*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 cdk1b.phase.inp cdk1b.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
cdk1b.phase.out_freqs : haplotype frequency estimates
cdk1b.phase.out_pairs : most likely haplotype pairs for each individual
cdk1b.phase.out_recom : estimates of recombination parameters
cdk1b.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 10
Positions of loci: 616 1020 1894 2406 3047 3158 3578 3673 4842 5391
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file cdk1b.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 CGTDDCTCAA 16.000000
2 CGTDDGCTCG 1.000000
3 CGTDIGCTCA 6.000000
4 CGTIDCCTAA 2.000000
5 CGADIGCTCA 1.000000
6 CGAIDCCTCA 2.000000
7 CTTDDCTCAA 47.000000
8 CTTDDGCCCA 10.000000
9 CTTDIGCTCA 22.000000
10 CTTIDCCTAA 4.000000
11 CTTIDCCTCA 1.000000
12 CTADDGCCCA 1.000000
13 CTADIGCTCA 11.000000
14 TGTDDCCTAA 1.000000
15 TGTDDCTCAA 2.000000
16 TGTDDGCCCA 1.000000
17 TGTDDGCTCA 5.000000
18 TGTDDGCTCG 7.000000
19 TGTDIGCTCA 3.000000
20 TGTIDCCTAA 1.000000
21 TGADDGCTCG 4.000000
22 TTTDDGCCCA 6.000000
23 TTTDDGCTCA 1.000000
24 TTTDIGCTCA 2.000000
25 TTTIDCCTAA 13.000000
26 TTTIDCCTCA 5.000000
27 TTADDGCCCA 1.000000
28 TTAIDCCTAA 2.000000
29 TTAIDCCTCA 2.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (1,3)
P002: (22,28)
P003: (1,9)
P004: (17,21)
P005: (26,29)
P006: (6,15)
P007: (9,22)
P008: (7,13)
P009: (9,26)
P010: (7,7)
P011: (10,21)
P012: (6,7)
P013: (7,9)
P014: (7,22)
P015: (4,7)
P016: (7,25)
P017: (9,18)
P018: (19,26)
P019: (3,25)
P020: (8,9)
P021: (1,3)
P022: (7,9)
P023: (9,25)
P024: (9,9)
P025: (1,16)
P026: (7,25)
P027: (7,13)
P028: (7,26)
P029: (7,23)
P030: (7,10)
P031: (7,8)
P032: (1,9)
P033: (1,5)
P034: (7,8)
P035: (7,8)
P036: (13,25)
P037: (7,25)
P038: (1,7)
P039: (9,9)
P040: (7,7)
P041: (15,25)
P042: (1,20)
P043: (1,8)
P044: (7,29)
P045: (7,28)
P046: (7,9)
P047: (7,7)
P048: (7,11)
P049: (7,24)
P050: (2,18)
P051: (7,13)
P052: (13,25)
P053: (9,22)
P054: (9,9)
P055: (25,25)
P056: (7,7)
P057: (19,24)
P058: (7,8)
P059: (1,7)
P060: (3,4)
P061: (7,17)
P062: (22,26)
P063: (7,13)
P064: (17,18)
P065: (1,17)
P066: (7,7)
P067: (13,25)
P068: (7,12)
P069: (7,7)
P070: (9,9)
P071: (7,25)
P072: (1,13)
P073: (1,7)
P074: (8,14)
P075: (7,27)
P076: (7,7)
P077: (1,25)
P078: (7,19)
P079: (1,9)
P080: (18,21)
P081: (10,13)
P082: (9,13)
P083: (1,8)
P084: (22,3)
P085: (7,9)
P086: (3,13)
P087: (10,18)
P088: (18,21)
P089: (17,18)
P090: (8,8)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
C G T D D C T C A A
C G T D I G C T C A
0 P002
T T (T) D D G C C C A
T T (A) I D C C T A A
0 P003
C (G) T D D C T C A A
C (T) T D I G C T C A
0 P004
T G T D D G C T C A
T G A D D G C T C G
0 P005
T T T I D C C T C A
T T A I D C C T C A
0 P006
(C) G A [I] D C C T C A
(T) G T D D C T C A A
0 P007
(C) T T D I G C T C A
(T) T T D D G C C C A
0 P008
C T (T) D D C T C A A
C T (A) D I G C T C A
0 P009
C T T D I G C T C A
T T T I D C C T C A
0 P010
C T T D D C T C A A
C T T D D C T C A A
0 P011
(C) T (T) I D C C T A A
(T) G (A) D D G C T C G
0 P012
C (G) (A) [I] D C C T C A
C (T) (T) D D C T C A A
0 P013
C T T D D C T C A A
C T [T] D I G C T C A
