*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 smug1.phase.inp smug1.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
smug1.phase.out_freqs : haplotype frequency estimates
smug1.phase.out_pairs : most likely haplotype pairs for each individual
smug1.phase.out_recom : estimates of recombination parameters
smug1.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 12
Positions of loci: 368 668 880 918 1046 1699 1709 2897 3100 6186 6528 7285
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file smug1.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 GTTCTCTCAGGT 9.000000
2 GTTCTCTCATGT 57.000000
3 GTTCTCTCGGGT 1.000000
4 ACCTCCCCGGGT 2.000000
5 ACCTCCCCGGGC 13.000000
6 ACCTCCCGGGGC 1.000000
7 ACCTCTCCGGGT 2.000000
8 ACCTCTCCGGAT 6.000000
9 ACCTCTCGGGGT 25.000000
10 ACCTCTCGGGGC 4.000000
11 ACCTCTCGGGAT 56.000000
12 ACCTCTCGGTGT 4.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (2,2)
P002: (5,11)
P003: (7,10)
P004: (2,9)
P005: (2,9)
P006: (11,11)
P007: (2,11)
P008: (2,11)
P009: (2,2)
P010: (11,11)
P011: (4,7)
P012: (3,11)
P013: (2,2)
P014: (5,11)
P015: (9,12)
P016: (2,5)
P017: (1,11)
P018: (9,11)
P019: (1,2)
P020: (2,11)
P021: (10,10)
P022: (1,9)
P023: (11,11)
P024: (2,11)
P025: (2,2)
P026: (2,12)
P027: (2,11)
P028: (2,9)
P029: (1,5)
P030: (5,9)
P031: (2,5)
P032: (5,11)
P033: (2,9)
P034: (2,11)
P035: (2,2)
P036: (2,11)
P037: (2,11)
P038: (1,5)
P039: (5,11)
P040: (2,2)
P041: (4,11)
P042: (2,5)
P043: (11,11)
P044: (2,2)
P045: (2,11)
P046: (9,9)
P047: (11,11)
P048: (2,11)
P049: (2,8)
P050: (9,9)
P051: (11,11)
P052: (10,11)
P053: (9,11)
P054: (2,5)
P055: (2,8)
P056: (9,11)
P057: (2,11)
P058: (2,11)
P059: (9,9)
P060: (2,2)
P061: (1,11)
P062: (9,11)
P063: (2,2)
P064: (9,9)
P065: (2,9)
P066: (5,11)
P067: (11,11)
P068: (2,11)
P069: (11,11)
P070: (2,11)
P071: (6,11)
P072: (12,12)
P073: (2,9)
P074: (2,11)
P075: (11,11)
P076: (2,8)
P077: (11,11)
P078: (2,8)
P079: (2,11)
P080: (9,9)
P081: (2,5)
P082: (2,11)
P083: (1,2)
P084: (2,8)
P085: (2,8)
P086: (2,11)
P087: (1,2)
P088: (1,9)
P089: (9,11)
P090: (11,11)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
G T T C T C T C A T G T
G T T C T C T C A [T] G T
0 P002
A C C T C C C C G G G C
A C C T C T C [G] G G A T
0 P003
A C C T C T C (C) G G G T
A C C T C T C (G) G G G C
0 P004
G T T C T C T C A T G T
A C C T C T C G G G G T
0 P005
G T T C T C T C A [T] G T
A C C T C T C G G G G T
0 P006
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P007
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P008
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P009
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P010
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P011
A C C T C C C C G G G T
A C C T C T C C G G G T
0 P012
G T T C T C T (C) G G (G) T
A C C T C T C (G) G G (A) T
0 P013
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P014
A C C T C C C C G G G C
A C C T C T C G G G A T
0 P015
A C C T C T C G G G G T
A C C T C T C G G T G T
0 P016
G T T C T C T C A T G T
A C C T C C C C G G G C
0 P017
G T T C T C T C A G G T
A C C T C T C G G G A T
0 P018
A C C T C T C G G G G T
A C C T C T C [G] G G A T
0 P019
G T T C T C T C A G G T
G T T C T C T C A T G T
0 P020
G T T C T C T C A T G T
A C C T C T C G G G [A] T
0 P021
A C C T C T C G G G G C
A C C T C T C G G G G C
0 P022
G T T C T C T C A G G T
A C C T C T C G G G G T
0 P023
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P024
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P025
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P026
G T T C T C T C A T G T
A C C T C T C G G T G T
0 P027
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P028
G T T C T C T C A T G T
A C C T C T C G G G G T
0 P029
G T T C T C T C A G G T
A C C T C C C C G G G C
0 P030
A C C T C C C C G G G C
A C C T C T C G G G G T
0 P031
G T T C T C T C A T G T
A C C T C C C C G G G C
0 P032
A C C T C C C C G G G C
A C C T C T C G G G A T
0 P033
G T T C T C T C A T G T
A C C T C T C G G G G T
0 P034
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P035
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P036
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P037
G T T C T C T C A T G T
A C C T C T C [G] G G A T
0 P038
G T T C T C T C A G G T
A C C T C C C C G G G C
0 P039
A C C T C C C C G G G C
A C C T C T C G G G A T
0 P040
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P041
A C C T C (C) C C G G G T
A C C T C (T) C G G G A T
0 P042
G T T C T C T C A T G T
