*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 junxx.phase.inp junxx.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
junxx.phase.out_freqs : haplotype frequency estimates
junxx.phase.out_pairs : most likely haplotype pairs for each individual
junxx.phase.out_recom : estimates of recombination parameters
junxx.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 8
Positions of loci: 535 922 1180 1214 2273 3413 3641 5519
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file junxx.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 ACCCDCAA 1.000000
2 ACCCDCGA 57.000000
3 ACCCDCGC 34.000000
4 ACCCICAA 1.000000
5 ACCGDCGA 1.000000
6 ACTGDCGA 38.000000
7 ACTGDCGC 1.000000
8 ATTGDCGA 2.000000
9 CCCCDCAC 1.000000
10 CCCCDCGA 3.000000
11 CCCCDCGC 2.000000
12 CCCCDTAC 1.000000
13 CCCCICAC 1.000000
14 CCCCICGA 1.000000
15 CCCCICGC 1.000000
16 CCCCITAA 1.000000
17 CCCCITAC 5.000000
18 CCTGDCGA 16.000000
19 CCTGDCGC 1.000000
20 CCTGICAC 1.000000
21 CTTGDCGA 10.000000
22 CTTGDCGC 1.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (2,6)
P002: (2,6)
P003: (2,10)
P004: (14,15)
P005: (3,6)
P006: (3,3)
P007: (2,6)
P008: (2,6)
P009: (2,6)
P010: (2,22)
P011: (2,20)
P012: (2,6)
P013: (1,2)
P014: (2,7)
P015: (3,21)
P016: (3,3)
P017: (3,18)
P018: (18,18)
P019: (2,17)
P020: (3,3)
P021: (16,18)
P022: (2,2)
P023: (3,21)
P024: (3,6)
P025: (3,17)
P026: (3,6)
P027: (2,3)
P028: (2,3)
P029: (17,18)
P030: (2,2)
P031: (2,2)
P032: (4,6)
P033: (2,6)
P034: (2,18)
P035: (2,2)
P036: (6,6)
P037: (2,11)
P038: (6,8)
P039: (2,6)
P040: (2,2)
P041: (18,19)
P042: (9,18)
P043: (2,3)
P044: (2,6)
P045: (3,5)
P046: (2,6)
P047: (6,6)
P048: (2,6)
P049: (3,21)
P050: (17,21)
P051: (3,6)
P052: (2,3)
P053: (2,6)
P054: (2,2)
P055: (3,12)
P056: (17,18)
P057: (10,18)
P058: (3,6)
P059: (13,21)
P060: (2,6)
P061: (3,18)
P062: (2,3)
P063: (3,21)
P064: (18,18)
P065: (11,18)
P066: (2,6)
P067: (2,3)
P068: (2,2)
P069: (2,2)
P070: (2,21)
P071: (6,6)
P072: (2,2)
P073: (6,6)
P074: (6,21)
P075: (2,2)
P076: (2,3)
P077: (2,3)
P078: (3,6)
P079: (2,6)
P080: (2,18)
P081: (6,21)
P082: (3,6)
P083: (2,3)
P084: (3,6)
P085: (3,6)
P086: (2,3)
P087: (18,21)
P088: (6,6)
P089: (10,8)
P090: (2,2)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
A C C C D C G A
A C [T] [G] D C G A
0 P002
A C C C D C G A
A C T G D C G A
0 P003
A C [C] [C] D C G A
C C [C] [C] D C G A
0 P004
C C C C I C G A
