*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 calca.phase.inp calca.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
calca.phase.out_freqs : haplotype frequency estimates
calca.phase.out_pairs : most likely haplotype pairs for each individual
calca.phase.out_recom : estimates of recombination parameters
calca.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 95
Number of Loci: 6
Positions of loci: 859 893 3053 3581 6262 6385
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file calca.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 TCGCAC 101.000000
2 TCGTAC 12.000000
3 TCACAC 9.000000
4 TGGCAC 1.000000
5 CGGCAC 2.000000
6 CGGCAT 12.000000
7 CGGCTT 52.000000
8 CGACTT 1.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (1,1)
D002: (6,6)
D003: (1,1)
D004: (3,6)
D005: (1,7)
D006: (1,6)
D007: (1,3)
D008: (1,6)
D009: (1,1)
D010: (1,1)
D011: (1,6)
D012: (1,7)
D013: (1,1)
D014: (1,1)
D015: (1,6)
DY01: (1,6)
DY02: (1,6)
DY03: (1,1)
DY04: (1,3)
DY05: (1,1)
DY06: (1,5)
DY07: (4,6)
DY08: (1,1)
DY09: (1,6)
DY10: (1,6)
DY11: (1,1)
DY12: (1,1)
E101: (1,7)
E102: (1,1)
E103: (7,7)
E104: (1,7)
E105: (1,7)
E106: (1,1)
E107: (7,8)
E108: (1,1)
E109: (1,7)
E110: (1,1)
E111: (1,1)
E112: (1,1)
E113: (1,7)
E114: (1,7)
E115: (1,3)
E116: (7,7)
E117: (1,1)
E118: (1,7)
E119: (1,1)
E120: (7,7)
E121: (1,1)
E122: (1,1)
H101: (1,7)
H102: (3,7)
H103: (1,7)
H104: (1,7)
H105: (7,7)
H106: (3,5)
H107: (7,7)
H108: (1,7)
H109: (7,7)
H110: (1,7)
H111: (1,7)
H112: (7,7)
H113: (1,7)
H114: (1,7)
H115: (7,7)
H116: (1,3)
H117: (1,7)
H118: (1,1)
H119: (1,7)
H120: (1,3)
H121: (7,7)
H122: (7,7)
X101: (1,2)
X102: (1,1)
X103: (1,2)
X104: (1,7)
X105: (1,1)
X106: (1,2)
X107: (2,2)
X108: (2,7)
X109: (2,7)
X110: (1,2)
X111: (1,2)
X112: (1,1)
X113: (1,7)
X114: (1,2)
X115: (1,7)
X116: (1,1)
X117: (7,7)
X118: (3,7)
X119: (2,7)
X120: (1,7)
X121: (1,1)
X122: (1,1)
X123: (1,2)
X124: (1,7)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
T C G C A C
T C G C A C
0 D002
C G G C A T
C G G C A T
0 D003
T C G C A C
T C G C A C
0 D004
T C A C A C
C G G C A T
0 D005
T C G C A C
C G G C T T
0 D006
T C G C A C
C G G C A T
0 D007
T C G C A C
T C A C A C
0 D008
T C G C A C
C G G C A T
0 D009
T C G C A C
T C G C A C
0 D010
T C G C A C
T C G C A C
0 D011
T C G C A C
C G G C A T
0 D012
T C G C A C
C G G C T T
0 D013
T C G C A C
T C G C A C
0 D014
T C G C A C
T C G C A C
0 D015
T C G C A C
C G G C A [T]
0 DY01
T C G C A C
C G G C A T
0 DY02
T C G C A C
C G G C A T
0 DY03
T C G C A C
T C G C A C
0 DY04
T C G C A C
T C A C A C
0 DY05
T C G C A C
T C G C A C
0 DY06
T C G C A C
C G G C A C
0 DY07
T G G C A C
C G G C A T
0 DY08
T C G C A C
T C G C A C
0 DY09
T C G C A C
C G G C A T
0 DY10
T C G C A C
