*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 hshin.phase.inp hshin.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
hshin.phase.out_freqs : haplotype frequency estimates
hshin.phase.out_pairs : most likely haplotype pairs for each individual
hshin.phase.out_recom : estimates of recombination parameters
hshin.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 23
Positions of loci: 579 9581 10783 12625 12881 14985 15956 16472 19354 20409 22747 22905 23202 23918 23958 24559 35499 35507 39548 40747 42269 43049 43379
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file hshin.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 DAGTTCGICDGTGCAGACICGII 6.000000
2 DAGTTCGICDGTGCAGACICCII 2.000000
3 DAGTTCGICDGTGCAGACICCID 1.000000
4 DAGTTCGICDGTACAGACICGID 6.000000
5 DAGTTCGICDGTACAGACICCII 1.000000
6 DAGTTCGICDGTACAGACDCGID 3.000000
7 DAGTTCGICIGTACAGACDCGID 1.000000
8 DAGTTCGITIGCGCAGTCICCII 4.000000
9 DAGGTCGICDGTACAGACDCGID 1.000000
10 DAAGTCGDTIGTGCTGTCITCDI 12.000000
11 DAAGTCGDTIGTGCTATCITCDI 5.000000
12 DTGTTGGICDGTATAGACICGID 7.000000
13 IAGTTCGITIGTGCAGTTICCII 2.000000
14 IAGTTCAITIGTGCAGTTICCII 30.000000
15 IAGTCCAITICTGCAGTTICCII 11.000000
16 ITGTTGGICDGTATAGACICGID 2.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
DY01: (1,12)
DY02: (1,12)
DY03: (14,14)
DY04: (6,12)
DY05: (1,4)
DY06: (7,16)
DY07: (3,4)
DY08: (14,16)
DY09: (1,13)
DY10: (8,14)
DY11: (1,15)
DY12: (8,15)
DY13: (12,14)
DY14: (1,4)
DY15: (12,12)
DY16: (14,14)
DY17: (6,14)
DY18: (14,14)
DY19: (6,13)
DY20: (14,15)
DY21: (12,14)
DY22: (2,8)
DY23: (2,15)
DY24: (4,8)
E101: (10,11)
E102: (10,14)
E103: (14,15)
E104: (10,14)
E105: (10,14)
E106: (10,14)
E107: (14,14)
E108: (10,11)
E109: (14,15)
E110: (10,14)
E111: (10,10)
E112: (11,14)
E113: (11,14)
E114: (14,14)
E115: (10,14)
E116: (11,14)
E117: (5,15)
E118: (9,15)
E119: (4,15)
E120: (10,15)
E121: (4,14)
E122: (10,14)
E123: (14,15)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 DY01
D A G T T C G I C D G T G C A G A C I C G I I
D T G T T G G I C D G T A T A G A C I C G I D
0 DY02
D A G T T C G I C D G T G C A G A C I C G I I
D T G T T G G I C D G T A T A G A C I C G I D
0 DY03
I A G T T C A I T I G T G C A G T T I C C I I
I A G T T C A I T I G T G C A G T T I C C I I
0 DY04
D A G T T C G I C D G T A C A G A C D C G I D
D T G T T G G I C D G T A T A G A C I C G I D
0 DY05
D A G T T C G I C D G T G C A G A C I C G I I
D A G T T C G I C D G T A C A G A C I C G I D
0 DY06
(D) A G T T C G I C (I) G T A C A G A C D C G I D
(I) T G T T G G I C (D) G T A T A G A C I C G I D
0 DY07
D A G T T C G I C D G T G C A G A C I C C I D
D A G T T C G I C D G T A C A G A C I C G I D
0 DY08
I A G T T C A I T I G T G C A G T T I C C I I
I T G T T G G I C D G T A T A G A C I C G I D
0 DY09
D A G T T C G I C D G T G C A G A C I C G I I
I A G T T C G I T I G T G C A G T T I C C I I
0 DY10
D A G T T C G I T I G C G C A G T C I C C I I
I A G T T C A I T I G T G C A G T T I C C I I
0 DY11
D A G T T C G I C D G T G C A G A C I C G I I
I A G T C C A I T I C T G C A G T T I C C I I
0 DY12
D A G T T C G I T I G C G C A G T C I C C I I
I A G T C C A I T I C T G C A G T T I C C I I
0 DY13
D T G T T G G I C D G T A T A G A C I C G I D
I A G T T C A I T I G T G C A G T T I C C I I
0 DY14
D A G T T C G I C D G T G C A G A C I C G I I
D A G T T C G I C D G T A C A G A C I C G I D
0 DY15
D T G T T G G I C D G T A T A G A C I C G I D
D T G T T G G I C D G T A T A G A C I C G I D
0 DY16
I A G T T C A I T I G T G C A G T T I C C I I