0 P014
(C) T T D D C T C A A
(T) T T D D G C C C A
0 P015
C (G) T I D C C T A A
C (T) T D D C T C A A
0 P016
C T T D D C T C A A
T T T I D C C T A A
0 P017
C T T D I G C T C A
T G T D D G C T C G
0 P018
T G T D I G C T C A
T T T I D C C T C A
0 P019
(C) (G) T D I G C T C A
(T) (T) T I D C C T A A
0 P020
C T T D D G C C C A
C T [T] D I G C T C A
0 P021
C G T D D C T C A A
C G T D I G C T C A
0 P022
C T T D D C T C A A
C T T D I G C T C A
0 P023
C T T D I G C T C A
T T T I D C C T A A
0 P024
C T T D I G C T C A
C T T D I G C T C A
0 P025
(C) G T D D C T C A A
(T) G T D D G C C C A
0 P026
C T T D D C T C A A
T T T I D C C T A A
0 P027
C T (T) D D C T C A A
C T (A) D I G C T C A
0 P028
C T T D D C T C A A
T T [T] I D C C T C A
0 P029
(C) T T D D C T C A A
(T) T T D D G C T C A
0 P030
C T T D D C T C A A
C T T I D C C T A A
0 P031
C T T D D C T C A A
C T T D D G C C C A
0 P032
C (G) T D D C T C A A
C (T) T D I G C T C A
0 P033
C G (T) D D C T C A A
C G (A) D I G C T C A
0 P034
C T T D D C T C A A
C T T D D G C C C A
0 P035
C T T D D C T C A A
C T T D D G C C C A
0 P036
C T (A) D I G C T C A
T T (T) I D C C T A A
0 P037
C T T D D C T C A A
T T T I D C C T A A
0 P038
C G T D D C T C A A
C T T D D C T C A A
0 P039
C T T D I G C T C A
C T T D I G C T C A
0 P040
C T T D D C T C A A
C T T D D C T C A A
0 P041
T (G) T D D C T C A A
T (T) T I D C C T A A
0 P042
(C) G T D D C T C A A
(T) G T I D C C T A A
0 P043
C (G) T D D C T C A A
C (T) T D D G C C C A
0 P044
C T (T) D D C T C A A
T T (A) I D C C T C A
0 P045
C T (T) D D C T C A A
T T (A) I D C C T A A
0 P046
C T T D D C T C A A
C T T D I G C T C A
0 P047
C T T D D C T C A A
C T T D D C T C A A
0 P048
C T T D D C T C A A
C T T [I] D C C T C A
0 P049
(C) T T D D C T C A A
(T) T T D I G C T C A
0 P050
C G T D D G C T C G
T G T D D G C T C G
0 P051
C T (T) D D C T C A A
C T (A) D I G C T C A
0 P052
C T (A) D I G C T C A
T T (T) I D C C T A A
0 P053
(C) T T D I G C T C A
(T) T T D D G C C C A
0 P054
C T T D I G C T C A
C T T D I G C T C A
0 P055
T T T I D C C T A A
T T T I D C C T A A
0 P056
C T T D D C T C A A
C T T D D C T C A A
0 P057
T G T D I G C T C A
T T T D I G C T C A
0 P058
C T T D D C T C A A
C T T D D G C C C A
0 P059
C G T D D C T C A A
C T T D D C T C A A
0 P060
C G T D I G C T C A
C G T I D C C T A A
0 P061
C T T D D C T C A A
T G T D D G C T C A
0 P062
T T T D D G C C C A
T T T I D C C T C A
0 P063
C T (T) D D C T C A A
C T (A) D I G C T C A
0 P064
T G T D D G C T C A
T G T D D G C T C G
0 P065
C G T D D C T C A A
T G T D D G C T C A
0 P066
C T T D D C T C A A
C T T D D C T C A A
0 P067
C T (A) D I G C T C A
T T (T) I D C C T A A
0 P068
C T (T) D D C T C A A
C T (A) D D G C C C A
0 P069
C T T D D C T C A A
C T T D D C T C A A
0 P070
C T T D I G C T C A
C T T D I G C T C A
0 P071
C T T D D C T C A A
T T T I D C C T A A
0 P072
C (G) (T) D D C T C A A
C (T) (A) D I G C T C A
0 P073
C G T D D C T C A A
C T T D D C T C A A
0 P074
(C) (T) T D D (G) C C (C) A
(T) (G) T D D (C) C T (A) A
0 P075
(C) T (T) D D C T C A A
(T) T (A) D D G C C C A
0 P076
C T T D D C T C A A
C T T D D C T C A A
0 P077
(C) (G) T D D C T C A A