C G G C A T
0 DY11
T C G C A C
T C G C A C
0 DY12
T C G C A C
T C G C A C
0 E101
T C G C A C
C G G C T T
0 E102
T C G C A C
T C G C A C
0 E103
C G G C T T
C G G C T T
0 E104
T C G C A C
C G G C T T
0 E105
T C G C A C
C G G C T T
0 E106
T C G C A C
T C G C A C
0 E107
C G G C T T
C G A C T T
0 E108
T C G C A C
T C G C A C
0 E109
T C G C A C
C G G C T T
0 E110
T C G C A C
T C G C A C
0 E111
T C G C A C
T C G C A C
0 E112
T C G C A C
T C G C A C
0 E113
T C G C A C
C G G C T T
0 E114
T C G C A C
C G G C T T
0 E115
T C G C A C
T C A C A C
0 E116
C G G C T T
C G G C T T
0 E117
T C G C A C
T C G C A C
0 E118
T C G C A C
C G G C T T
0 E119
T C G C A C
T C G C A C
0 E120
C G G C T T
C G G C T T
0 E121
T C G C A C
T C G C A C
0 E122
T C G C A C
T C G C A C
0 H101
T C G C A C
C G G C T T
0 H102
T C (A) C A C
C G (G) C T T
0 H103
T C G C A C
C G G C T T
0 H104
T C G C A C
C G G C T T
0 H105
C G G C T T
C G G C T T
0 H106
T C A C A C
C G G C A C
0 H107
C G G C T T
C G G C T T
0 H108
T C G C A C
C G G C T T
0 H109
C G G C T T
C G G C T T
0 H110
T C G C A C
C G G C T T
0 H111
T C G C A C
C G G C T T
0 H112
C G G C T T
C G G C T T
0 H113
T C G C A C
C G G C T T
0 H114
T C G C A C
C G G C T T
0 H115
C G G C T T
C G G C T T
0 H116
T C G C A C
T C A C A C
0 H117
T C G C A C
C G G C T T
0 H118
T C G C A C
T C G C A C
0 H119
T C G C A C
C G G C T T
0 H120
T C G C A C
T C A C A C
0 H121
C G G C T T
C G G C T T
0 H122
C G G C T T
C G G C T T
0 X101
T C G C A C
T C G T A C
0 X102
T C G C A C
T C G C A C
0 X103
T C G C A C
T C G T A C
0 X104
T C G C A C
C G G C T T
0 X105
T C G C A C
T C G C A C
0 X106
T C G C A C
T C G T A C
0 X107
T C G T A C
T C G T A C
0 X108
T C G T A C
C G G C T T
0 X109
T C G T A C
C G G C T T
0 X110
T C G C A C
T C G T A C
0 X111
T C G C A C
T C G T A C
0 X112
T C G C A C
T C G C A C
0 X113
T C G C A C
C G G C T T
0 X114
T C G C A C
T C G T A C
0 X115
T C G C A C
C G G C T T
0 X116
T C G C A C
T C G C A C
0 X117
C G G C T T
C G G C T T
0 X118
T C (A) C A C
C G (G) C T T
0 X119
T C G T A C
C G G C T T
0 X120
T C G C A C
C G G C T T
0 X121
T C G C A C
T C G C A C
0 X122
T C G C A C
T C G C A C
0 X123
T C G C A C
T C G T A C
0 X124
T C G C A C
C G G C T 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
? ? = = = =
? ? = = = =
0 D002
? ? = = = =
? ? = = = =
0 D003
= = = = = =
= = = = = =
0 D004
T C A = = C
C G G = = T
0 D005
T C = = A C
C G = = T T
0 D006
T C = = = C
C G = = = T
0 D007
= = G = = =
= = A = = =
0 D008
T C = = = C
C G = = = T
0 D009
= = = = = =
= = = = = =
0 D010
? ? = = = =
? ? = = = =
0 D011
T C = = = C
C G = = = T
0 D012
T C = = A C
C G = = T T
0 D013
= = = = = =
= = = = = =
0 D014
= = = = = =
= = = = = =
0 D015
T C = = = ?
C G = = = ?
