*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 cdc6x.phase.inp cdc6x.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
cdc6x.phase.out_freqs : haplotype frequency estimates
cdc6x.phase.out_pairs : most likely haplotype pairs for each individual
cdc6x.phase.out_recom : estimates of recombination parameters
cdc6x.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 6
Positions of loci: 1368 4301 5306 5753 13084 14890
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file cdc6x.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 AATDIG 140.000000
2 AGTDIA 1.000000
3 GGTDIG 2.000000
4 GGTDIA 22.000000
5 GGCIDA 15.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (1,1)
P002: (1,4)
P003: (1,5)
P004: (1,5)
P005: (1,1)
P006: (1,1)
P007: (1,1)
P008: (1,1)
P009: (1,4)
P010: (1,1)
P011: (1,1)
P012: (1,3)
P013: (1,1)
P014: (4,4)
P015: (1,1)
P016: (1,1)
P017: (1,1)
P018: (1,5)
P019: (1,5)
P020: (1,4)
P021: (4,5)
P022: (1,1)
P023: (1,1)
P024: (1,1)
P025: (1,1)
P026: (1,2)
P027: (1,1)
P028: (1,1)
P029: (1,5)
P030: (1,1)
P031: (1,1)
P032: (1,1)
P033: (1,1)
P034: (1,1)
P035: (1,1)
P036: (1,1)
P037: (1,1)
P038: (1,5)
P039: (1,1)
P040: (1,1)
P041: (1,5)
P042: (1,5)
P043: (1,1)
P044: (1,1)
P045: (1,4)
P046: (1,1)
P047: (1,1)
P048: (4,4)
P049: (1,1)
P050: (1,1)
P051: (1,1)
P052: (1,1)
P053: (1,1)
P054: (1,1)
P055: (1,1)
P056: (1,5)
P057: (1,1)
P058: (1,4)
P059: (1,1)
P060: (1,3)
P061: (1,5)
P062: (1,1)
P063: (1,4)
P064: (4,5)
P065: (1,5)
P066: (1,1)
P067: (1,4)
P068: (1,4)
P069: (1,1)
P070: (1,1)
P071: (1,1)
P072: (1,1)
P073: (1,1)
P074: (1,4)
P075: (1,1)
P076: (4,4)
P077: (1,1)
P078: (1,1)
P079: (1,1)
P080: (1,5)
P081: (1,1)
P082: (1,1)
P083: (1,4)
P084: (1,4)
P085: (1,1)
P086: (1,1)
P087: (1,5)
P088: (1,4)
P089: (1,1)
P090: (4,4)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
A A T D I G
A A T D I G
0 P002
A A T D I G
G G T D I [A]
0 P003
A A T D I G
G G C I D A
0 P004
A A T D I G
G G C I D A
0 P005
A A T D I G
A A T D I G
0 P006
A A T D I G
A A T D I G
0 P007
A A T D I G
A A T D I G
0 P008
A A T D I G
A A T D I G
0 P009
A A T D I G
G G T D I [A]
0 P010
A A T D I G
A A T D I G
0 P011
A A T D I G
A A T D I G
0 P012
A A T D I G
G G T D I G
0 P013
A A T D I G
A A T D I G
0 P014
G G T D I A
G G T D I A
0 P015
A A T D I G
A A T D I G
0 P016
A A T D I G
A A T D I G
0 P017
A A T D I G
A A T D I G
0 P018
A A T D I G
G G C I D A
0 P019
A A T D I G
G G C I D A
0 P020
A A T D I G
G G T D I A
0 P021
G G T D I A