(T) (T) T I D C C T A A
0 P078
(C) (T) T D D C T C A A
(T) (G) T D I G C T C A
0 P079
C (G) T D D C T C A A
C (T) T D I G C T C A
0 P080
T G T D D G C T C G
T G A D D G C T C G
0 P081
C T (T) I D C C T A A
C T (A) D I G C T C A
0 P082
C T T D I G C T C A
C T A D I G C T C A
0 P083
C (G) T D D C T C A A
C (T) T D D G C C C A
0 P084
(T) (T) T D D G C C C A
(C) (G) T D I G C T C A
0 P085
C T T D D C T C A A
C T T D I G C T C A
0 P086
C (G) T D I G C T C A
C (T) A D I G C T C A
0 P087
(C) T T I D C C T A A
(T) G T D D G C T C G
0 P088
T G T D D G C T C G
T G A D D G C T C G
0 P089
T G T D D G C T C A
T G [T] D D G C T C G
0 P090
C T T D D G C C C A
C [T] T D D G C C C A
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 P001
= = = ? ? C T C A =
= = = ? ? G C T C =
0 P002
= = (T) ? = G = C C =
= = (A) ? = C = T A =
0 P003
= (G) = = D C T C A =
= (T) = = I G C T C =
0 P004
= = T = = = = = = A
= = A = = = = = = G
0 P005
= = T = = = = = = =
= = A = = = = = = =
0 P006
(C) = A ? = = C T C =
(T) = T ? = = T C A =
0 P007
(C) = = = I = = T = =
(T) = = = D = = C = =
0 P008
= = (T) = D C T C A =
= = (A) = I G C T C =
0 P009
C = = D I G = = = ?
T = = I D C = = = ?
0 P010
= = = = = = = = = =
= = = = = = = = = =
0 P011
(C) T (T) I = C = = A A
(T) G (A) D = G = = C G
0 P012
= (G) (A) ? = = C T C =
= (T) (T) ? = = T C A =
0 P013
= = ? = D C T C A =
= = ? = I G C T C =
0 P014
(C) = = = = C T = A ?
(T) = = = = G C = C ?
0 P015
= (G) = I = = C T = =
= (T) = D = = T C = =
0 P016
C = = D = = T C = =
T = = I = = C T = =
0 P017
C T = = I = = = = A
T G = = D = = = = G
0 P018
= G = ? I G = = = =
= T = ? D C = = = =
0 P019
(C) (G) = D I G = = C =
(T) (T) = I D C = = A =
0 P020
= = ? = D = = C = =
= = ? = I = = T = =
0 P021
= = ? = D C ? C A =
= = ? = I G ? T C =
0 P022
= = = = D C T C A =
= = = = I G C T C =
0 P023
C = = D I G = = C =
T = = I D C = = A =
0 P024
= = = = = = = = = =
= = = = = = = = = =
0 P025
(C) = = = = C T = A =
(T) = = = = G C = C =
0 P026
C = = D = = T C = =
T = = I = = C T = =
0 P027
= = (T) = D C T C A =
= = (A) = I G C T C =
0 P028
C = ? D = = T C A =
T = ? I = = C T C =
0 P029
(C) = = = = C T C A =
(T) = = = = G C T C =
0 P030
= = = D = = T C = =
= = = I = = C T = =
0 P031
= = = = = C T = A =
= = = = = G C = C =
0 P032
= (G) = = D C T C A =
= (T) = = I G C T C =
0 P033
= = (T) = D C T C A =
= = (A) = I G C T C =
0 P034
= = = = = C T = A =
= = = = = G C = C =
0 P035
= = = = = C T = A =
= = = = = G C = C =
0 P036
C = (A) D I G = = C =
T = (T) I D C = = A =
0 P037
C = = D = = T C = =
T = = I = = C T = =
0 P038
= G = = = = = = = =
= T = = = = = = = =
0 P039
= = = = = = = = = =
= = = = = = = = = =
0 P040
= = = = = = = = = =
= = = = = = = = = =
0 P041
= (G) = D = = T C = =
= (T) = I = = C T = =
0 P042
(C) = = D = = T C = =
(T) = = I = = C T = =
0 P043
= (G) = = = C T = A =
= (T) = = = G C = C =
0 P044
C = (T) D = = T C A =
T = (A) I = = C T C =
0 P045
C = (T) D = = T C = =
T = (A) I = = C T = =
0 P046
= = = = D C T C A =
= = = = I G C T C =
0 P047
= = = = = = = = = =
= = = = = = = = = =
0 P048
= = = ? = = T C A =
= = = ? = = C T C =
0 P049
(C) = = = D C T C A ?
