*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 ptge4.phase.inp ptge4.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
ptge4.phase.out_freqs : haplotype frequency estimates
ptge4.phase.out_pairs : most likely haplotype pairs for each individual
ptge4.phase.out_recom : estimates of recombination parameters
ptge4.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 22
Positions of loci: 1410 1479 1600 1701 1757 2876 3166 4462 5479 6588 9381 9949 9977 10470 10918 11914 14858 16072 16715 16884 16988 17118
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file ptge4.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 CCGTGCCTACCAAATGGTCACD 16.000000
2 CCGTGCCTACCAAATGACCCTI 1.000000
3 CTGTGCCTACCAAATGGTCACD 1.000000
4 TCGCACCCGTCGAGGAGTTATD 1.000000
5 TCGCACCTGCCAAATGGCCATD 4.000000
6 TCGCACCTGCCAAATGGCCCTI 1.000000
7 TCGCACCTGCTAGATGGCCCTI 12.000000
8 TCGCACCTGCTAGATGACCCTI 5.000000
9 TCGCACCTGTCAAATGGCCATD 1.000000
10 TCGCGGTTACTAGATGGCCCTI 8.000000
11 TCGTGGTTATCAAATGGTCATD 1.000000
12 TCGTGGTTATCAAGGAGTCATD 1.000000
13 TTGCACCCGCTAGATGGCCCTI 3.000000
14 TTGCACCCGTCAAGGAGTTATD 2.000000
15 TTGCACCCGTCGAGGAGTTATD 16.000000
16 TTGCACCTGTCAAGGAGTCATD 1.000000
17 TTACACCCGTCGAGGAGTTATD 18.000000
18 TTACACCCGTCGAGGGGTTATD 1.000000
19 TTACACCTACCAAATGACCCTI 1.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
DY01: (1,15)
DY02: (15,15)
DY03: (4,15)
DY04: (7,15)
DY05: (7,7)
DY06: (5,16)
DY07: (15,15)
DY08: (7,15)
DY09: (14,15)
DY10: (12,15)
DY11: (1,15)
DY12: (7,15)
DY13: (1,7)
DY14: (7,11)
DY15: (10,13)
DY16: (7,9)
DY17: (7,13)
DY18: (5,10)
DY19: (6,14)
DY20: (7,15)
DY21: (7,10)
DY22: (1,5)
DY23: (1,10)
DY24: (5,7)
E101: (10,17)
E102: (17,17)
E103: (17,17)
E104: (10,17)
E105: (1,2)
E106: (1,17)
E107: (8,17)
E108: (8,17)
E109: (8,15)
E110: (1,8)
E111: (1,17)
E112: (1,10)
E113: (1,17)
E114: (1,13)
E115: (3,17)
E116: (17,18)
E117: (1,1)
E118: (10,15)
E119: (15,17)
E120: (1,1)
E121: (8,17)
E122: (17,17)
E123: (17,19)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 DY01
C C G T G C C T A C C A A A T G G T C A C D
T T G C A C C C G T C G A G G A G T T A T D
0 DY02
T T G C A C C C G T C G A G G A G T T A T D
T T G C A C C C G T C G A G G A G T T A T D
0 DY03
T C G C A C C C G T C G A G G A G T T A T D
T T G C A C C C G T C G A G G A G T T A T D
0 DY04
T C G C A C C T G C T A G A T G G C C C T I
T T G C A C C C G T C G A G G A G T T A T D
0 DY05
T C G C A C C T G C T A G A T G G C C C T I
T C G C A C C T G C T A G A T G G C C C T I
0 DY06
T (C) G C A C C T G C C A A A T G G C C A T D
T (T) G C A C C T G T C A A G G A G T C A T D
0 DY07
T T G C A C C C G T C G A G G A G T T A T D
T T G C A C C C G T C G A G G A G T T A T D
0 DY08
T C G C A C C T G C T A G A T G G C C C T I
T T G C A C C C G T C G A G G A G T T A T D
0 DY09
T T G C A C C C G T C A A G G A G T T A T D
T T G C A C C C G T C G A G G A G T T A T D
0 DY10
T C G T G G T T A T C A A G G A G T C A T D
T T G C A C C C G T C [G] A G G A G T T A T D
0 DY11
C C G T G C C T A C C A A A T G G T C A C D
T T G C A C C C G T C [G] A G G A G T T A T D
0 DY12
T C G C A C C T G C T A G A T G G C C C T I
T T G C A C C C G T C G A G G A G T T A T D
0 DY13
C C G T G C C T A C C A A A T G G T C A C D
T C G C A C C T G C T A G A T G G C C C T I
0 DY14
T C G C (A) (C) (C) T (G) (C) (T) A (G) A T G G C C (C) T (I)
T C G T (G) (G) (T) T (A) (T) (C) A (A) A T G G T C (A) T (D)
0 DY15
T C G C G G T T A C T A G A T G G C C C T I
T T G C A C C C G C T A G A T G G C C C T I
0 DY16
T C G C A C C T G (C) T A G A T G G C C C T I
T C G C A C C T G (T) C A A A T G G C C A T D
0 DY17
T C G C A C C T G C T A G A T G G C C C T I
T T G C A C C C G C T A G A T G G C C C T I
0 DY18
T C G C A C C T G C C A A A T G G C C A T D
T C G C G G T T A C T A G A T G G C C C T I
0 DY19
T C G C A C C T G C C A A A T G G C C C T I
T T G C A C C C G T C A A G G A G T T A T D
0 DY20
T C G C A C C T G C T A G A T G G C C C T I
T T G C A C C C G T C G A G G A G T T A T D
0 DY21
T C G C A C C T G C T A G A T G G C C C T I