C C C C I C G C
0 P005
A C C C D C G (C)
A C T G D C G (A)
0 P006
A C C C D C G C
A C C C D C G C
0 P007
A C C C D C G A
A C [T] [G] D C G A
0 P008
A C C C D C G A
A C T G D C G A
0 P009
A C C C D C G A
A C T G D C G A
0 P010
(A) (C) (C) (C) D C G (A)
(C) (T) (T) (G) D C G (C)
0 P011
(A) C (C) C (D) C (G) (A)
(C) C (T) [G] (I) C (A) (C)
0 P012
A C C C D C G A
A C T G D C G A
0 P013
A C [C] [C] D C A A
A C [C] [C] D C G A
0 P014
A C C C D C G (A)
A C T G D C G (C)
0 P015
(A) (C) C C D C G (C)
(C) (T) T G D C G (A)
0 P016
A C C C D C G C
A C C C D C [G] C
0 P017
(A) C C C D C G (C)
(C) C T G D C G (A)
0 P018
C C T G D C G A
C C T G D C G A
0 P019
(A) C C C (D) (C) (G) (A)
(C) C C C (I) (T) (A) (C)
0 P020
A C C C D C G C
A C C C D C G C
0 P021
C C (C) (C) (I) (T) (A) A
C C (T) (G) (D) (C) (G) A
0 P022
A C C C D C G A
A C C C D C G A
0 P023
(A) (C) (C) (C) D C G (C)
(C) (T) (T) (G) D C G (A)
0 P024
A C C C D C G (C)
A C T G D C G (A)
0 P025
(A) C C C (D) C G C
(C) C C C (I) T A C
0 P026
A C C C D C G (C)
A C T G D C G (A)
0 P027
A C C C D C G A
A C C C D C G C
0 P028
A C C C D C G A
A C C C D C G C
0 P029
C C (C) C (I) (T) (A) (C)
C C (T) [G] (D) (C) (G) (A)
0 P030
A C C C D C G A
A C C C D C G A
0 P031
A C C C D C G A
A C C C D C G A
0 P032
A C (C) (C) (I) C (A) A
A C (T) (G) (D) C (G) A
0 P033
A C C C D C G A
A C T G D C G A
0 P034
(A) C C C D C G A
(C) C T G D C G A
0 P035
A C C C D C G A
A C C C D C G A
0 P036
A C T G D C G A
A C T G D C G A
0 P037
(A) C C C D C G A
(C) C C C D C G C
0 P038
A C T G D C G A
A T T G D C G A
0 P039
A C C C D C G A
A C T G D C G A
0 P040
A C C C D C G A
A C C C D C G A
0 P041
C C T G D C G A
C C T G D C G C
0 P042
C C (C) (C) D C (A) (C)
C C (T) (G) D C (G) (A)
0 P043
A C C C D C G A
A C C C D C G C
0 P044
A C C C D C G A
A C T G D C G A
0 P045
[A] C C (C) D C G C
A C C (G) D C G A
0 P046
A C C C D C G A
A C T G D C G A
0 P047
A C T G D C G A
A C T G D C G A
0 P048
A C C C D C G A
A C T G D C G A
0 P049
(A) (C) (C) (C) D C G (C)
(C) (T) (T) (G) D C G (A)
0 P050
C (C) (C) (C) (I) (T) (A) (C)
C (T) (T) (G) (D) (C) (G) (A)
0 P051
A C C C D C G (C)
A C T G D C G (A)
0 P052
A C C C D C G A
A C C C D C G C
0 P053
A C C C D C G A
A C T G D C G A
0 P054
A C C C D C G A
A C C C D C G A
0 P055
(A) C C C D C G C
(C) C C C D T A C
0 P056
C C (C) (C) (I) (T) (A) (C)
C C (T) (G) (D) (C) (G) (A)
0 P057
C C C C D C G A