0 DY01
T C = = = C
C G = = = T
0 DY02
T C = = = C
C G = = = T
0 DY03
= = = = = =
= = = = = =
0 DY04
= = G = = =
= = A = = =
0 DY05
= = = = = =
= = = = = =
0 DY06
T C = = = =
C G = = = =
0 DY07
T = = = = C
C = = = = T
0 DY08
= = = = = =
= = = = = =
0 DY09
? ? = = = C
? ? = = = T
0 DY10
T C = = = C
C G = = = T
0 DY11
= = = = = =
= = = = = =
0 DY12
= = = = = =
= = = = = =
0 E101
T C = = A C
C G = = T T
0 E102
= = = = = =
= = = = = =
0 E103
= = = = = =
= = = = = =
0 E104
T C = = A C
C G = = T T
0 E105
T C = = A C
C G = = T T
0 E106
= = = = = =
= = = = = =
0 E107
? ? G = = =
? ? A = = =
0 E108
= = = = = =
= = = = = =
0 E109
T C = = A C
C G = = T T
0 E110
= = = = = =
= = = = = =
0 E111
= = = = = =
= = = = = =
0 E112
= = = = = =
= = = = = =
0 E113
T C = = A C
C G = = T T
0 E114
T C = = A C
C G = = T T
0 E115
? ? G = = =
? ? A = = =
0 E116
= = = = = =
= = = = = =
0 E117
= = = = = =
= = = = = =
0 E118
T C = = A C
C G = = T T
0 E119
= = = = = =
= = = = = =
0 E120
= = = = = =
= = = = = =
0 E121
= = = = = =
= = = = = =
0 E122
= = = = = =
= = = = = =
0 H101
T C = = A C
C G = = T T
0 H102
T C (A) = A C
C G (G) = T T
0 H103
T C = = A C
C G = = T T
0 H104
T C = = A C
C G = = T T
0 H105
= = = = = =
= = = = = =
0 H106
T C A = = =
C G G = = =
0 H107
= = = = = =
= = = = = =
0 H108
T C = = A C
C G = = T T
0 H109
? ? = = = =
? ? = = = =
0 H110
T C = = A C
C G = = T T
0 H111
T C = = A C
C G = = T T
0 H112
= = = = = =
= = = = = =
0 H113
T C = = A C
C G = = T T
0 H114
T C = = A C
C G = = T T
0 H115
= = = = = =
= = = = = =
0 H116
= = G = = =
= = A = = =
0 H117
T C = = A C
C G = = T T
0 H118
= = = = = =
= = = = = =
0 H119
T C = = A C
C G = = T T
0 H120
= = G = = =
= = A = = =
0 H121
= = = = = =
= = = = = =
0 H122
= = = = = =
= = = = = =
0 X101
= = = C = =
= = = T = =
0 X102
= = = = = =
= = = = = =
0 X103
= = = C = =
= = = T = =
0 X104
T C = = A C
C G = = T T
0 X105
= = = = = =
= = = = = =
0 X106
= = = C = =
= = = T = =
0 X107
= = = = = =
= = = = = =
0 X108
? C = T A C
? G = C T T
0 X109
T C = T A C
C G = C T T
0 X110
= = = C = =
= = = T = =
0 X111
= = = C = =
= = = T = =
0 X112
= = = = = =
= = = = = =
0 X113
T C = = A C
C G = = T T
0 X114
= = = C = =
= = = T = =
0 X115
T C = = A C
C G = = T T
0 X116
= = = = = =
= = = = = =
0 X117
= = = = = =
= = = = = =
0 X118
T C (A) = A C
C G (G) = T T
0 X119
T C = T A C
C G = C T T
0 X120
T C = = A C
C G = = T T
0 X121
= = = = = =
= = = = = =
0 X122
= = = = = =
= = = = = =
0 X123
= = = C = =
= = = T = =
0 X124
T C = = A C
C G = = T T
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 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 = = = =
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 0.77 = 1.00 1.00
1.00 1.00 = = 1.00 1.00
1.00 1.00 = = 1.00 1.00
= = = = = =
1.00 1.00 0.96 = = =
= = = = = =
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 = 0.99 1.00 1.00
1.00 1.00 = 0.99 1.00 1.00
= = = 1.00 = =
= = = 1.00 = =
= = = = = =
1.00 1.00 = = 1.00 1.00
= = = 1.00 = =
1.00 1.00 = = 1.00 1.00
= = = = = =
= = = = = =
1.00 1.00 0.76 = 1.00 1.00
1.00 1.00 = 0.99 1.00 1.00
1.00 1.00 = = 1.00 1.00
= = = = = =
= = = = = =
= = = 1.00 = =
1.00 1.00 = = 1.00 1.00
END PHASEPROBS