A C C T C C C C G G G C
0 P043
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P044
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P045
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P046
A C C T C T C G G G G T
A C C T C T C G G G G T
0 P047
A C C T C T C G G G A T
A C C T C T C [G] G G A T
0 P048
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P049
G T T C T C T C A T G T
A C C T C T C C G G A T
0 P050
A C C T C T C G G G G T
A C C T C T C G G G G T
0 P051
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P052
A C C T C [T] C G G G G C
A C C T C T C G G G A T
0 P053
A C C T C T C G G G G T
A C C T C T C [G] G G A T
0 P054
G T T C T C T C A T G T
A C C T C C C C G G G C
0 P055
G T T C T C T C A T G T
A C C T C T C C G G A T
0 P056
A C C T C T C G G G G T
A C C T C T C G G G A T
0 P057
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P058
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P059
A C C T C T C G G G G T
A C C T C T C G G G G T
0 P060
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P061
G T T C T C T C A G G T
A C C T C T C G G G A T
0 P062
A C C T C T C G G G G T
A C C T C T C G G G A T
0 P063
G T T C T C T C A T G T
G T T C T C T C A T G T
0 P064
A C C T C T C G G G G T
A C C T C T C G G G G T
0 P065
G T T C T C T C A T G T
A C C T C T C G G G G T
0 P066
A C C T C C C C G G G C
A C C T C T C G G G A T
0 P067
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P068
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P069
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P070
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P071
A C C T C (C) C G G G G C
A C C T C (T) C G G G A T
0 P072
A C C T C T C G G T G T
A C C T C T C G G T G T
0 P073
G T T C T C T C A T G T
A C C T C T C G G G G T
0 P074
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P075
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P076
G T T C T C T C A T G T
A C C T C T C C G G A T
0 P077
A C C T C T C G G G A T
A C C T C T C G G G A T
0 P078
G T T C T C T C A T G T
A C C T C T C C G G A T
0 P079
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P080
A C C T C T C G G G G T
A C C T C T C G G G G T
0 P081
G T T C T C T C A T G T
A C C T C C C C G G G C
0 P082
G T T C T C T C A T G T
A C C T C T C [G] G G A T
0 P083
G T T C T C T C A G G T
G T T C T C T C A T G T
0 P084
G T T C T C T C A T G T
A C C T C T C C G G A T
0 P085
G T T C T C T C A T G T
A C C T C T C C G G A T
0 P086
G T T C T C T C A T G T
A C C T C T C G G G A T
0 P087
G T T C T C T C A G G T
G T T C T C T C A T G T
0 P088
G T T C T C T C A G G T
A C C T C T C G G G G T
0 P089
A C C T C T C G G G G T
A C C T C T C G G G A T
0 P090
A C C T C T C G G G A T
A C C T C T C G G G A 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
= = = = = = = = = ? = =
= = = = = = = = = ? = =
0 P002
? = = = ? C = ? = = G C
? = = = ? T = ? = = A T
0 P003
= = = = = = = (C) = = = T
= = = = = = = (G) = = = C
0 P004
G T T C T C T C A T = =
A C C T C T C G G G = =
0 P005
G T T C T ? ? C ? ? = =
A C C T C ? ? G ? ? = =
0 P006
= = = = ? = = = = = = =
= = = = ? = = = = = = =
0 P007
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P008
G T T C ? C T C A T G =
A C C T ? T C G G G A =
0 P009
= ? = = = = = = ? = = =
= ? = = = = = = ? = = =
0 P010
= = = = = ? ? = ? = = =
= = = = = ? ? = ? = = =
0 P011
= = = = = C = = = = = =
= = = = = T = = = = = =
0 P012
G T T C T C T (C) = = (G) =
A C C T C T C (G) = = (A) =
0 P013
= = = = ? = = = = = = =
= = = = ? = = = = = = =
0 P014
= = = = = C = C = = G C
= = = = = T = G = = A T
0 P015
= ? = = = = = = = G = =
= ? = = = = = = = T = =
0 P016
G T T C T = T = A T = T
A C C T C = C = G G = C
0 P017
G T T C T C T C A = G =
A C C T C T C G G = A =
0 P018
= = = = = = = ? = = G =
= = = = = = = ? = = A =
0 P019
= ? = = = = = = = G = =
= ? = = = = = = = T = =
0 P020
G T T C T C T C A T ? =
A C C T C T C G G G ? =
0 P021
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P022
? T T C T C T ? A = = =
? C C T C T C ? G = = =
0 P023
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P024
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P025
? = = = = = = = = = = =
? = = = = = = = = = = =
0 P026
G ? T C T C T C A = = =
A ? C T C T C G G = = =
0 P027
G ? T C T C T C A T G =
A ? C T C T C G G G A =
0 P028
G ? T C T C T C A T = =
A ? C T C T C G G G = =
0 P029
G ? T C T = T = A = = T
A ? C T C = C = G = = C
0 P030
? = = = = C = C = = = C
? = = = = T = G = = = T
