)
0 E105
= = = = =
= = = = =
0 E106
? ? = = C
? ? = = T
0 E107
= = = = C
= = = = T
0 E108
= = = = =
= = = = =
0 E109
A G C (C) =
C C T (A) =
0 E110
= = = = =
= = = = =
0 E111
? G C (C) =
? C T (A) =
0 E112
= = = = =
= = = = =
0 E113
A G C (C) =
C C T (A) =
0 E114
= = = = C
= = = = T
0 E115
= = = = =
= = = = =
0 E116
= = = = =
= = = = =
0 E117
= = = = =
= = = = =
0 E118
? = = = =
? = = = =
0 E119
= = = = C
= = = = T
0 E120
= = = = =
= = = = =
0 E121
= = = = =
= = = = =
0 E122
= = = = C
= = = = T
0 H101
? ? = = C
? ? = = T
0 H102
= = ? = C
= = ? = T
0 H103
= = = = =
= = = = =
0 H104
= = = = C
= = = = T
0 H105
= = ? = C
= = ? = T
0 H106
= = = = =
= = = = =
0 H107
= = = = =
= = = = =
0 H108
= (C) = = C
= (G) = = T
0 H109
= = = = C
= = = = T
0 H110
= = = = =
= = = = =
0 H111
? G (C) (C) =
? C (T) (A) =
0 H112
= = = = =
= = = = =
0 H113
= = = = =
= = = = =
0 H114
= = = = C
= = = = T
0 H115
= = = = C
= = = = T
0 H116
? ? = = =
? ? = = =
0 H117
A G C (C) =
C C T (A) =
0 H118
= = = = C
= = = = T
0 H119
A G (C) (C) (T)
C C (T) (A) (C)
0 H120
= = = = =
= = = = =
0 H121
= = = = C
= = = = T
0 H122
= = = = C
= = = = T
0 X101
= ? = = =
= ? = = =
0 X102
= = = = C
= = = = T
0 X103
= = = = =
= = = = =
0 X104
= = = = =
= = = = =
0 X105
= = = = C
= = = = T
0 X106
= = = = =
= = = = =
0 X107
= = = = C
= = = = T
0 X108
= = = = C
= = = = T
0 X109
= = = = =
= = = = =
0 X110
A ? C (C) (T)
C ? T (A) (C)
0 X111
= = = = C
= = = = T
0 X112
A G C (C) =
C C T (A) =
0 X113
= = = = =
= = = = =
0 X114
= = = = =
= = = = =
0 X115
= = = = =
= = = = =
0 X116
= = = = C
= = = = T
0 X117
= = = = C
= = = = T
0 X118
? ? (C) (C) (T)
? ? (T) (A) (C)
0 X119
A G C (C) =
C C T (A) =
0 X120
A ? C (C) =
C ? T (A) =
0 X121
= = ? = =
= = ? = =
0 X122
= = = = C
= = = = T
0 X123
= = = = =
= = = = =
0 X124
= = = = C
= = = = T
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
? ? 0.68 0.95 =
? ? ? = 1.00
0.97 0.97 ? 0.56 =
= = = = =
0.93 0.93 0.93 0.62 =
1.00 = = = =
? ? ? 0.55 0.92
? ? ? 1.00 =
? ? 0.59 0.97 =
= = = = 1.00
0.93 0.93 0.93 0.62 =
? ? 1.00 1.00 =
= ? = = =
? ? = = 1.00
= = = = =
= = = = 1.00
? ? = = =
? = = = =
? 0.95 0.89 0.70 0.56
0.96 0.96 0.90 0.58 0.54
0.96 0.96 0.90 0.58 0.54
? ? = = =
= = 0.55 1.00 =
= 1.00 = = =
? ? = = 1.00
= = = = =
= = = = 1.00
? = = = 1.00
0.96 0.96 0.90 0.58 0.54
? = = = =
0.96 0.96 0.90 0.58 0.54
= = = = =
? ? = = 1.00
= = = = 1.00
= = = = =
0.93 0.93 0.93 0.62 =
= = = = =
? 0.98 0.92 0.54 =
= = = = =
0.93 0.93 0.93 0.62 =
= = = = 1.00
= = = = =
= = = = =
= = = = =
? = = = =
= = = = 1.00
= = = = =
= = = = =
= = = = 1.00
? ? = = 1.00
= = ? = 1.00
= = = = =
= = = = 1.00
= = ? = 1.00
= = = = =
= = = = =
= 0.50 = = 1.00
= = = = 1.00
= = = = =
? 0.98 0.87 0.57 =
= = = = =
= = = = =
= = = = 1.00
= = = = 1.00
? ? = = =
0.93 0.93 0.93 0.62 =
= = = = 1.00
0.96 0.96 0.90 0.58 0.54
= = = = =
= = = = 1.00
= = = = 1.00
= ? = = =
= = = = 1.00
= = = = =
= = = = =
= = = = 1.00
= = = = =
= = = = 1.00
= = = = 1.00
= = = = =
0.97 ? 0.94 0.55 0.54
= = = = 1.00
0.93 0.93 0.93 0.62 =
= = = = =
= = = = =
= = = = =
= = = = 1.00
= = = = 1.00
? ? 0.79 0.79 0.71
0.93 0.93 0.93 0.62 =
0.99 ? 0.98 0.57 =
= = ? = =
= = = = 1.00
= = = = =
= = = = 1.00
END PHASEPROBS