*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 casp2.phase.inp casp2.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
casp2.phase.out_freqs : haplotype frequency estimates
casp2.phase.out_pairs : most likely haplotype pairs for each individual
casp2.phase.out_recom : estimates of recombination parameters
casp2.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 6
Positions of loci: 3367 4108 7143 7832 14099 14494
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file casp2.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 TDGGCC 4.000000
2 TDGGTT 128.000000
3 TDAGCC 1.000000
4 TDACCC 6.000000
5 TIGGCC 1.000000
6 TIGGTT 28.000000
7 TIACCC 1.000000
8 TIACTT 1.000000
9 GDGGTT 10.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (1,2)
P002: (2,2)
P003: (2,2)
P004: (6,6)
P005: (2,2)
P006: (2,9)
P007: (2,2)
P008: (2,6)
P009: (2,2)
P010: (2,9)
P011: (6,6)
P012: (2,9)
P013: (2,2)
P014: (2,2)
P015: (2,6)
P016: (2,2)
P017: (2,4)
P018: (2,9)
P019: (2,2)
P020: (2,2)
P021: (2,6)
P022: (6,6)
P023: (2,6)
P024: (2,2)
P025: (2,2)
P026: (2,2)
P027: (2,2)
P028: (2,2)
P029: (2,2)
P030: (2,2)
P031: (2,2)
P032: (1,2)
P033: (3,4)
P034: (2,6)
P035: (2,2)
P036: (2,2)
P037: (2,2)
P038: (6,6)
P039: (6,7)
P040: (2,9)
P041: (6,6)
P042: (6,6)
P043: (4,9)
P044: (2,4)
P045: (2,2)
P046: (2,4)
P047: (2,2)
P048: (2,2)
P049: (2,9)
P050: (6,8)
P051: (2,2)
P052: (2,2)
P053: (2,2)
P054: (2,2)
P055: (2,2)
P056: (2,2)
P057: (2,2)
P058: (2,2)
P059: (1,2)
P060: (2,2)
P061: (6,6)
P062: (2,6)
P063: (2,2)
P064: (5,6)
P065: (2,2)
P066: (2,2)
P067: (2,2)
P068: (2,2)
P069: (2,2)
P070: (2,2)
P071: (2,2)
P072: (2,4)
P073: (2,2)
P074: (2,2)
P075: (2,6)
P076: (2,2)
P077: (2,6)
P078: (2,2)
P079: (2,2)
P080: (1,2)
P081: (2,2)
P082: (2,9)
P083: (6,9)
P084: (2,2)
P085: (2,2)
P086: (2,2)
P087: (2,6)
P088: (6,9)
P089: (2,2)
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
T D [G] [G] C C
T D G G T T
0 P002
T [D] G G T T
T D G G T T
0 P003
T D G G T T
T D G G T T
0 P004
T I G G T T
T I G G T T
0 P005
T D G G T T
T D G G T T
0 P006
T D G G T T
G D G G T T
0 P007
T D G G T T
T D G G T T
0 P008
T D G G T T
T I G G T T
0 P009
T [D] G G T T
T D G G T T
0 P010
T D G G T T
G D G G T T
0 P011
T I G G T T
T I G G T T
0 P012
T D G G T T
G D G G T T
0 P013
T D G G T T
T D G G T T
0 P014
T [D] G G T T
T D G G T T
0 P015
T D G G T T
T I G G T T
0 P016
T [D] G G T T
T D G G T T
0 P017
T D G G T T
T D A C C C
0 P018
T D G G T T
G D G G T T
0 P019
T [D] G G T T
T D G G T T
0 P020
T D G G T T
T D G G T T
0 P021
T D G G T T
T I G G T T
0 P022
T I G G T T
T I G G T T
0 P023
T D G G T T
T I G G T T
0 P024
T D G G T T
T D G G T T
0 P025
T [D] G G T T
T D G G T T
0 P026
T [D] G G T T
T D G G T T
0 P027
T D G G T T
T D G G T T
0 P028
T D G G T T
T D G G T T
0 P029
T D G G T T
T D G G T T
0 P030
T D G G T T
T D G G T T
0 P031
T [D] G G T T
T D G G T T
0 P032
T D G G C C
T D G G T T
0 P033
T D A G C C
T D A C C C
0 P034
T D G G T T
T I G G T T
0 P035
T [D] G G T T
T D G G T T
0 P036
T D G G T T
T D G G T T