I A G T T C A I T I G T G C A G T T I C C I I
0 DY17
D A G T T C G I C D G T A C A G A C D C G I D
I A G T T C A I T I G T G C A G T T I C C I I
0 DY18
I A G T T C A I T I G T G C A G T T I C C I I
I A G T T C A I T I G T G C A G T T I C C I I
0 DY19
D A G T T C G I C D G T A C A G A C D C G I D
I A G T T C G I T I G T G C A G T T I C C I I
0 DY20
I A G T T C A I T I G T G C A G T T I C C I I
I A G T C C A I T I C T G C A G T T I C C I I
0 DY21
D T G T T G G I C D G T A T A G A C I C G I D
I A G T T C A I T I G T G C A G T T I C C I I
0 DY22
D A G T T C G I C D G T G C A G A C I C C I I
D A G T T C G I T I G C G C A G T C I C C I I
0 DY23
D A G T T C G I C D G T G C A G A C I C C I I
I A G T C C A I T I C T G C A G T T I C C I I
0 DY24
D A G T T C G I C D G T A C A G A C I C G I D
D A G T T C G I T I G C G C A G T C I C C I I
0 E101
D A A G T C G D T I G T G C T G T C I T C D I
D A A G T C G D T I G T G C T A T C I T C D I
0 E102
D A A G T C G D T I G T G C T G T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E103
I A G T T C A I T I G T G C A G T T I C C I I
I A G T C C A I T I C T G C A G T T I C C I I
0 E104
D A A G T C G D T I G T G C T G T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E105
D A A G T C G D T I G T G C T G T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E106
D A A G T C G D T I G T G C T G T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E107
I A G T T C A I T I G T G C A G T T I C C I I
I A G T T C A I T I G T G C A G T T I C C I I
0 E108
D A A G T C G D T I G T G C T G T C I T C D I
D A A G T C G D T I G T G C T A T C I T C D I
0 E109
I A G T T C A I T I G T G C A G T T I C C I I
I A G T C C A I T I C T G C A G T T I C C I I
0 E110
D A A G T C G D T I G T G C T [G] T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E111
D A A G T C G D T I G T G C T G T C I T C D I
D A A G T C G D T I G T G C T G T C I T C D I
0 E112
D A A G T C G D T I G T G C T A T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E113
D A A G T C G D T I G T G C T A T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E114
I A G T T C A I T I G T G C A G T T I C C I I
I A G T T C A I T I G T G C A G T T I C C I I
0 E115
D A A G T C G D T I G T G C T G T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E116
D A A G T C G D T I G T G C T A T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E117
D A G T T C G I C D G T A C A G A C I C C I I
I A G T C C A I T I C T G C A G T T I C C I I
0 E118
D A G (G) T C G I C D G T A C A G A C D C G I D
I A G (T) C C A I T I C T G C A G T T I C C I I
0 E119
D A G T T C G I C D G T A C A G A C I C G I D
I A G T C C A I T I C T G C A G T T I C C I I
0 E120
D A A G T C G D T I G T G C T [G] T C I T C D I
I A G T C C A I T I C T G C A G T T I C C I I
0 E121
D A G T T C G I C D G T A C A G A C I C G I D
I A G T T C A I T I G T G C A G T T I C C I I
0 E122
D A A G T C G D T I G T G C T [G] T C I T C D I
I A G T T C A I T I G T G C A G T T I C C I I
0 E123
I A G T T C A I T I G T G C A G T T I C C I I
I A G T C C A I T I C T G C A G T T I C C I 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
= A = = = C = ? = = ? ? ? C = = = = = = = = I
= T = = = G = ? = = ? ? ? T = = = = = = = = D
0 DY02
= A = ? = ? = ? ? = = ? ? C = = = = = = = = I
= T = ? = ? = ? ? = = ? ? T = = = = = = = = D
0 DY03
= = = = = ? = = = = = = = = = = = = = = = = =
= = = = = ? = = = = = = = = = = = = = = = = =
0 DY04
= A = = = C = = = = = = = C = = = = D = = = =
= T = = = G = = = = = = = T = = = = I = = = =
0 DY05
= = = = = = = = = = = ? ? = = = = = = = = = I