G G C I D A
0 P022
A A T D I G
A A T D I G
0 P023
A A T D I G
A A T D I G
0 P024
A A T D I G
A A T D I G
0 P025
A A T D I G
A A T D I G
0 P026
A A T D I G
A G T D I A
0 P027
A A T D I G
A A T D I G
0 P028
A A T D I G
A A T D I G
0 P029
A A T D I G
G G C I D A
0 P030
A A T D I G
A A T D I G
0 P031
A A T D I G
A A T D I G
0 P032
A A T D I G
A A T D I G
0 P033
A A T D I G
A A T D I G
0 P034
A A T D I G
A A T D I G
0 P035
A A T D I G
A A T D I G
0 P036
A A T D I G
A A T D I G
0 P037
A A T D I G
A A T D I G
0 P038
A A T D I G
G G C I D A
0 P039
A A T D I G
A A T D I G
0 P040
A A T D I G
A A T D I G
0 P041
A A T D I G
G G C I D A
0 P042
A A T D I G
G G C I D A
0 P043
A A T D I G
A A T D I G
0 P044
A A T D I G
A A T D I G
0 P045
A A T D I G
G G T D I A
0 P046
A A T D I G
A A T D I G
0 P047
A A T D I G
A A T D I G
0 P048
G G T D I A
G G T D I A
0 P049
A A T D I G
A A T D I G
0 P050
A A T D I G
A A T D I G
0 P051
A A T D I G
A A T D I G
0 P052
A A T D I G
A A T D I G
0 P053
A A T D I G
A A T D I G
0 P054
A A T D I G
A A T D I G
0 P055
A A T D I G
A A T D I G
0 P056
A A T D I G
G G C I D A
0 P057
A A T D I G
A A T D I G
0 P058
A A T D I G
G G T D I A
0 P059
A A T D I G
A A T D I G
0 P060
A A T D I G
G G T D I G
0 P061
A A T D I G
G G C I D A
0 P062
A A T D I G
A A T D I G
0 P063
A A T D I G
G G T D I A
0 P064
G G T D I A
G G C I D A
0 P065
A A T D I G
G G C I D A
0 P066
A A T D I G
A A T D I G
0 P067
A A T D I G
G G T D I A
0 P068
A A T D I G
G G T D I A
0 P069
A A T D I G
A A T D I G
0 P070
A A T D I G
A A T D I G
0 P071
A A T D I G
A A T D I G
0 P072
A A T D I G
A A T D I G
0 P073
A A T D I G
A A T D I G
0 P074
A A T D I G
G G T D I A
0 P075
A A T D I G
A A T D I G
0 P076
G G T D I A
G G T D I A
0 P077
A A T D I G
A A T D I G
0 P078
A A T D I G
A A T D I G
0 P079
A A T D I G
A A T D I G
0 P080
A A T D I G
G G C I D A
0 P081
A A T D I G
A A T D I G
0 P082
A A T D I G
A A T D I G
0 P083
A A T D I G
G G T D I A
0 P084
A A T D I G
G G T D I A
0 P085
A A T D I G
A A T D I G
0 P086
A A T D I G
A A T D I G
0 P087
A A T D I G
G G C I D A
0 P088
A A T D I G
G G T D I A
0 P089
A A T D I G
A A T D I G
0 P090
G G T D I A
[G] G T D I A
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
? A ? = = ?
? G ? = = ?
0 P003
? A T D I G
? G C I D A
0 P004
A A T D I G
G G C I D A
0 P005
= = = = = =
= = = = = =
0 P006
= = = = = =
= = = = = =
0 P007
? = = = = =
? = = = = =
0 P008
? = = = = =
? = = = = =
0 P009
? A ? = ? ?
? G ? = ? ?