0 P037
T [D] G G T T
T D G G T T
0 P038
T I G G T T
T I G G T T
0 P039
T I G G T T
T I A C C C
0 P040
T D G G T T
G D G G T T
0 P041
T I G G T T
T I G G T T
0 P042
T I G G T T
T I G G T T
0 P043
(T) D A C C C
(G) D G G T T
0 P044
T D G G T T
T D A C C C
0 P045
T D G G T T
T D G G T T
0 P046
T D G G T T
T D A C C C
0 P047
T D G G T T
T D G G T T
0 P048
T D G G T T
T D G G T T
0 P049
T D G G T T
G D G G T T
0 P050
T I G G T T
T I A C T T
0 P051
T [D] G G T T
T D G G T T
0 P052
T D G G T T
T D G G T T
0 P053
T [D] G G T T
T D G G T T
0 P054
T D G G T T
T D G G T T
0 P055
T D G G T T
T D G G T T
0 P056
T [D] G G T T
T D G G T T
0 P057
T [D] G G T T
T D G G T T
0 P058
T [D] G G T T
T D G G T T
0 P059
T D G G C C
T D G G T T
0 P060
T D G G T T
T D G G T T
0 P061
T I G G T T
T I G G T T
0 P062
T D G G T T
T I G G T T
0 P063
T [D] G G T T
T D G G T T
0 P064
T I G G C C
T I G G T T
0 P065
T D G G T T
T D G G T T
0 P066
T D G G T T
T D G G T T
0 P067
T D G G T T
T D G G T T
0 P068
T [D] G G T T
T D G G T T
0 P069
T [D] G G T T
T D G G T T
0 P070
T [D] G G T T
T D G G T T
0 P071
T [D] G G T T
T D G G T T
0 P072
T D G G T T
T D A C C C
0 P073
T D G G T T
T D G G T T
0 P074
T D G G T T
T D G G T T
0 P075
T D G G T T
T I G G T T
0 P076
T D G G T T
T D G G T T
0 P077
T D G G T T
T I G G T T
0 P078
T [D] G G T T
T D G G T T
0 P079
T D G G T T
T D G G T T
0 P080
T D G G C C
T D G G T T
0 P081
T D G G T T
T D G G T T
0 P082
T D G G T T
G D G G T T
0 P083
(T) I G G T T
(G) D G G T T
0 P084
T [D] G G T T
T D G G T T
0 P085
T D G G T T
T D G G T T
0 P086
T [D] G G T T
T D G G T T
0 P087
T D G G T T
T I G G T T
0 P088
(T) I G G T T
(G) D G G T T
0 P089
T D G G T T
T D G G T T
0 P090
T D G G T T
T D G G 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 ?
? ? ? ? T ?
0 P002
? ? = ? = =
? ? = ? = =
0 P003
= = = ? = =
= = = ? = =
0 P004
= = ? ? = =
= = ? ? = =
0 P005
= = ? ? = =
= = ? ? = =
0 P006
T = = ? ? =
G = = ? ? =
0 P007
? = = = = =
? = = = = =
0 P008
= D ? ? = =
= I ? ? = =
0 P009
? ? = = = =
? ? = = = =
0 P010
T = = = = =
G = = = = =
0 P011
= = = = = =
= = = = = =
0 P012
T = = = = =
G = = = = =
0 P013
= = ? ? = =
= = ? ? = =
0 P014
= ? = = = =
= ? = = = =
0 P015
= D = = = =
= I = = = =
0 P016
= ? ? = = =
= ? ? = = =
0 P017
= ? G G T T
= ? A C C C
0 P018
T = = = = =
G = = = = =
0 P019
= ? = = = =
= ? = = = =
0 P020
= = = = = =
= = = = = =
0 P021
= D = = ? ?
= I = = ? ?
0 P022
? = = = = =
? = = = = =
0 P023
= D = = = =
= I = = = =
0 P024
= = = = = =
= = = = = =
0 P025
= ? = = = =
= ? = = = =
0 P026
? ? = = ? =
? ? = = ? =
0 P027
= = = = = =
= = = = = =
0 P028
= = = = = =
= = = = = =
0 P029
= = = = = =
= = = = = =
0 P030
? = = = = =
? = = = = =
0 P031
= ? = = = =
= ? = = = =
0 P032
? ? = = C C
? ? = = T T
0 P033
? ? = G ? =
? ? = C ? =
0 P034
= D = = = =
= I = = = =
0 P035
= ? = = = =
= ? = = = =
0 P036
= = = = = =
= = = = = =
0 P037
? ? = = = =
? ? = = = =
0 P038
= = = = = =
= = = = = =
0 P039
= = G G T T
= = A C C C
0 P040
T = = = = =
G = = = = =
0 P041
= = = ? = ?