0 P031
? T T C T = T ? A T = T
? C C T C = C ? G G = C
0 P032
= = = = = C = C = = G C
= = = = = T = G = = A T
0 P033
G T T C T C T C A T = =
A C C T C T C G G G = =
0 P034
G ? T C T C T C A T G =
A ? C T C T C G G G A =
0 P035
= ? = = = = = = = = = =
= ? = = = = = = = = = =
0 P036
? T T C T C T C A T G =
? C C T C T C G G G A =
0 P037
G T T C ? C T ? A T G =
A C C T ? T C ? G G A =
0 P038
G T T C T = T = A = = T
A C C T C = C = G = = C
0 P039
= = = = = C = C = = G C
= = = = = T = G = = A T
0 P040
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P041
= = = = = (C) = ? = = G =
= = = = = (T) = ? = = A =
0 P042
G T T C T ? ? = A T = T
A C C T C ? ? = G G = C
0 P043
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P044
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P045
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P046
= ? = = = = = = ? = = =
= ? = = = = = = ? = = =
0 P047
= = = = = ? ? ? ? = = =
= = = = = ? ? ? ? = = =
0 P048
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P049
G T T C T C T = ? T G =
A C C T C T C = ? G A =
0 P050
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P051
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P052
= = = = = ? ? = = = G C
= = = = = ? ? = = = A T
0 P053
= = = = = = = ? = = G =
= = = = = = = ? = = A =
0 P054
G T T C T = T = A T ? T
A C C T C = C = G G ? C
0 P055
G T T C T C T = A T G =
A C C T C T C = G G A =
0 P056
= = = = = = = = = = G =
= = = = = = = = = = A =
0 P057
G T T C ? C T C ? T G =
A C C T ? T C G ? G A =
0 P058
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P059
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P060
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P061
G T T C T C T C A = G =
A C C T C T C G G = A =
0 P062
= = = = = = = = = = G =
= = = = = = = = = = A =
0 P063
? = = = ? = = = = = = =
? = = = ? = = = = = = =
0 P064
? = = = = = = = = = = =
? = = = = = = = = = = =
0 P065
? ? T C T C T C ? T = =
? ? C T C T C G ? G = =
0 P066
= = = = = C = C = = G C
= = = = = T = G = = A T
0 P067
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P068
G T T C ? C T C ? T G =
A C C T ? T C G ? G A =
0 P069
= = = = ? = = = = = = =
= = = = ? = = = = = = =
0 P070
G ? T C T C T C A T G =
A ? C T C T C G G G A =
0 P071
= = = = = (C) = = ? = G C
= = = = = (T) = = ? = A T
0 P072
= ? = = = = = = ? = = =
= ? = = = = = = ? = = =
0 P073
G T T C T C T ? A T = =
A C C T C T C ? G G = =
0 P074
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P075
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P076
G T T C T C T = A T G =
A C C T C T C = G G A =
0 P077
= = = = = ? ? = = = = =
= = = = = ? ? = = = = =
0 P078
G T T C T C T = A T G =
A C C T C T C = G G A =
0 P079
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P080
= = = = = ? ? = = = = =
= = = = = ? ? = = = = =
0 P081
G T T C T = T = A T = T
A C C T C = C = G G = C
0 P082
G T T C T C T ? A T G =
A C C T C T C ? G G A =
0 P083
? ? = = = = = = ? G = =
? ? = = = = = = ? T = =
0 P084
G T T C T C T = A T G =
A C C T C T C = G G A =
0 P085
? T T C T C T = A T G =
? C C T C T C = G G A =
0 P086
G T T C T C T C A T G =
A C C T C T C G G G A =
0 P087
= = = = = = = = = G = =
= = = = = = = = = T = =
0 P088
G T T C T C T ? ? = = =
A C C T C T C ? ? = = =
0 P089
= = = = = = = = = = G ?
= = = = = = = = = = A ?
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
= = = = = = = 0.78 = = = 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 0.87 = = 0.67 =
= = = = ? = = = = = = =
= = = = = 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 = 0.99 =
= = = = = = = ? = = 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 0.97 = =
1.00 ? 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00
? = = = = 1.00 = 0.99 = = = 0.97
? 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 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 = 0.99 = = 1.00 1.00
= = = = = = = = = = = =
= = = = = 0.87 = ? = = 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 =
= = = = = = = = = = = =
= = = = = = = = = = = =
= = = = = ? ? = = = 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 = 0.99 =
= = = = = = = = = = 1.00 =
? = = = ? = = = = = = =
? = = = = = = = = = = =
? ? 1.00 1.00 1.00 1.00 1.00 1.00 ? 0.97 = =
= = = = = 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 =
= = = = = 0.73 = = ? = 1.00 1.00
= ? = = = = = = ? = = =
1.00 1.00 1.00 1.00 1.00 1.00 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 ?
= = = = = = = = = = = ?
END PHASEPROBS