*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 e2f1x.phase.inp e2f1x.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
e2f1x.phase.out_freqs : haplotype frequency estimates
e2f1x.phase.out_pairs : most likely haplotype pairs for each individual
e2f1x.phase.out_recom : estimates of recombination parameters
e2f1x.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 11
Positions of loci: 1722 3901 4247 4513 5996 10263 10355 10589 11569 12478 13140
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file e2f1x.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 CCTACCACGCC 13.000000
2 CCTACCACGCT 1.000000
3 CCTACTATGCC 61.000000
4 CCTACTATTCC 14.000000
5 CCTACTTTGCC 31.000000
6 CCTATTATGCC 1.000000
7 CCTTCTTTGCC 1.000000
8 CCGACCACGCC 3.000000
9 CCGTTCACGCC 8.000000
10 CTTACCACGCT 9.000000
11 TCTACCACGCT 1.000000
12 TCTACTTTGCC 1.000000
13 TTTACCACGCT 13.000000
14 TTTACCACGGT 23.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (3,14)
P002: (14,14)
P003: (5,13)
P004: (1,1)
P005: (4,13)
P006: (3,14)
P007: (3,5)
P008: (9,9)
P009: (3,5)
P010: (3,13)
P011: (8,10)
P012: (13,14)
P013: (9,14)
P014: (5,5)
P015: (3,5)
P016: (5,5)
P017: (3,11)
P018: (3,13)
P019: (3,5)
P020: (3,4)
P021: (1,3)
P022: (3,4)
P023: (9,10)
P024: (14,14)
P025: (5,10)
P026: (3,14)
P027: (3,5)
P028: (4,13)
P029: (3,10)
P030: (3,3)
P031: (3,3)
P032: (3,3)
P033: (4,13)
P034: (1,4)
P035: (5,14)
P036: (3,12)
P037: (3,7)
P038: (1,3)
P039: (3,4)
P040: (3,10)
P041: (3,3)
P042: (1,1)
P043: (5,13)
P044: (5,5)
P045: (3,14)
P046: (5,5)
P047: (2,14)
P048: (3,5)
P049: (3,14)
P050: (1,3)
P051: (9,13)
P052: (6,14)
P053: (3,3)
P054: (5,9)
P055: (3,4)
P056: (3,3)
P057: (3,10)
P058: (3,4)
P059: (1,8)
P060: (3,14)
P061: (1,13)
P062: (5,5)
P063: (3,9)
P064: (1,13)
P065: (1,3)
P066: (4,14)
P067: (4,14)
P068: (5,10)
P069: (9,10)
P070: (4,5)
P071: (5,14)
P072: (5,14)
P073: (3,10)
P074: (5,14)
P075: (3,5)
P076: (5,14)
P077: (3,3)
P078: (3,3)
P079: (3,3)
P080: (3,3)
P081: (3,13)
P082: (3,14)
P083: (3,3)
P084: (3,4)
P085: (3,5)
P086: (3,3)
P087: (8,13)
P088: (4,5)
P089: (1,3)
P090: (5,14)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
C C T A C T A T G C C
T T T A C C A C G G T
0 P002
T T T A C C A C G G T
T T T A C C A C G G T
0 P003
C C T A C T T T G C C
T T T A C C A C G C T
0 P004
C C T A C C A C G C C
C C T A C C A C G C C
0 P005
C C T A C T A T T C C
T T T A C C A C G C T
0 P006
C C T A C T A T G C C
T T T A C C A C G G T
0 P007
C C T A C T A T G C C
C C T A C T T T G C C
0 P008
C C G T T C A C G C C
C C G T T C A C G C C
0 P009
C C T A C T A T G C C
C C T A C T [T] T G C C
0 P010
C C T A C T [A] T G C C
T T T A C C A C G C T
0 P011
C C G A C C A C G C C
C T T A C C A C G C T
0 P012
T T T A C C A C G C T
T T T A C C A C G G T
0 P013
C C G T T C A C G C C
T T T A C C A C G G T
0 P014
C C T A C T T T G C C
C C T A C T T T G C C
0 P015
C C T A C T A T G C C
C C T A C T T T G C C
0 P016
C C T A C T T T G C C
C C T A C T T T G C C
0 P017
(C) C T A C T [A] T G C C
(T) C T A C C A C G C T
0 P018
C C T A C T A T G C C
T T T A C C A C G C T
0 P019
C C T A C T A T G C C
C C T A C T T T G C C
0 P020
C C T A C T A T G C C
C C T A C T A T T C C
0 P021
C C T A C C A C G C C
C C T A C T A T G C C
0 P022
