*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 ccnhx.phase.inp ccnhx.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
ccnhx.phase.out_freqs : haplotype frequency estimates
ccnhx.phase.out_pairs : most likely haplotype pairs for each individual
ccnhx.phase.out_recom : estimates of recombination parameters
ccnhx.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 6
Positions of loci: 367 483 9663 11817 12128 13933
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file ccnhx.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 TGCCTT 17.000000
2 TGTCTT 19.000000
3 TGTCTC 15.000000
4 TGTTAT 97.000000
5 TGTTTT 6.000000
6 TTTTAT 10.000000
7 GGTCTT 16.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (1,4)
P002: (4,4)
P003: (4,4)
P004: (4,4)
P005: (4,4)
P006: (1,3)
P007: (4,4)
P008: (4,4)
P009: (1,4)
P010: (4,4)
P011: (2,4)
P012: (4,4)
P013: (6,7)
P014: (7,7)
P015: (1,4)
P016: (4,7)
P017: (4,4)
P018: (4,5)
P019: (3,4)
P020: (2,4)
P021: (2,4)
P022: (3,4)
P023: (2,4)
P024: (2,4)
P025: (2,3)
P026: (3,7)
P027: (2,6)
P028: (4,4)
P029: (4,4)
P030: (3,4)
P031: (1,4)
P032: (4,4)
P033: (1,1)
P034: (2,4)
P035: (6,6)
P036: (2,3)
P037: (4,7)
P038: (2,4)
P039: (4,4)
P040: (1,3)
P041: (1,5)
P042: (2,4)
P043: (3,4)
P044: (4,4)
P045: (4,4)
P046: (2,2)
P047: (4,7)
P048: (4,4)
P049: (4,4)
P050: (4,4)
P051: (4,4)
P052: (4,4)
P053: (1,4)
P054: (6,7)
P055: (3,4)
P056: (4,5)
P057: (4,5)
P058: (4,4)
P059: (5,6)
P060: (3,4)
P061: (4,7)
P062: (1,4)
P063: (2,6)
P064: (2,4)
P065: (2,4)
P066: (4,4)
P067: (4,7)
P068: (4,4)
P069: (6,7)
P070: (1,6)
P071: (3,7)
P072: (2,4)
P073: (1,4)
P074: (1,4)
P075: (4,7)
P076: (2,7)
P077: (3,4)
P078: (1,4)
P079: (4,6)
P080: (4,5)
P081: (4,4)
P082: (4,4)
P083: (4,4)
P084: (4,7)
P085: (3,4)
P086: (1,4)
P087: (4,4)
P088: (3,4)
P089: (1,4)
P090: (2,7)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
T G C C T T
T G T T A T
0 P002
T G T T A T
T G T T A T
0 P003
T G T T A T
T G T T A T
0 P004
T G T T A T
T G T T A T
0 P005
T G T T A T
T G T T A T
0 P006
T G C C T T
T G T C T C
0 P007
T G T T A T
T G T T A T
0 P008
T G T T A T
T G T T A T
0 P009
T G C C T T
T G T T A T
0 P010
T G T T A T
T G T T A T
0 P011
T G T C T T
T G T T A T
0 P012
T G T T A T
T G T T A T
0 P013
T T T T A T
G G T C T T
0 P014
G G T C T T
G G T C T T
0 P015
T G C C T T
T G T T A T
0 P016
T G T T A T
G G T C T T
0 P017
T G T T A T
T G T T A T
0 P018
T G T T A T
T G T T T T
0 P019
T G T C T C
T G T T A T
0 P020
T G T C T T
T G T T A T
0 P021
[T] G T C T T
T G T T A T
0 P022
T G T C T C
T G T T A T
0 P023
T G T C T T
T G T T A T
0 P024
T G T C T T
T G T T A T
0 P025
T G T C T T
T G T C T C
0 P026
T G T C T C
G G T C T T
0 P027
T G T C T T
T T T T A T
0 P028
T G T T A T
T G T T A T
0 P029
T G T T A T
T G T T A T
0 P030
T G T C T C
T G T T A T
0 P031
T G C C T T
T G T T A T
0 P032
T G T T A T
T G T T A T
0 P033
T G C C T T
T G C C T T
0 P034
[T] G T C T T
T G T T A T
0 P035
T T T T A T