T C G C G G T T A C T A G A T G G C C C T I
0 DY22
C C G T G C C T A C C A A A T G G T C A C D
T C G C A C C T G C C A A A T G G C C A T D
0 DY23
C C G T G C C T A C C A A A T G G T C A C D
T C G C G G T T A C T A G A T G G C C C T I
0 DY24
T C G C A C C T G C C A A A T G G C C A T D
T C G C A C C T G C T A G A T G G C C C T I
0 E101
T C G C G G T T A C T A G A T G G C C C T I
T T A C A C C C G T C G A G G A G T T A T D
0 E102
T T A C A C C C G T C G A G G A G T T A T D
T T A C A C C C G T C G A G G A G T T A T D
0 E103
T T A C A C C C G T C G A G G A G T T A T D
T T A C A C C C G T C G A G G A G T T A T D
0 E104
T C G C G G T T A C T A G A T G G C C C T I
T T A C A C C C G T C G A G G A G T T A T D
0 E105
C C G T G C C T A C C A A A T G G T C A C D
C C G T G C C T A C C A A A T G A C C C T I
0 E106
C C G T G C C T A C C A A A T G G T C A C D
T T A C A C C C G T C G A G G A G T T A T D
0 E107
T C G C A C C T G C T A G A T G A C C C T I
T T A C A C C C G T C G A G G A G T T A T D
0 E108
T C G C A C C T G C T A G A T G A C C C T I
T T A C A C C C G T C G A G G A G T T A T D
0 E109
T C G C A C C T G C T A G A T G A C C C T I
T T G C A C C C G T C G A G G A G T T A T D
0 E110
C C G T G C C T A C C A A A T G G T C A C D
T C G C A C C T G C T A G A T G A C C C T I
0 E111
C C G T G C C T A C C A A A T G G T C A C D
T T A C A C C C G T C G A G G A G T T A T D
0 E112
C C G T G C C T A C C A A A T G G T C A C D
T C G C G G T T A C T A G A T G G C C C T I
0 E113
C C G T G C C T A C C A A A T G G T C A C D
T T A C A C C C G T C G A G G A G T T A T D
0 E114
C C G T G C C T A C C A A A T G G T C A C D
T T G C A C C C G C T A G A T G G C C C T I
0 E115
C T G T G C C T A C C A A A T G G T C A C D
T T A C A C C C G T C G A G G A G T T A T D
0 E116
T T A C A C C C G T C G A G G A G T T A T D
T T A C A C C C G T C G A G G G G T T A T D
0 E117
C C G T G C C T A C C A A A T G G T C A C D
C C G T G C C T A C C A A A T G G T C A C D
0 E118
T C G C G G T T A C T A G A T G G C C C T I
T T G C A C C C G T C G A G G A G T T A T D
0 E119
T T G C A C C C G T C G A G G A G T T A T D
T T [A] C A C C C G T C G A G G A G T T A T D
0 E120
C C G T G C C T A C C A A A T G G T C A C D
C C G T G C C T A C C A A A T G G T C A C D
0 E121
T C G C A C C T G C T A G A T G A C C C T I
T T A C A C C C G T C G A G G A G T T A T D
0 E122
T T A C A C C C G T C G A G G A G T T A T D
T T A C A C C C G T C G A G G A G T T A T D
0 E123
T T A C A C C C G T C G A G G A G T T A T D
T T A C A C C T A C C A A A T G A C C C T 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 DY01
C C = T G = = T A C = A = A ? G = = C = C =
T T = C A = = C G T = G = G ? A = = T = T =
0 DY02
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 DY03
= C = = = = = = = = = = = = = = = = = = = =
= T = = = = = = = = = = = = = = = = = = = =
0 DY04
= C = = = = = T = C T A G A T ? = C C C = I
= T = = = = = C = T C G A G G ? = T T A = D
0 DY05
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 DY06
= (C) = = = = = = = C = = = A T ? = C = = = =
= (T) = = = = = = = T = = = G G ? = T = = = =
0 DY07
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 DY08
= C = = = = = T = C T A G A T ? = ? C C = I
= T = = = = = C = T C G A G G ? = ? T A = D
0 DY09
= = = = = = = = = = ? A = = = = = = = = = =
= = = = = = = = = = ? G = = = = = = = = = =
0 DY10
= C = T G G T T A = = ? ? = = ? = = C = = =
= T = C A C C C G = = ? ? = = ? = = T = = =
0 DY11
C C = T G = = T A C = ? ? ? T G = = C = C =
T T = C A = = C G T = ? ? ? G A = = T = T =
0 DY12
= C = = = = = T = C T A G A T G = C C C = I
= T = = = = = C = T C G A G G A = T T A = D
0 DY13
C = = T G = = = A = C = A = = = = T = A C D
T = = C A = = = G = T = G = = = = C = C T I
0 DY14
= = = C (A) (C) (C) = (G) (C) (T) = (G) = = = = C = (C) = (I)
= = = T (G) (G) (T) = (A) (T) (C) = (A) = = = = T = (A) = (D)
0 DY15
= C = = G G T T A = = = = = = = = = = = = =
= T = = A C C C G = = = = = = = = = = = = =
0 DY16
= = = = = = = = = (C) T = G = = = = = = C = I