C C [T] [G] D C G A
0 P058
A C C C D C G (C)
A C T G D C G (A)
0 P059
C (C) (C) (C) (I) C (A) (C)
C (T) (T) (G) (D) C (G) (A)
0 P060
A C C C D C G A
A C T G D C G A
0 P061
(A) C C C D C G (C)
(C) C T G D C G (A)
0 P062
A C C C D C G A
A C C C D C G C
0 P063
(A) (C) (C) (C) D C G (C)
(C) (T) (T) (G) D C G (A)
0 P064
C C T G D C G A
C C T G D C G A
0 P065
C C C C D C G (C)
C C T G D C G (A)
0 P066
A C C C D C G A
A C T G D C G A
0 P067
A C C C D C G A
A C C C D C G C
0 P068
A C C C D C G A
A C C C D C G A
0 P069
A C C C D C G A
A C C C D C G A
0 P070
(A) (C) C C D C G A
(C) (T) T G D C G A
0 P071
A C T G D C G A
A C T G D C G A
0 P072
A C C C D C G A
A C C C D C G A
0 P073
A C T G D C G A
A C T G D C G A
0 P074
(A) C T G D C G A
(C) T T G D C G A
0 P075
A C C C D C G A
A C C C D C G A
0 P076
A C C C D C G A
A C C C D C G C
0 P077
A C C C D C G A
A C C C D C G C
0 P078
A C C C D C G (C)
A C T G D C G (A)
0 P079
A C C C D C G A
A C T G D C G A
0 P080
(A) C C C D C G A
(C) C T G D C G A
0 P081
(A) C T G D C G A
(C) T T G D C G A
0 P082
A C C C D C G (C)
A C T G D C G (A)
0 P083
A C C C D C G A
A C C C D C G C
0 P084
A C C C D C G (C)
A C T G D C G (A)
0 P085
A C C C D C G (C)
A C T G D C G (A)
0 P086
A C C C D C G A
A C C C D C G C
0 P087
C C T G D C G A
C T T G D C G A
0 P088
A C T G D C G A
A C T G D C [G] A
0 P089
(C) (C) C C D C G A
(A) (T) T G D C G A
0 P090
A C C C D C G A
A C C C D C G 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
= = ? ? ? ? ? =
= = ? ? ? ? ? =
0 P002
= = C ? = ? ? =
= = T ? = ? ? =
0 P003
A = ? ? = ? ? =
C = ? ? = ? ? =
0 P004
= = = = = ? ? A
= = = = = ? ? C
0 P005
= ? C C ? ? ? (C)
= ? T G ? ? ? (A)
0 P006
= ? = = ? ? ? =
= ? = = ? ? ? =
0 P007
= = ? ? ? ? ? =
= = ? ? ? ? ? =
0 P008
= = C C ? ? ? =
= = T G ? ? ? =
0 P009
= ? C C = ? ? =
= ? T G = ? ? =
0 P010
(A) (C) (C) (C) = ? ? (A)
(C) (T) (T) (G) = ? ? (C)
0 P011
(A) = (C) ? (D) = (G) (A)
(C) = (T) ? (I) = (A) (C)
0 P012
= = C C = = = =
= = T G = = = =
0 P013
= = ? ? ? = A ?
= = ? ? ? = G ?
0 P014
? ? C C = = = (A)
? ? T G = = = (C)
0 P015
(A) (C) C C = ? ? (C)
(C) (T) T G = ? ? (A)
0 P016
= = = = = ? ? =
= = = = = ? ? =
0 P017
(A) = C C = ? ? (C)
(C) = T G = ? ? (A)
0 P018
= = = = = = = =
= = = = = = = =
0 P019
(A) = = = (D) (C) (G) (A)
(C) = = = (I) (T) (A) (C)
0 P020
= = = = ? = = =
= = = = ? = = =
0 P021
= = (C) (C) (I) (T) (A) ?
= = (T) (G) (D) (C) (G) ?