C C T A C T A T G C C
C C T A C T A T T C C
0 P023
C C G T T C A C G C C
C T T A C C A C G C T
0 P024
T T T A C C A C G G T
T T T A C C A C G G T
0 P025
C C T A C T T T G C C
C T T A C C A C G C T
0 P026
C C T A C T A T G C C
T T T A C C A C G G T
0 P027
C C T A C T A T G C C
C C T A C T T T G C C
0 P028
C C T A C T A T T C C
T T T A C C A C G C T
0 P029
C C T A C T A T G C C
C T T A C C A C G C T
0 P030
C C T A C T A T G C C
C C T A C T A T G C C
0 P031
C C T A C T A T G C C
C C T A C T A T G C C
0 P032
C C T A C T A T G C C
C C T A C T A T G C C
0 P033
C C T A C T A T T C C
T T T A C C A C G C T
0 P034
C C T A C C A C G C C
C C T A C T A T T C C
0 P035
C C T A C T T T G C C
T T T A C C A C G G T
0 P036
(C) C T A C T A T G C C
(T) C T A C T T T G C C
0 P037
C C T (A) C T A T G C C
C C T (T) C T T T G C C
0 P038
C C T A C C A C G C C
C C T A C T A T G C C
0 P039
C C T A C T A T G C C
C C T A C T A T T C C
0 P040
C C T A C T A T G C C
C T T A C C A C G C T
0 P041
C C T A C T A T G C C
C C T A C T A T G C C
0 P042
C C [T] A C C A C G C C
C C T A C C A C G C C
0 P043
C C T A C T T T G C C
T T T A C C A C G C T
0 P044
C C T A C T T T G C C
C C T A C T T T G C C
0 P045
C C T A C T A T G C C
T T T A C C A C G G T
0 P046
C C T A C T T T G C C
C C T A C T T T G C C
0 P047
C C T A C C A C G (C) T
T T T A C C A C G (G) T
0 P048
C C T A C T A T G C C
C C T A C T T T G C C
0 P049
C C T A C T A T G C C
T T T A C C A C G G T
0 P050
C C T A C C A C G C C
C C T A C T A T G C C
0 P051
C C G T T C A C G C C
T T T A C C A C G C T
0 P052
C C T A (T) T A T G C C
T T T A (C) C A C G G T
0 P053
C C T A C T A T G C C
C C T A C T A T G C C
0 P054
C C T A C T T T G C C
C C G T T C A C G C C
0 P055
C C T A C T A T G C C
C C T A C T A T T C C
0 P056
C C T A C T A T G C C
C C T A C T A T G C C
0 P057
C C T A C T A T G C C
C T T A C C A C G C T
0 P058
C C T A C T A T G C C
C C T A C T A T T C C
0 P059
C C T A C C A C G C C
C C G A C C A C G C C
0 P060
C C T A C T A T G C C
T T T A C C A C G G T
0 P061
C C T A C C A C G C C
T T T A C C A C G C T
0 P062
C C T A C T T T G C C
C C T A C T T T G C C
0 P063
C C T A C T A T G C C
C C G T T C A C G C C
0 P064
C C T A C C A C G C C
T T T A C C A C G C T
0 P065
C C T A C C A C G C C
C C T A C T A T G C C
0 P066
C C T A C T A T T C C
T T T A C C A C G G T
0 P067
C C T A C T A T T C C
T T T A C C A C G G T
0 P068
C C T A C T T T G C C
C T T A C C A C G C T
0 P069
C C G T T C A C G C C
C T T A C C A C G C T
0 P070
C C T A C T A T T C C
C C T A C T T T G C C
0 P071
C C T A C T T T G C C
T T T A C C A C G G T
0 P072
C C T A C T T T G C C
T T T A C C A C G G T
0 P073
C C T A C T A T G C C
C T T A C C A C G C T
0 P074
C C T A C T T T G C C
T T T A C C A C G G T
0 P075
C C T A C T A T G C C
C C T A C T T T G C C
0 P076
C C T A C T T T G C C
T T T A C C A C G G T
0 P077
C C T A C T A T G C C
C C T A C T A T G C C
0 P078
C C T A C T A T G C C
C C T A C T A T G C C
0 P079
C C T A C T A T G C C
C C T A C T A T G C C
0 P080
C C T A C T A T G C C
C C T A C T A T G C C
0 P081
C C T A C T A T G C C
T T T A C C A C G C T
0 P082
C C T A C T A T G C C
T T T A C C A C G G T
0 P083
C C T A C T A T G C C
C C T A C T A T G C C
0 P084
C C T A C [T] [A] [T] G C C
