*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 trex1.phase.inp trex1.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
trex1.phase.out_freqs : haplotype frequency estimates
trex1.phase.out_pairs : most likely haplotype pairs for each individual
trex1.phase.out_recom : estimates of recombination parameters
trex1.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 3
Positions of loci: 161 1864 2782
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file trex1.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 ATC 6.000000
2 ATT 51.000000
3 CTC 104.000000
4 CTT 1.000000
5 CCC 18.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (2,3)
P002: (3,3)
P003: (3,3)
P004: (3,3)
P005: (3,5)
P006: (2,3)
P007: (3,5)
P008: (3,3)
P009: (2,2)
P010: (2,3)
P011: (3,3)
P012: (2,3)
P013: (3,5)
P014: (2,3)
P015: (2,3)
P016: (2,2)
P017: (3,3)
P018: (2,3)
P019: (2,2)
P020: (3,5)
P021: (1,2)
P022: (2,3)
P023: (3,3)
P024: (3,3)
P025: (3,5)
P026: (2,3)
P027: (2,3)
P028: (2,5)
P029: (3,3)
P030: (3,3)
P031: (3,3)
P032: (3,3)
P033: (2,3)
P034: (3,5)
P035: (3,3)
P036: (3,4)
P037: (2,3)
P038: (2,3)
P039: (3,3)
P040: (3,3)
P041: (3,3)
P042: (3,3)
P043: (2,2)
P044: (2,3)
P045: (2,3)
P046: (2,3)
P047: (3,3)
P048: (3,3)
P049: (2,3)
P050: (2,3)
P051: (2,3)
P052: (2,3)
P053: (2,3)
P054: (2,3)
P055: (2,3)
P056: (2,3)
P057: (1,1)
P058: (3,5)
P059: (2,3)
P060: (1,2)
P061: (3,3)
P062: (3,5)
P063: (3,5)
P064: (2,3)
P065: (2,5)
P066: (3,3)
P067: (3,5)
P068: (3,3)
P069: (3,3)
P070: (3,3)
P071: (2,3)
P072: (3,5)
P073: (2,2)
P074: (3,5)
P075: (2,2)
P076: (2,3)
P077: (1,3)
P078: (3,3)
P079: (3,5)
P080: (2,3)
P081: (2,3)
P082: (2,3)
P083: (2,5)
P084: (3,5)
P085: (2,5)
P086: (3,3)
P087: (1,2)
P088: (3,3)
P089: (2,3)
P090: (3,3)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
A T T
C T C
0 P002
C T C
C T C
0 P003
C T C
C T C
0 P004
C T C
C T C
0 P005
C T C
C C C
0 P006
A T T
C T C
0 P007
C T C
C C C
0 P008
C T C
C T C
0 P009
A T T
A T T
0 P010
A T T
C T C
0 P011
C T C
C T C
0 P012
A T T
C T C
0 P013
C T C
C C C
0 P014
A T T
C T C
0 P015
A T T
C T C
0 P016
A T T
A T T
0 P017
C T C
C T C
0 P018
A T T
C T C
0 P019
A T T
A T T
0 P020
C T C
C C C
0 P021
A T C
A T T
0 P022
A T T
C T C
0 P023
C T C
C T C
0 P024
C T C
C T C
0 P025
C T C
C C C
0 P026
A T T
C T C
0 P027
A T T
C T C
0 P028
A T T
C C C
0 P029
C T C
C T C
0 P030
C T C
C T C
0 P031
C T C
C T C
0 P032
C [T] C
C T C
0 P033
A T T
C T C
0 P034
C T C
C C C
0 P035
C T C
C T C
0 P036
C T C
C T T
0 P037
A T T
C T C
0 P038
A T T
C T C
0 P039
C T C
[C] T C
0 P040
C T C
C T C
0 P041
C T C
C T C
0 P042
C T C
C T C
0 P043
A T T
A T T
0 P044
A T T
C T C
0 P045
A T T
C T C
0 P046
A T T
C T C
0 P047
C T C
C T C
0 P048
C T C
C T C
0 P049
A T T
C T C
0 P050
A T T
C T C
0 P051
A T T
C T C
0 P052
A T T
C T C
0 P053
A T T