0 P022
= = = = = = = =
= = = = = = = =
0 P023
(A) (C) (C) (C) ? = = (C)
(C) (T) (T) (G) ? = = (A)
0 P024
= = C C ? ? = (C)
= = T G ? ? = (A)
0 P025
(A) = = = (D) C G =
(C) = = = (I) T A =
0 P026
= ? C C = = = (C)
= ? T G = = = (A)
0 P027
= = = = = = = A
= = = = = = = C
0 P028
= = = = = = = A
= = = = = = = C
0 P029
= = (C) ? (I) (T) (A) (C)
= = (T) ? (D) (C) (G) (A)
0 P030
= = = = = = = =
= = = = = = = =
0 P031
= = = = = = = =
= = = = = = = =
0 P032
? ? (C) (C) (I) = (A) =
? ? (T) (G) (D) = (G) =
0 P033
= ? C C = = = =
= ? T G = = = =
0 P034
(A) = C C = = = =
(C) = T G = = = =
0 P035
= = = = = = = =
= = = = = = = =
0 P036
= = = = = = = =
= = = = = = = =
0 P037
(A) ? = = = = = A
(C) ? = = = = = C
0 P038
? C = = = = = =
? T = = = = = =
0 P039
= = C C = = = =
= = T G = = = =
0 P040
= = = = = = = =
= = = = = = = =
0 P041
= = = = ? ? ? A
= = = = ? ? ? C
0 P042
= = (C) (C) ? = (A) (C)
= = (T) (G) ? = (G) (A)
0 P043
= = = = = = = A
= = = = = = = C
0 P044
= = C C = = = =
= = T G = = = =
0 P045
? ? = (C) = ? ? C
? ? = (G) = ? ? A
0 P046
= = C C = = = =
= = T G = = = =
0 P047
= = = = = = = =
= = = = = = = =
0 P048
= = C C = = = =
= = T G = = = =
0 P049
(A) (C) (C) (C) = = = (C)
(C) (T) (T) (G) = = = (A)
0 P050
= (C) (C) (C) (I) (T) (A) (C)
= (T) (T) (G) (D) (C) (G) (A)
0 P051
= = C C = = = (C)
= = T G = = = (A)
0 P052
= = = = ? = = A
= = = = ? = = C
0 P053
= = C C = = = =
= = T G = = = =
0 P054
= = = = = = = =
= = = = = = = =
0 P055
(A) = = = ? C G =
(C) = = = ? T A =
0 P056
= = (C) (C) (I) (T) (A) (C)
= = (T) (G) (D) (C) (G) (A)
0 P057
= = ? ? = = = =
= = ? ? = = = =
0 P058
= = C C = = = (C)
= = T G = = = (A)
0 P059
= (C) (C) (C) (I) = (A) (C)
= (T) (T) (G) (D) = (G) (A)
0 P060
= = C C = = = =
= = T G = = = =
0 P061
(A) = C C = = = (C)
(C) = T G = = = (A)
0 P062
= = = = = = = A
= = = = = = = C
0 P063
(A) (C) (C) (C) = = = (C)
(C) (T) (T) (G) = = = (A)
0 P064
= = = = = = = =
= = = = = = = =
0 P065
= = C C = = = (C)
= = T G = = = (A)
0 P066
= = C C = = = =
= = T G = = = =
0 P067
= = = = = = = A
= = = = = = = C
0 P068
= = = = = = = =
= = = = = = = =
0 P069
= = = = = = = =
= = = = = = = =
0 P070
(A) (C) C C = = = =
(C) (T) T G = = = =
0 P071
= = = = = = = =
= = = = = = = =
0 P072
= = = = = = = =
= = = = = = = =
0 P073
= = = = ? ? ? =
= = = = ? ? ? =
0 P074
(A) C = = = = = =
(C) T = = = = = =
0 P075
= = = = ? = = =
= = = = ? = = =
0 P076
= = = = = = = A
= = = = = = = C
0 P077
= = = = ? = = A
= = = = ? = = C
0 P078
= = C C = = = (C)
= = T G = = = (A)
0 P079
= = C C = = = =
= = T G = = = =
0 P080
(A) = C C = = = =
(C) = T G = = = =
0 P081
(A) C = = = ? ? =
(C) T = = = ? ? =
0 P082
= = C C = = = (C)
= = T G = = = (A)
0 P083
= = = = = = = A
= = = = = = = C
0 P084
= = C C = = = (C)
= = T G = = = (A)
0 P085
= = C C = = = (C)
= = T G = = = (A)
0 P086
= = = = = = = A
= = = = = = = C
0 P087
= C = = = = = =
= T = = = = = =
0 P088
= = = = = ? ? =
= = = = = ? ? =
0 P089
(C) (C) C C = ? ? =
(A) (T) T G = ? ? =
0 P090
= ? = = = ? ? =
= ? = = = ? ? =
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
= = ? ? ? ? ? =
= = 0.99 ? = ? ? =
1.00 = ? ? = ? ? =
= = = = = ? ? 1.00
= ? 1.00 1.00 ? ? ? 0.50
= ? = = ? ? ? =
= = ? ? ? ? ? =
= = 1.00 1.00 ? ? ? =
= ? 1.00 1.00 = ? ? =
0.58 0.81 0.82 0.82 = ? ? 0.88
0.64 = 0.86 ? 0.69 = 0.71 0.57
= = 0.99 1.00 = = = =
= = ? ? ? = 1.00 ?