= = = ? = ?
0 P042
= = = = = =
= = = = = =
0 P043
(T) ? A C C C
(G) ? G G T T
0 P044
= ? G G T T
= ? A C C C
0 P045
= = = = = =
= = = = = =
0 P046
= ? G G ? T
= ? A C ? C
0 P047
= = = = = =
= = = = = =
0 P048
= = = = = =
= = = = = =
0 P049
T ? = ? ? =
G ? = ? ? =
0 P050
= = G G ? =
= = A C ? =
0 P051
= ? = = = =
= ? = = = =
0 P052
= = = = = =
= = = = = =
0 P053
= ? = = = =
= ? = = = =
0 P054
= = = = = =
= = = = = =
0 P055
= = = = = =
= = = = = =
0 P056
= ? = = = =
= ? = = = =
0 P057
= ? = = = =
= ? = = = =
0 P058
= ? = = = =
= ? = = = =
0 P059
= ? = = C C
= ? = = T T
0 P060
= = = = = =
= = = = = =
0 P061
= = = = = ?
= = = = = ?
0 P062
= D = = = =
= I = = = =
0 P063
= ? = = = =
= ? = = = =
0 P064
= = = = C C
= = = = T T
0 P065
= = = = = =
= = = = = =
0 P066
= = = = = =
= = = = = =
0 P067
= = = = = =
= = = = = =
0 P068
= ? = = = =
= ? = = = =
0 P069
= ? = = = =
= ? = = = =
0 P070
= ? = = = =
= ? = = = =
0 P071
= ? = = = =
= ? = = = =
0 P072
= ? G G T T
= ? A C C C
0 P073
= = = = = =
= = = = = =
0 P074
= = = = = =
= = = = = =
0 P075
= D ? = = =
= I ? = = =
0 P076
= = = = = =
= = = = = =
0 P077
= D = = = =
= I = = = =
0 P078
= ? = = = =
= ? = = = =
0 P079
= = = = = =
= = = = = =
0 P080
= ? = = C C
= ? = = T T
0 P081
= = = = ? ?
= = = = ? ?
0 P082
T = = = = ?
G = = = = ?
0 P083
(T) I = = = =
(G) D = = = =
0 P084
= ? = = = =
= ? = = = =
0 P085
= = = = = =
= = = = = =
0 P086
? ? = = = =
? ? = = = =
0 P087
= D = = = =
= I = = = =
0 P088
(T) I = = = =
(G) D = = = =
0 P089
= = = = = =
= = = = = =
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 = = = = =
= = = = = =
1.00 = = = = =
= = ? ? = =
= ? = = = =
= 1.00 = = = =
= ? ? = = =
= ? 0.98 0.98 1.00 1.00
1.00 = = = = =
= ? = = = =
= = = = = =
= 1.00 = = ? ?
? = = = = =
= 1.00 = = = =
= = = = = =
= ? = = = =
? ? = = ? =
= = = = = =
= = = = = =
= = = = = =
? = = = = =
= ? = = = =
? ? = = 1.00 1.00
? ? = 1.00 ? =
= 1.00 = = = =
= ? = = = =
= = = = = =
? ? = = = =
= = = = = =
= = 0.94 0.94 1.00 1.00
1.00 = = = = =
= = = ? = ?
= = = = = =
0.62 ? 0.99 0.99 1.00 1.00
= ? 0.98 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
= = = = = =
= = = = = =
= = = = = =
= ? = = = =
= ? = = = =
= ? = = = =
= ? = = = =
= ? 0.98 0.98 1.00 1.00
= = = = = =
= = = = = =
= 1.00 ? = = =
= = = = = =
= 1.00 = = = =
= ? = = = =
= = = = = =
= ? = = 1.00 1.00
= = = = ? ?
1.00 = = = = ?
0.89 1.00 = = = =
= ? = = = =
= = = = = =
? ? = = = =
= 1.00 = = = =
0.88 1.00 = = = =
= = = = = =
= = = = = =
END PHASEPROBS