(T) = = = I G C T C ?
0 P050
C = = = = = = = ? =
T = = = = = = = ? =
0 P051
= = (T) = D C T C A =
= = (A) = I G C T C =
0 P052
C = (A) D I G = = C =
T = (T) I D C = = A =
0 P053
(C) = = = I = = T ? =
(T) = = = D = = C ? =
0 P054
= = = = = = = = = =
= = = = = = = = = =
0 P055
= = = = = = = = = =
= = = = = = = = = =
0 P056
= = = = = = = = = =
= = = = = = = = = =
0 P057
= G ? = = = = = = =
= T ? = = = = = = =
0 P058
= = = = = C T = A =
= = = = = G C = C =
0 P059
= G ? ? = = = = = =
= T ? ? = = = = = =
0 P060
= = = D I G = = C =
= = = I D C = = A =
0 P061
C T = = = C T C A =
T G = = = G C T C =
0 P062
= = = D = G = C = =
= = = I = C = T = =
0 P063
= = (T) = D C T C A =
= = (A) = I G C T C =
0 P064
= = = = = = = = = A
= = = = = = = = = G
0 P065
C = = = = C T C A =
T = = = = G C T C =
0 P066
= = ? = = = = = = =
= = ? = = = = = = =
0 P067
C = (A) ? I G = = C =
T = (T) ? D C = = A =
0 P068
= = (T) = = C T = A =
= = (A) = = G C = C =
0 P069
= = = = = = = = = =
= = = = = = = = = =
0 P070
= = = = = = = = = =
= = = = = = = = = =
0 P071
C = = D = = T C = =
T = = I = = C T = =
0 P072
= (G) (T) = D C T C A =
= (T) (A) = I G C T C =
0 P073
= G = = = = = = = =
= T = = = = = = = =
0 P074
(C) (T) = = = (G) = C (C) =
(T) (G) = = = (C) = T (A) =
0 P075
(C) = (T) = = C T = A =
(T) = (A) = = G C = C =
0 P076
= = = = = = = = = =
= = = = = = = = = =
0 P077
(C) (G) = D = = T C = =
(T) (T) = I = = C T = =
0 P078
(C) (T) = = D C T C A =
(T) (G) = = I G C T C =
0 P079
= (G) ? = D C T C A =
= (T) ? = I G C T C =
0 P080
= = T = = = = = = =
= = A = = = = = = =
0 P081
= = (T) I D C = = A =
= = (A) D I G = = C =
0 P082
= = T = = = = = = =
= = A = = = = = = =
0 P083
= (G) ? = = C T = A =
= (T) ? = = G C = C =
0 P084
(T) (T) = = D = = C = =
(C) (G) = = I = = T = =
0 P085
= = = = D C T C A =
= = = = I G C T C =
0 P086
= (G) T = = = = = = =
= (T) A = = = = = = =
0 P087
(C) T = I = C = = A A
(T) G = D = G = = C G
0 P088
= = T = = = = = = =
= = A = = = = = = =
0 P089
= = ? = = = = = = A
= = ? = = = = = = G
0 P090
= ? ? = = = = = = =
= ? ? = = = = = = =
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 =
= = 0.55 ? = 1.00 = 1.00 0.98 =
= 0.53 = = 1.00 1.00 1.00 1.00 1.00 =
= = 0.95 = = = = = = 1.00
= = 1.00 = = = = = = =
0.53 = 0.92 ? = = 1.00 1.00 1.00 =
0.71 = = = 1.00 = = 1.00 = =
= = 0.90 = 1.00 1.00 1.00 1.00 1.00 =
0.95 = = 1.00 1.00 1.00 = = = ?
= = = = = = = = = =
0.79 0.98 0.75 1.00 = 1.00 = = 1.00 1.00
= 0.67 0.89 ? = = 1.00 1.00 1.00 =
= = ? = 1.00 1.00 1.00 1.00 1.00 =
0.85 = = = = 1.00 1.00 = 1.00 ?