C C T A C T A T T C C
0 P085
C C T A C T A T G C C
C C T A C T T T G C C
0 P086
C C T A C T A T G C C
C C T A C T A T G C C
0 P087
C C G A C C A C G C C
T T T A C C A C G C T
0 P088
C C T A C T A T T C C
C C T A C T T T G C C
0 P089
C C T A C C A C G C C
C C T A C T A T G C C
0 P090
C C T A C T T T G C C
T T T A C C A C G [G] 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 P001
C C = = = ? = T = C C
T T = = = ? = C = G T
0 P002
= = = = = ? = = = = =
= = = = = ? = = = = =
0 P003
C C = = = T T T = = C
T T = = = C A C = = T
0 P004
= = = = = = = = = = =
= = = = = = = = = = =
0 P005
C C = = = ? ? ? T = C
T T = = = ? ? ? G = T
0 P006
C C = = = T = T = C C
T T = = = C = C = G T
0 P007
= = = = = = A = = = =
= = = = = = T = = = =
0 P008
= = = = = = = = = = =
= = = = = = = = = = =
0 P009
= = = = = ? ? = = = =
= = = = = ? ? = = = =
0 P010
C C = = = T ? ? = = C
T T = = = C ? ? = = T
0 P011
= C G = = = = = = = C
= T T = = = = = = = T
0 P012
= = = = = = = = = C =
= = = = = = = = = G =
0 P013
C C G T T = = = = C C
T T T A C = = = = G T
0 P014
= = = = = = = = = = =
= = = = = = = = = = =
0 P015
= = = = = = A = = = =
= = = = = = T = = = =
0 P016
= = = = = = = = = = =
= = = = = = = = = = =
0 P017
(C) = = = = ? ? ? ? = C
(T) = = = = ? ? ? ? = T
0 P018
C C = = = T = T = = C
T T = = = C = C = = T
0 P019
= = = = = = A = ? = =
= = = = = = T = ? = =
0 P020
= = = = = = = = G = =
= = = = = = = = T = =
0 P021
= = = = = C = C = = =
= = = = = T = T = = =
0 P022
= = = = = = = = G = =
= = = = = = = = T = =
0 P023
= C G T T = = = = = C
= T T A C = = = = = T
0 P024
= = = = = = = = = = =
= = = = = = = = = = =
0 P025
= C = = = T T T = = C
= T = = = C A C = = T
0 P026
C C = = = T = T = C C
T T = = = C = C = G T
0 P027
= = = = = = A = = = =
= = = = = = T = = = =
0 P028
C C = = = T = T T = C
T T = = = C = C G = T
0 P029
= C = = = T = T = = C
= T = = = C = C = = T
0 P030
= = = = = = = = = = =
= = = = = = = = = = =
0 P031
= = = = = = = = = = =
= = = = = = = = = = =
0 P032
= = = = = = = = = = =
= = = = = = = = = = =
0 P033
C C = = = T = T T = C
T T = = = C = C G = T
0 P034
= = ? = = C = C G = =
= = ? = = T = T T = =
0 P035
C C = = = T T T = C C
T T = = = C A C = G T
0 P036
(C) = = = = = A = = = =
(T) = = = = = T = = = =
0 P037
= = = (A) = = A = = = =
= = = (T) = = T = = = =
0 P038
= = ? = = C = C = = =
= = ? = = T = T = = =
0 P039
= = = = = = = = G = =
= = = = = = = = T = =
0 P040
= C = = = T = T = = C
= T = = = C = C = = T
0 P041
= = = = = = = = = = =
= = = = = = = = = = =
0 P042
= = ? = = = = = = = =
= = ? = = = = = = = =
0 P043
C C = = = T T T = = C
T T = = = C A C = = T
0 P044
= = = = = = = = = = =
= = = = = = = = = = =
0 P045
C C = = = T = T = C C
T T = = = C = C = G T
0 P046
= ? ? = = = = = = = =
= ? ? = = = = = = = =
0 P047
C C = = = = = = = (C) =
T T = = = = = = = (G) =
0 P048
= = = = = = A = = = =
= = = = = = T = = = =
0 P049
C C = = = T = T = C C
T T = = = C = C = G T
0 P050
= = ? = = C = C = = =
= = ? = = T = T = = =
0 P051
C C G T T = = = = = C
T T T A C = = = = = T
0 P052
C C = = (T) T = T = C C
T T = = (C) C = C = G T
0 P053
= = = = = = = = = = =
= = = = = = = = = = =
0 P054
= = ? A C T T T = = =
= = ? T T C A C = = =
0 P055
= = = = = = = = G = =
= = = = = = = = T = =
0 P056