= = = = = = = = = (T) C = A = = = = = = A = D
0 DY17
= C = = = = = T = = = = = = = = = = = = = =
= T = = = = = C = = = = = = = = = = = = = =
0 DY18
= = = = A C C = G ? C = A = = = = = = A = D
= = = = G G T = A ? T = G = = = = = = C = I
0 DY19
= C = = = = = T = C = = = A T G = C C C = I
= T = = = = = C = T = = = G G A = T T A = D
0 DY20
= C = = = = = T = C T A G A T G = C C C = I
= T = = = = = C = T C G A G G A = T T A = D
0 DY21
= = = = A C C = G = ? = = = = = = = = = = =
= = = = G G T = A = ? = = = = = = = = = = =
0 DY22
C = = T G = = = A = = = = = ? = = T = = C =
T = = C A = = = G = = = = = ? = = C = = T =
0 DY23
C = = T = C C = = = C = A = ? = = T = A C D
T = = C = G T = = = T = G = ? = = C = C T I
0 DY24
= = = = = = = = = = C = A = = = = ? = A = D
= = = = = = = = = = T = G = = = = ? = C = I
0 E101
= C G = G G T T A C T A G A T G = C C C = I
= T A = A C C C G T C G A G G A = T T A = D
0 E102
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 E103
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 E104
= C G = G G T T A C T A G A T G = C C C = I
= T A = A C C C G T C G A G G A = T T A = D
0 E105
= = = = = = = = = = = = = = = = G T = A C D
= = = = = = = = = = = = = = = = A C = C T I
0 E106
C C G T G = = T A C = A = A T G = = C = C =
T T A C A = = C G T = G = G G A = = T = T =
0 E107
= C G = = = = T = C T A G A T G A C C C = I
= T A = = = = C = T C G A G G A G T T A = D
0 E108
= C G = = = = T = C T A G A T G A C C C = I
= T A = = = = C = T C G A G G A G T T A = D
0 E109
= C = = = = = T = C T A G A T G A C C C = I
= T = = = = = C = T C G A G G A G T T A = D
0 E110
? ? ? ? ? = = = A = C = A = = = G T = A C D
? ? ? ? ? = = = G = T = G = = = A C = C T I
0 E111
C C G T G = = T A C = A = A T G = = C = C =
T T A C A = = C G T = G = G G A = = T = T =
0 E112
C = = T = C C = = = C = A = = = = T = A C D
T = = C = G T = = = T = G = = = = C = C T I
0 E113
C C G T G = = T A C = A = A T G = = C = C =
T T A C A = = C G T = G = G G A = = T = T =
0 E114
C C = T G = = T A = C = A = = = = ? = A C D
T T = C A = = C G = T = G = = = = ? = C T I
0 E115
C = G T G = = T A C = A = A T G = = C = C =
T = A C A = = C G T = G = G G A = = T = T =
0 E116
= = = = = = = = = = = = = = = A = = = = = =
= = = = = = = = = = = = = = = G = = = = = =
0 E117
= = = = = = = ? = = = = = ? = = = = = = = =
= = = = = = = ? = = = = = ? = = = = = = = =
0 E118
= C = ? G G T T A C T A G A T G = C C C = I
= T = ? A C C C G T C G A G G A = T T A = D
0 E119
? ? ? ? ? = = = = = = = = = = = = = = = = =
? ? ? ? ? = = = = = = = = = = = = = = = = =
0 E120
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 E121
= C G = = = = T = C T A G A T G A C C C = I
= T A = = = = C = T C G A G G A G T T A = D
0 E122
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = =
0 E123
= = = = = = = C G T = G = G G A G T T A = D
= = = = = = = T A C = A = A T G A C C C = I
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
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 1.00 1.00 1.00 1.00 ? = 1.00 1.00 1.00 = 1.00
= = = = = = = = = = = = = = = = = = = = = =
= 0.83 = = = = = = = 0.92 = = = 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 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
= = = 0.91 0.68 0.68 0.68 = 0.68 0.78 0.85 = 0.85 = = = = 0.93 = 0.85 = 0.85
= 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = =
= = = = = = = = = 0.63 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 = ? = = = = = = = = = = =
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 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 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 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 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 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 = 1.00 = 1.00 = = = = ? = 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 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
= = = = = = = = = = = = = = = = = = = = = =
= = = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00
END PHASEPROBS