= = = = = = = = = = = ? ? = = = = = = = = = D
0 DY06
(D) A = = = C = = = (I) = ? ? C = = = = D = = = =
(I) T = = = G = = = (D) = ? ? T = = = = I = = = =
0 DY07
= = = = = ? = = = = = ? G = = = = = = = C = =
= = = = = ? = = = = = ? A = = = = = = = G = =
0 DY08
= ? ? = = C A = ? I ? ? G C = = T T = = C = I
= ? ? = = G G = ? D ? ? A T = = A C = = G = D
0 DY09
D = = = = = = = C D = ? ? = = = A C = = G ? =
I = = = = = = = T I = ? ? = = = T T = = C ? =
0 DY10
D = = = = = G = = = = C = = = = = C = = = = =
I = = = = = A = = = = T = = = = = T = = = = =
0 DY11
D ? = = T = ? = C D G = = = = = A C = = G = =
I ? = = C = ? = T I C = = = = = T T = = C = =
0 DY12
D = = = T = G = = = G C = = = = = C = = = = =
I = = = C = A = = = C T = = = = = T = = = = =
0 DY13
D T = = = G G = C D = = A T = = A C = = G = D
I A = = = C A = T I = = G C = = T T = = C = I
0 DY14
= = = = = = = = = = = = G = = = = = = = = = I
= = = = = = = = = = = = A = = = = = = = = = D
0 DY15
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = =
0 DY16
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = =
0 DY17
D = = = = = G = C D = = A = = = A C D = G = D
I = = = = = A = T I = = G = = = T T I = C = I
0 DY18
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = =
0 DY19
D = = = = = = = C D = = A = = = A C D = G = D
I = = = = = = = T I = = G = = = T T I = C = I
0 DY20
= = = = T = = = = = G = = = = = = = = = = = =
= = = = C = = = = = C = = = = = = = = = = = =
0 DY21
D T ? = = G G = C D = = A T = = A C = = G = D
I A ? = = C A = T I = = G C = = T T = = C = I
0 DY22
= = = = = = = = C D = T = = = = A = = = = = =
= = = = = = = = T I = C = = = = T = = = = = =
0 DY23
D = = = T = G = C D G = = = = = A C = = = = =
I = = = C = A = T I C = = = = = T T = = = = =
0 DY24
= = = = = = = = C D = T A = = = A = = = G = D
= = = = = = = = T I = C G = = = T = = = C = I
0 E101
= = = = = = = = = = = = = = = G = = = = = = =
= = = = = = = = = = = = = = = A = = = = = = =
0 E102
D = A G = = G D = = = = = = T = = C = T = D =
I = G T = = A I = = = = = = A = = T = C = I =
0 E103
= = = = T = = = = = G = = = = = = = = = = = =
= = = = C = = = = = C = = = = = = = = = = = =
0 E104
D = A G = = G D = = = = = = T = = C = T = D =
I = G T = = A I = = = = = = A = = T = C = I =
0 E105
D = A G = = G D = = = = = = T = = C = T = D =
I = G T = = A I = = = = = = A = = T = C = I =
0 E106
D = A G = = G D = = = = = = T = = C = T = D =
I = G T = = A I = = = = = = A = = T = C = I =
0 E107
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = =
0 E108
= = = = = = = = = = = = = = = G = = = = = = =
= = = = = = = = = = = = = = = A = = = = = = =
0 E109
= = = = T = = = = = G = = ? ? ? = = = = = = =
= = = = C = = = = = C = = ? ? ? = = = = = = =
0 E110
D = A G = ? G D = = = = = = T ? = C = T = D =
I = G T = ? A I = = = = = = A ? = T = C = I =
0 E111
= = = = = = = = = = = ? = = = = = = = = = = =
= = = = = = = = = = = ? = = = = = = = = = = =
0 E112
D = A G = = G D = = = = = = T A = C = T = D =
I = G T = = A I = = = = = = A G = T = C = I =
0 E113
D = A G = = G D = = = = = = T A = C = T = D =
I = G T = = A I = = = = = = A G = T = C = I =
0 E114
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = =
0 E115
D = A G = = G D = = = = = = T = = C = T = D =
I = G T = = A I = = = = = = A = = T = C = I =
0 E116
D ? A G = = G D = = = = = = T A = C = T = D =
I ? G T = = A I = = = = = = A G = T = C = I =
0 E117
D = = = T = G = C D G = A = = ? A C = = = = =
I = = = C = A = T I C = G = = ? T T = = = = =
0 E118
D = = (G) T = G = C D G = A = = = A C D ? G ? ?