= = = = = = = = = = =
= = = = = = = = = = =
0 P057
= C = = = T = T = = C
= T = = = C = C = = T
0 P058
= = ? = = = = = G = =
= = ? = = = = = T = =
0 P059
= = T = ? = = = = = =
= = G = ? = = = = = =
0 P060
C C = = = T = T = C C
T T = = = C = C = G T
0 P061
C C = = ? = = = = = C
T T = = ? = = = = = T
0 P062
= = ? = = = = = = = =
= = ? = = = = = = = =
0 P063
= = T A C T = T = = =
= = G T T C = C = = =
0 P064
C C = = ? = = = = = C
T T = = ? = = = = = T
0 P065
= = = = ? C = C = = =
= = = = ? T = T = = =
0 P066
C C = = = T = T T C C
T T = = = C = C G G T
0 P067
C C = = = T = T T C C
T T = = = C = C G G T
0 P068
= C = = = T T T = = C
= T = = = C A C = = T
0 P069
= C G T T = = = = = C
= T T A C = = = = = T
0 P070
= = = = = = A = T = =
= = = = = = T = G = =
0 P071
C C = = = T T T = C C
T T = = = C A C = G T
0 P072
C C = = = T T T = C C
T T = = = C A C = G T
0 P073
= C = = = T = T = = C
= T = = = C = C = = T
0 P074
C C = = = T T T = C C
T T = = = C A C = G T
0 P075
= = = = = = A = = = =
= = = = = = T = = = =
0 P076
C C = = = T T T = C C
T T = = = C A C = G T
0 P077
= = = = = = = = = = =
= = = = = = = = = = =
0 P078
= = ? ? ? = = = = ? ?
= = ? ? ? = = = = ? ?
0 P079
= = = = = = = = = = =
= = = = = = = = = = =
0 P080
= = = = = = = = = = =
= = = = = = = = = = =
0 P081
C C = = = T = T = = C
T T = = = C = C = = T
0 P082
C C = = = T = T = C C
T T = = = C = C = G T
0 P083
= = = = = = = = = = =
= = = = = = = = = = =
0 P084
= = = = = ? ? ? G = =
= = = = = ? ? ? T = =
0 P085
= = = = = = A = = = =
= = = = = = T = = = =
0 P086
= = ? ? ? = = = = ? ?
= = ? ? ? = = = = ? ?
0 P087
C C G = ? = = = = = C
T T T = ? = = = = = T
0 P088
= = = = = = A = T = =
= = = = = = T = G = =
0 P089
= = = = = C = C = = =
= = = = = T = T = = =
0 P090
C C ? ? = T T T = ? C
T T ? ? = C A C = ? 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 = = = ? = 1.00 = 1.00 1.00
= = = = = ? = = = = =
0.98 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 = = = =
= = = = = = = = = = =
= = = = = ? ? = = = =
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 = = = =
= = = = = = = = = = =
0.67 = = = = ? ? ? ? = 0.99
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 0.98 = 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 0.99 = =
1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00
0.52 = = = = = 1.00 = = = =
= = = 0.51 = = 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
= ? ? = = = = = = = =
0.98 0.96 = = = = = = = 0.73 =
= = = = = = 1.00 = = = =
1.00 1.00 = = = 1.00 = 1.00 = 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 = = = 1.00 = 1.00 = = 1.00
= = ? = = = = = 1.00 = =
= = 1.00 = ? = = = = = =
1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00
1.00 1.00 = = ? = = = = = 1.00
= = ? = = = = = = = =
= = 1.00 1.00 1.00 1.00 = 1.00 = = =
1.00 1.00 = = ? = = = = = 1.00
= = = = ? 1.00 = 1.00 = = =
1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00
1.00 1.00 = = = 1.00 = 1.00 1.00 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
= = = = = = = = = = =
= = ? ? ? = = = = ? ?
= = = = = = = = = = =
= = = = = = = = = = =
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
= = = = = = 0.99 = 1.00 = =
= = = = = 1.00 = 1.00 = = =
0.99 1.00 ? ? = 1.00 1.00 1.00 = ? 1.00
END PHASEPROBS