T T T T A T
0 P036
T G T C T T
T G T C T C
0 P037
T G T T A T
G G T C T T
0 P038
[T] G T C T [T]
T G T T A T
0 P039
T G T T A T
T G T T A T
0 P040
T G C C T T
T G T C T C
0 P041
T G C C T T
T G T T T T
0 P042
T G T C T T
T G T T A T
0 P043
T G T C T C
T G T T A T
0 P044
T G T T A T
T G T T A T
0 P045
T G T T A T
T G T T A T
0 P046
T G T C T T
T G T C T T
0 P047
T G T T A T
G G T C T T
0 P048
T G T T A T
T G T T A T
0 P049
T G T T A T
T G T T A T
0 P050
T G T T A T
T G T T A T
0 P051
T G T T A T
T G T T A T
0 P052
T G T T A T
T G T T A T
0 P053
T G C C T T
T G T T A T
0 P054
T T T T A T
G G T C T T
0 P055
T G T C T C
T G T T A T
0 P056
T G T T A T
T G T T T T
0 P057
T G T T A T
T G T T T T
0 P058
T G T T A T
T G T T A T
0 P059
T G T T T T
T T T T A T
0 P060
T G T C T C
T G T T A T
0 P061
T G T T A T
G G T C T T
0 P062
T G C C T T
T G T T A T
0 P063
T G T C T T
T T T T A T
0 P064
T G T C T T
T G T T A T
0 P065
T G T C T T
T G T T A T
0 P066
T G T T A T
T G T T A T
0 P067
T G T T A T
G G T C T T
0 P068
T G T T A T
T G T T A T
0 P069
T T T T A T
G G T C T T
0 P070
T G C C T T
T T T T A T
0 P071
T G T C T C
G G T C T T
0 P072
T G T C T T
T G T T A T
0 P073
T G C C T T
T G T T A T
0 P074
T G C C T T
T G T T A T
0 P075
T G T T A T
G G T C T T
0 P076
T G T C T T
G G T C T T
0 P077
T G T C T C
T G T T A T
0 P078
T G C C T T
T G T T A T
0 P079
T G T T A T
T T T T A T
0 P080
T G T T A T
T G T T T T
0 P081
T G T T A T
T G T T A T
0 P082
T G T T A T
T G T T A T
0 P083
T G T T A T
T G T T A T
0 P084
T G T T A T
G G T C T T
0 P085
T G T C T C
T G T T A T
0 P086
T G C C T T
T G T T A T
0 P087
T G T T A T
T G T T A T
0 P088
T G T C T C
T G T T A T
0 P089
T G C C T T
T G T T A T
0 P090
T G T C T T
G G T C T 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 =
= = T T A =
0 P002
= ? = = = =
= ? = = = =
0 P003
= = = = = =
= = = = = =
0 P004
= = = = ? =
= = = = ? =
0 P005
= = = = = =
= = = = = =
0 P006
= = C = = T
= = T = = C
0 P007
= = = = ? =
= = = = ? =
0 P008
= = = = = =
= = = = = =
0 P009
= = C C T =
= = T T A =
0 P010
= = = = = =
= = = = = =
0 P011
= = = C T =
= = = T A =
0 P012
= = = = ? =
= = = = ? =
0 P013
T T = T A =
G G = C T =
0 P014
= = = = = =
= = = = = =
0 P015
= = C C ? =
= = T T ? =
0 P016
T = = T A =
G = = C T =
0 P017
= = = = = =
= = = = = =
0 P018
= = = = A =
= = = = T =
0 P019
? ? = C T C
? ? = T A T
0 P020
= = = C T =
= = = T A =
0 P021
? ? = C T =
? ? = T A =
0 P022
= = = C T C
= = = T A T
0 P023
= ? = C T =
= ? = T A =
0 P024
= = = C T =
= = = T A =
0 P025
= = = = = T
= = = = = C
0 P026
T = = = = C
G = = = = T
0 P027
= G = C T =
= T = T A =
0 P028
= = = = = =
= = = = = =
0 P029
= = = = = =
= = = = = =
0 P030
= = = C T C
= = = T A T
0 P031
= = C C T =
= = T T A =
0 P032
= = = = = =
= = = = = =
0 P033
= = = = = =
= = = = = =
0 P034
? ? = C T =
? ? = T A =
0 P035
= = = = ? =
= = = = ? =
0 P036
= ? = = = T
= ? = = = C
0 P037
T = = T A =
G = = C T =
0 P038
? = = C T ?