= 0.55 = 1.00 = = 1.00 1.00 = =
0.96 = = 1.00 = = 1.00 1.00 = =
0.93 0.97 = = 1.00 = = = = 1.00
= 0.91 = ? 0.99 1.00 = = = =
0.77 0.70 = 1.00 1.00 1.00 = = 1.00 =
= = ? = 1.00 = = 1.00 = =
= = ? = 1.00 1.00 ? 1.00 1.00 =
= = = = 1.00 1.00 1.00 1.00 1.00 =
0.92 = = 1.00 1.00 1.00 = = 1.00 =
= = = = = = = = = =
0.74 = = = = 1.00 1.00 = 1.00 =
0.97 = = 1.00 = = 1.00 1.00 = =
= = 0.89 = 1.00 1.00 1.00 1.00 1.00 =
0.98 = ? 1.00 = = 1.00 1.00 0.98 =
0.84 = = = = 1.00 1.00 0.96 1.00 =
= = = 1.00 = = 1.00 1.00 = =
= = = = = 1.00 1.00 = 1.00 =
= 0.53 = = 1.00 1.00 1.00 1.00 1.00 =
= = 0.75 = 1.00 1.00 1.00 1.00 1.00 =
= = = = = 1.00 1.00 = 1.00 =
= = = = = 1.00 1.00 = 1.00 =
0.97 = 0.73 1.00 1.00 1.00 = = 1.00 =
0.97 = = 1.00 = = 1.00 1.00 = =
= 1.00 = = = = = = = =
= = = = = = = = = =
= = = = = = = = = =
= 0.87 = 1.00 = = 1.00 1.00 = =
0.57 = = 1.00 = = 1.00 1.00 = =
= 0.78 = = = 1.00 1.00 = 1.00 =
0.98 = 0.87 1.00 = = 1.00 1.00 0.99 =
0.93 = 0.62 1.00 = = 1.00 1.00 = =
= = = = 1.00 1.00 1.00 1.00 1.00 =
= = = = = = = = = =
= = = ? = = 1.00 1.00 0.95 =
0.69 = = = 1.00 1.00 1.00 1.00 1.00 ?
1.00 = = = = = = = ? =
= = 0.89 = 1.00 1.00 1.00 1.00 1.00 =
0.96 = 0.73 1.00 1.00 1.00 = = 1.00 =
0.70 = = = 1.00 = = 1.00 ? =
= = = = = = = = = =
= = = = = = = = = =
= = = = = = = = = =
= 1.00 ? = = = = = = =
= = = = = 1.00 1.00 = 1.00 =
= 1.00 ? ? = = = = = =
= = = 1.00 1.00 1.00 = = 1.00 =
0.98 0.92 = = = 1.00 1.00 1.00 1.00 =
= = = 1.00 = 1.00 = 1.00 = =
= = 0.90 = 1.00 1.00 1.00 1.00 1.00 =
= = = = = = = = = 1.00
0.98 = = = = 1.00 1.00 1.00 1.00 =
= = ? = = = = = = =
0.96 = 0.71 ? 1.00 1.00 = = 1.00 =
= = 0.51 = = 1.00 1.00 = 1.00 =
= = = = = = = = = =
= = = = = = = = = =
0.97 = = 1.00 = = 1.00 1.00 = =
= 0.66 0.86 = 1.00 1.00 1.00 1.00 1.00 =
= 1.00 = = = = = = = =
0.63 0.80 = = = 0.72 = 0.96 0.73 =
0.76 = 0.59 = = 1.00 1.00 = 1.00 =
= = = = = = = = = =
0.88 0.75 = 1.00 = = 1.00 1.00 = =
0.66 0.55 = = 1.00 1.00 1.00 1.00 1.00 =
= 0.56 ? = 1.00 1.00 1.00 1.00 1.00 =
= = 1.00 = = = = = = =
= = 0.83 1.00 1.00 1.00 = = 1.00 =
= = 1.00 = = = = = = =
= 0.79 ? = = 1.00 1.00 = 1.00 =
0.58 0.66 = = 1.00 = = 1.00 = =
= = = = 1.00 1.00 1.00 1.00 1.00 =
= 0.66 1.00 = = = = = = =
0.61 0.96 = 1.00 = 1.00 = = 1.00 1.00
= = 1.00 = = = = = = =
= = ? = = = = = = 1.00
= ? ? = = = = = = =
END PHASEPROBS