I = = (T) C = A = T I C = G = = = T T I ? C ? ?
0 E119
D = = = T = G = C D ? ? A = = = A C = = G = D
I = = = C = A = T I ? ? G = = = T T = = C = I
0 E120
D = A G T = G D = = G = = = T ? = C = T = D =
I = G T C = A I = = C = = = A ? = T = C = I =
0 E121
D = = = = = G = C D = ? ? = = = A C = = G = D
I = = = = = A = T I = ? ? = = = T T = = C = I
0 E122
D ? A G = = G D = = = = = = ? ? = C = T = ? =
I ? G T = = A I = = = = = = ? ? = T = C = ? =
0 E123
= = = = T = = = = = G = = ? ? = = = = = = = =
= = = = C = = = = = C = = ? ? = = = = = = = =
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
= 1.00 = ? = ? = ? ? = = ? ? 1.00 = = = = = = = = 1.00
= = = = = ? = = = = = = = = = = = = = = = = =
= 1.00 = = = 1.00 = = = = = = = 1.00 = = = = 1.00 = = = =
= = = = = = = = = = = ? ? = = = = = = = = = 1.00
0.88 0.99 = = = 1.00 = = = 0.50 = ? ? 1.00 = = = = 1.00 = = = =
= = = = = ? = = = = = ? 0.97 = = = = = = = 1.00 = =
= ? ? = = 1.00 1.00 = ? 1.00 ? ? 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00
1.00 = = = = = = = 1.00 1.00 = ? ? = = = 1.00 1.00 = = 1.00 ? =
1.00 = = = = = 1.00 = = = = 1.00 = = = = = 1.00 = = = = =
1.00 ? = = 1.00 = ? = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = 1.00 = =
1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = = = =
1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00
= = = = = = = = = = = = 1.00 = = = = = = = = = 1.00
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = =
1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00
= = = = = = = = = = = = = = = = = = = = = = =
1.00 = = = = = = = 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00
= = = = 1.00 = = = = = 1.00 = = = = = = = = = = = =
1.00 1.00 ? = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00
= = = = = = = = 1.00 1.00 = 1.00 = = = = 1.00 = = = = = =
1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = = =
= = = = = = = = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = 1.00 = 1.00
= = = = = = = = = = = = = = = 1.00 = = = = = = =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 =
= = = = 1.00 = = = = = 1.00 = = = = = = = = = = = =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 =
= = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = 1.00 = = = = = = =
= = = = 1.00 = = = = = 1.00 = = ? ? ? = = = = = = =
1.00 = 1.00 1.00 = ? 1.00 1.00 = = = = = = 1.00 ? = 1.00 = 1.00 = 1.00 =
= = = = = = = = = = = ? = = = = = = = = = = =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 =
= = = = = = = = = = = = = = = = = = = = = = =
1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 =
1.00 ? 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 =
1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 = = ? 1.00 1.00 = = = = =
1.00 = = 0.50 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 = = ? ? = = = = = = = =
END PHASEPROBS