? ? 1.00 1.00 = = = 0.54
0.80 0.64 1.00 1.00 = ? ? 0.52
= = = = = ? ? =
0.67 = 1.00 1.00 = ? ? 0.66
= = = = = = = =
0.64 = = = 0.64 0.83 0.83 0.64
= = = = ? = = =
= = 0.76 0.76 0.73 0.74 0.74 ?
= = = = = = = =
0.63 0.72 0.89 0.89 ? = = 0.61
= = 1.00 1.00 ? ? = 0.52
0.50 = = = 0.57 0.94 0.94 =
= ? 1.00 1.00 = = = 0.50
= = = = = = = 1.00
= = = = = = = 1.00
= = 0.84 ? 0.61 0.65 0.65 0.61
= = = = = = = =
= = = = = = = =
? ? 0.77 0.77 0.69 = 0.72 =
= ? 0.99 1.00 = = = =
0.51 = 1.00 1.00 = = = =
= = = = = = = =
= = = = = = = =
0.50 ? = = = = = 1.00
? 1.00 = = = = = =
= = 0.99 1.00 = = = =
= = = = = = = =
= = = = ? ? ? 1.00
= = 0.75 0.75 ? = 0.75 0.75
= = = = = = = 1.00
= = 0.99 1.00 = = = =
? ? = 0.60 = ? ? 0.90
= = 0.99 1.00 = = = =
= = = = = = = =
= = 0.99 1.00 = = = =
0.63 0.72 0.89 0.89 = = = 0.61
= 0.69 0.80 0.80 0.63 0.71 0.70 0.62
= = 1.00 1.00 = = = 0.50
= = = = ? = = 1.00
= = 0.99 1.00 = = = =
= = = = = = = =
0.57 = = = ? 0.94 0.94 =
= = 0.64 0.64 0.65 0.83 0.83 0.64
= = ? ? = = = =
= = 1.00 1.00 = = = 0.50
= 0.58 0.87 0.87 0.63 = 0.63 0.62
= = 0.99 1.00 = = = =
0.51 = 1.00 1.00 = = = 0.50
= = = = = = = 1.00
0.63 0.72 0.89 0.89 = = = 0.61
= = = = = = = =
= = 1.00 1.00 = = = 0.50
= = 0.99 1.00 = = = =
= = = = = = = 1.00
= = = = = = = =
= = = = = = = =
0.52 0.62 1.00 0.99 = = = =
= = = = = = = =
= = = = = = = =
= = = = ? ? ? =
0.57 1.00 = = = = = =
= = = = ? = = =
= = = = = = = 1.00
= = = = ? = = 1.00
= = 1.00 1.00 = = = 0.50
= = 0.99 1.00 = = = =
0.51 = 1.00 1.00 = = = =
0.56 1.00 = = = ? ? =
= = 1.00 1.00 = = = 0.50
= = = = = = = 1.00
= = 1.00 1.00 = = = 0.50
= = 1.00 1.00 = = = 0.50
= = = = = = = 1.00
= 1.00 = = = = = =
= = = = = ? ? =
0.57 0.74 1.00 1.00 = ? ? =
= ? = = = ? ? =
END PHASEPROBS