C T C
0 P054
A T T
C T C
0 P055
A T T
C T C
0 P056
A T T
C T C
0 P057
A T C
A T C
0 P058
C T C
C C C
0 P059
A T T
C T C
0 P060
A T C
A T T
0 P061
C T C
C T C
0 P062
C T C
C C C
0 P063
C T C
C C C
0 P064
A T T
C T C
0 P065
A T T
C C C
0 P066
C T C
C T C
0 P067
C T C
C C C
0 P068
C T C
C T C
0 P069
C T C
C T C
0 P070
C T C
C T C
0 P071
A T T
C T C
0 P072
C T C
C C C
0 P073
A T T
A T T
0 P074
C T C
C C C
0 P075
A T T
A T T
0 P076
A T T
C T C
0 P077
A T C
C T C
0 P078
C T C
C T C
0 P079
C T C
C C C
0 P080
A T T
C T C
0 P081
A T T
C T C
0 P082
A T T
C T C
0 P083
A T T
C C C
0 P084
C T C
C C C
0 P085
A T T
C C C
0 P086
C T C
C T C
0 P087
A T C
A T T
0 P088
C [T] C
C T C
0 P089
A T T
C T C
0 P090
C [T] C
C T C
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
A = T
C = C
0 P002
= = =
= = =
0 P003
= = =
= = =
0 P004
= = =
= = =
0 P005
= T =
= C =
0 P006
A = T
C = C
0 P007
= T =
= C =
0 P008
= = =
= = =
0 P009
= ? =
= ? =
0 P010
A = T
C = C
0 P011
= = ?
= = ?
0 P012
A = T
C = C
0 P013
= T =
= C =
0 P014
A = T
C = C
0 P015
A = T
C = C
0 P016
= = =
= = =
0 P017
= = =
= = =
0 P018
A ? T
C ? C
0 P019
= ? =
= ? =
0 P020
= T =
= C =
0 P021
= = C
= = T
0 P022
A ? T
C ? C
0 P023
= = =
= = =
0 P024
= = =
= = =
0 P025
= T =
= C =
0 P026
A = T
C = C
0 P027
A = T
C = C
0 P028
A T T
C C C
0 P029
= = =
= = =
0 P030
= = =
= = =
0 P031
= = =
= = =
0 P032
= ? =
= ? =
0 P033
A ? T
C ? C
0 P034
= T =
= C =
0 P035
= = =
= = =
0 P036
= ? C
= ? T
0 P037
A = T
C = C
0 P038
A = T
C = C
0 P039
? = =
? = =
0 P040
= = =
= = =
0 P041
= = =
= = =
0 P042
= = =
= = =
0 P043
= ? =
= ? =
0 P044
A = T
C = C
0 P045
A = T
C = C
0 P046
A = T
C = C
0 P047
= = =
= = =
0 P048
= = =
= = =
0 P049
A = T
C = C
0 P050
A = T
C = C
0 P051
A = T
C = C
0 P052
A = T
C = C
0 P053
A = T
C = C
0 P054
A = T
C = C
0 P055
A = T
C = C
0 P056
A ? T
C ? C
0 P057
= = =
= = =
0 P058
= T =
= C =
0 P059
A = T
C = C
0 P060
= = C
= = T
0 P061
= = =
= = =
0 P062
= T =
= C =
0 P063
= T =
= C =
0 P064
A = T
C = C
0 P065
A T T
C C C
0 P066
= = =
= = =
0 P067
= T =
= C =
0 P068
= = =
= = =
0 P069
= = =
= = =
0 P070
= = =
= = =
0 P071
A = T
C = C
0 P072
= T =
= C =
0 P073
= = =
= = =
0 P074
= T =
= C =
0 P075
= = =
= = =
0 P076
A = T
C = C
0 P077
A = =
C = =
0 P078
= = =
= = =
0 P079
= T =
= C =
0 P080
A = T
C = C
0 P081
A = T
C = C
0 P082
A = T
C = C
0 P083
A T T
C C C
0 P084
= T =
= C =
0 P085
A T T
C C C
0 P086
= = =
= = =
0 P087
= = C
= = T
0 P088
= ? =
= ? =
0 P089
? = T
? = C
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 =
= = =
= ? =
1.00 = 1.00
= = ?
1.00 = 1.00
= 1.00 =
1.00 = 1.00
1.00 = 1.00
= = =
= = =
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 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 0.99 1.00
= 1.00 =
1.00 0.99 1.00
= = =
= = 1.00
= ? =
? = 1.00
= ? =
END PHASEPROBS