? = = T A ?
0 P039
= = = = = =
= = = = = =
0 P040
= = C = = T
= = T = = C
0 P041
= = C C = =
= = T T = =
0 P042
= = = C ? =
= = = T ? =
0 P043
? = = C T C
? = = T A T
0 P044
= = = = = =
= = = = = =
0 P045
= = = = = =
= = = = = =
0 P046
= = = = = =
= = = = = =
0 P047
T = = T A =
G = = C T =
0 P048
= = = ? = =
= = = ? = =
0 P049
= = = ? = =
= = = ? = =
0 P050
= = = = = =
= = = = = =
0 P051
= = = = = =
= = = = = =
0 P052
= = = = = =
= = = = = =
0 P053
= = C C T =
= = T T A =
0 P054
T T = T A =
G G = C T =
0 P055
= = = C T C
= = = T A T
0 P056
= = = = A =
= = = = T =
0 P057
= = = = A =
= = = = T =
0 P058
= = = = ? =
= = = = ? =
0 P059
= G = = T =
= T = = A =
0 P060
= = = C T C
= = = T A T
0 P061
T = = T A =
G = = C T =
0 P062
= = C C T =
= = T T A =
0 P063
= G = C T =
= T = T A =
0 P064
= = = C T =
= = = T A =
0 P065
= = = C T =
= = = T A =
0 P066
= = = = = =
= = = = = =
0 P067
T ? = T A =
G ? = C T =
0 P068
= = = = ? =
= = = = ? =
0 P069
T T = T A =
G G = C T =
0 P070
= G C C T =
= T T T A =
0 P071
T = = = = C
G = = = = T
0 P072
= = = C T =
= = = T A =
0 P073
? = C C T =
? = T T A =
0 P074
= = C C T =
= = T T A =
0 P075
T = = T A =
G = = C T =
0 P076
T = = = = =
G = = = = =
0 P077
? = = C T C
? = = T A T
0 P078
= = C C ? =
= = T T ? =
0 P079
= G = = = =
= T = = = =
0 P080
= = = = A =
= = = = T =
0 P081
? = = = = =
? = = = = =
0 P082
= = = = = =
= = = = = =
0 P083
= = = = = =
= = = = = =
0 P084
T = = T A =
G = = C T =
0 P085
= = = C T C
= = = T A T
0 P086
= = C C T =
= = T T A =
0 P087
= = = = = =
= = = = = =
0 P088
= = = C T C
= = = T A T
0 P089
= = C ? T =
= = T ? A =
0 P090
T = = = = =
G = = = = =
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 0.95 = 1.00 1.00 =
= = = = = =
= = 1.00 1.00 ? =
1.00 = = 1.00 1.00 =
= = = = = =
= = = = 1.00 =
? ? = 1.00 1.00 1.00
= = = 1.00 1.00 =
? ? = 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 1.00 =
= = = = ? =
= ? = = = 1.00
1.00 = = 1.00 1.00 =
? = = 1.00 1.00 ?
= = = = = =
= = 1.00 = = 1.00
= = 1.00 1.00 = =
= = = 1.00 ? =
? = = 1.00 1.00 1.00
= = = = = =
= = = = = =
= = = = = =
1.00 = = 1.00 1.00 =
= = = ? = =
= = = ? = =
= = = = = =
= = = = = =
= = = = = =
= = 1.00 1.00 1.00 =
1.00 0.94 = 1.00 1.00 =
= = = 1.00 1.00 1.00
= = = = 1.00 =
= = = = 1.00 =
= = = = ? =
= 0.96 = = 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 =
= = = = ? =
1.00 0.96 = 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 = = = = =
END PHASEPROBS