0 P010
? = ? = = =
? = ? = = =
0 P011
= = = = = =
= = = = = =
0 P012
A A = = = =
G G = = = =
0 P013
= = = = = =
= = = = = =
0 P014
= = = = = =
= = = = = =
0 P015
= = = = = =
= = = = = =
0 P016
= = = = = =
= = = = = =
0 P017
? = ? = = =
? = ? = = =
0 P018
? A ? D I G
? G ? I D A
0 P019
A A T D I G
G G C I D A
0 P020
A A = = = G
G G = = = A
0 P021
= = T D I =
= = C I D =
0 P022
= = = = = =
= = = = = =
0 P023
= = = = = =
= = = = = =
0 P024
= = = = = =
= = = = = =
0 P025
= = = = = =
= = = = = =
0 P026
= A = = = G
= G = = = A
0 P027
= = = = = =
= = = = = =
0 P028
= = = = = =
= = = = = =
0 P029
A A T D I G
G G C I D A
0 P030
= = = = = =
= = = = = =
0 P031
= = = = = =
= = = = = =
0 P032
= = = = = =
= = = = = =
0 P033
= = = = = =
= = = = = =
0 P034
= = = = = =
= = = = = =
0 P035
= = = = = =
= = = = = =
0 P036
= = = = = =
= = = = = =
0 P037
= = = = = =
= = = = = =
0 P038
A A T D I G
G G C I D A
0 P039
= = = = = =
= = = = = =
0 P040
= = = = = =
= = = = = =
0 P041
A A T D I G
G G C I D A
0 P042
A A T D I G
G G C I D A
0 P043
= = = = = =
= = = = = =
0 P044
= = = = = =
= = = = = =
0 P045
A A = = = G
G G = = = A
0 P046
= = = = = =
= = = = = =
0 P047
= = = = = =
= = = = = =
0 P048
= = = = = =
= = = = = =
0 P049
? = ? = = =
? = ? = = =
0 P050
= = = = = =
= = = = = =
0 P051
= = = = = =
= = = = = =
0 P052
= = = = = =
= = = = = =
0 P053
= = = = = =
= = = = = =
0 P054
= = = = = =
= = = = = =
0 P055
= = = = = =
= = = = = =
0 P056
A A T D I G
G G C I D A
0 P057
= = = = = =
= = = = = =
0 P058
A A = = = G
G G = = = A
0 P059
= = = = = =
= = = = = =
0 P060
A A = = = =
G G = = = =
0 P061
A A T ? I G
G G C ? D A
0 P062
= = = = = =
= = = = = =
0 P063
A A = = = G
G G = = = A
0 P064
= = T D I =
= = C I D =
0 P065
A A T D I G
G G C I D A
0 P066
= = = = = =
= = = = = =
0 P067
A A = = = G
G G = = = A
0 P068
A A = = = G
G G = = = A
0 P069
= = = = = =
= = = = = =
0 P070
= = = = = =
= = = = = =
0 P071
? = ? = = =
? = ? = = =
0 P072
= = = = = =
= = = = = =
0 P073
? = ? = = =
? = ? = = =
0 P074
? A = = = G
? G = = = A
0 P075
= = = = = =
= = = = = =
0 P076
= = = = = =
= = = = = =
0 P077
= = = = = =
= = = = = =
0 P078
= = = = = =
= = = = = =
0 P079
= = = = = =
= = = = = =
0 P080
A A T D I G
G G C I D A
0 P081
= = = = = =
= = = = = =
0 P082
= = = = = =
= = = = = =
0 P083
A A = = = G
G G = = = A
0 P084
A A = = = G
G G = = = A
0 P085
= = = = = =
= = = = = =
0 P086
= = = = = =
= = = = = =
0 P087
A A T D I G
G G C I D A
0 P088
A A = = = G
G G = = = A
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
1.00 1.00 1.00 1.00 1.00 1.00
= = = = = =
= = = = = =
? = = = = =
? = = = = =
? 1.00 ? = ? ?
? = ? = = =
= = = = = =
1.00 1.00 = = = =
= = = = = =
= = = = = =
= = = = = =
= = = = = =
? = ? = = =
? 1.00 ? 1.00 1.00 1.00
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 1.00 1.00 1.00 1.00 1.00
= = = = = =
1.00 1.00 = = = 1.00
1.00 1.00 = = = 1.00
= = = = = =
= = = = = =
? = ? = = =
= = = = = =
? = ? = = =
? 1.00 = = = 1.00
= = = = = =
= = = = = =
= = = = = =
= = = = = =
= = = = = =
1.00 1.00 1.00 1.00 1.00 1.00
= = = = = =
= = = = = =
1.00 1.00 = = = 1.00
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