*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 cdk2c.phase.inp cdk2c.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
cdk2c.phase.out_freqs : haplotype frequency estimates
cdk2c.phase.out_pairs : most likely haplotype pairs for each individual
cdk2c.phase.out_recom : estimates of recombination parameters
cdk2c.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 5
Positions of loci: 1227 4789 5907 6423 7635
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file cdk2c.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 TACTC 116.000000
2 TATTT 3.000000
3 TATCT 4.000000
4 TGCTC 45.000000
5 AATTT 3.000000
6 AATCT 9.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (1,4)
P002: (1,6)
P003: (2,4)
P004: (1,6)
P005: (1,4)
P006: (4,6)
P007: (1,1)
P008: (1,1)
P009: (1,4)
P010: (1,1)
P011: (1,1)
P012: (1,4)
P013: (1,4)
P014: (1,1)
P015: (1,1)
P016: (1,1)
P017: (1,1)
P018: (4,4)
P019: (1,4)
P020: (1,4)
P021: (1,4)
P022: (1,1)
P023: (1,1)
P024: (1,1)
P025: (1,1)
P026: (1,4)
P027: (1,1)
P028: (1,1)
P029: (4,4)
P030: (1,1)
P031: (1,1)
P032: (4,4)
P033: (1,1)
P034: (1,1)
P035: (1,4)
P036: (1,1)
P037: (1,1)
P038: (4,4)
P039: (1,4)
P040: (1,6)
P041: (3,3)
P042: (1,1)
P043: (1,4)
P044: (1,4)
P045: (1,1)
P046: (1,1)
P047: (4,6)
P048: (1,1)
P049: (1,4)
P050: (1,4)
P051: (1,1)
P052: (1,1)
P053: (1,4)
P054: (1,1)
P055: (1,1)
P056: (1,5)
P057: (1,4)
P058: (1,1)
P059: (1,4)
P060: (1,1)
P061: (1,5)
P062: (1,1)
P063: (1,1)
P064: (2,5)
P065: (2,4)
P066: (1,4)
P067: (1,1)
P068: (1,4)
P069: (1,4)
P070: (1,1)
P071: (1,1)
P072: (1,4)
P073: (1,1)
P074: (1,4)
P075: (1,1)
P076: (1,1)
P077: (1,4)
P078: (1,4)
P079: (1,6)
P080: (3,4)
P081: (1,6)
P082: (1,4)
P083: (1,4)
P084: (1,1)
P085: (4,4)
P086: (4,4)
P087: (1,6)
P088: (1,6)
P089: (1,3)
P090: (1,4)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
T A C T C
T G C T C
0 P002
T A C T C
A A T C T
0 P003
T A T T T
T G C T C
0 P004
T A C T C
A A T C T
0 P005
T A C T C
T G C T C
0 P006
T G C T C
A A T C T
0 P007
T A C T C
T A C T C
0 P008
T A C T C
T A C T C
0 P009
T A C T C
T G C T C
0 P010
T A C T C
T A C T C
0 P011
T A C T C
T A C T C
0 P012
T A C T C
T G C T C
0 P013
T A C T C
T G C T C
0 P014
T A C T C
T A C T C
0 P015
T A C T C
T A C T C
0 P016
T A C T C
T A C T C
0 P017
T [A] C T C
T A C T C
0 P018
T G C T C
T G C T C
0 P019
T A C T C
T G C T C
0 P020
T A C T C
T G C T C
0 P021
T A C T C
T G C T C
0 P022
T A C T C
T A C T C
0 P023
T A C T C
T A C T C
0 P024
T A C T C
T A C T C
0 P025
T A C T C
T A C T C
0 P026
T A C T C
T G C T C
0 P027
T A C T C
T A C T C
0 P028
T [A] C T C
T A C T C
0 P029
T G C T C
T G C T C
0 P030
T A C T C
T A C T C
0 P031
T A C T C
T A C T C
0 P032
T G C T C
T G C T C
0 P033
T A C T C
T A C T C
0 P034
T A C T C
T A C T C
0 P035
T A C T C
T G C T C
0 P036
T A C T C
T A C T C
0 P037
T A C T C
T A C T C
0 P038
T G C T C
T G C T C
0 P039
T A C T C
T G C T C
0 P040
T A C T C
A A T C T
0 P041
T A T C T
T A T C T
0 P042
T A C T C
T A C T C
0 P043
T A C T C
T G C T C
0 P044
T A C T C
T G C T C
0 P045
T A C T C
T A C T C
0 P046
T [A] C T C
T A C T C
0 P047
T G C T C
A A T C T
0 P048
T [A] C T C
T A C T C
0 P049
T A C T C
T G C T C
0 P050
T A C T C
T G C T C
0 P051
T A C T C
T A C T C
0 P052
T A C T C
T A C T C
0 P053
T A C T C
T G C T C
0 P054
T A C T C
T A C T C
0 P055
T A C T C
T A C T C
0 P056
T A C T C
A A T T T
0 P057
T A C T C
T G C T C
0 P058
T A C T C
T A C T C
0 P059
T A C T C
T G C T C
0 P060
T A C T C
T A C T C
0 P061
T A C T C
A A T T T
0 P062
T A C T C
T A C T C
0 P063
T A C T C
T A C T C
0 P064
T A T T T
A A T T T
0 P065
T A [T] T T
T G C T C
0 P066
T A C T C
T G C T C
0 P067
T A C T C
T A C T C
0 P068
T A C T C
T G C T C
0 P069
T A C T C
T G C T C
0 P070
T A C T C
T A C T C
0 P071
T A C T C
T A C T C
0 P072
T A C T C
T G C T C
0 P073
T A C T C
T A C T C
0 P074
T A C T C
T G C T C
0 P075
T A C T C
T A C T C
0 P076
T [A] C T C
T A C T C
0 P077
T A C T C
T G C T C
0 P078
T A C T C
T G C T C
0 P079
T A C T C
A A T C T
0 P080
T A T C T
T G C T C
0 P081
T A C T C
A A T C T
0 P082
T A C T C
T G C T C
0 P083
T A C T C
T G C T C
0 P084
T A C T C
T A C T C
0 P085
T G C T C
T G C T C
0 P086
T G C T C
T G C T C
0 P087
T A C T C
A A T C T
0 P088
T [A] C T C
[A] A T C T
0 P089
T A C T C
T A T C T
0 P090
T A C T C
T G 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 = = =
= G = = =
0 P002
T = C T C
A = T C T
0 P003
= A T = T
= G C = C
0 P004
T = C T C
A = T C T
0 P005
= A = = =
= G = = =
0 P006
T G C T C
A A T C T
0 P007
? = = = =
? = = = =
0 P008
= = = = =
= = = = =
0 P009
= A = = =
= G = = =
0 P010
= = = = =
= = = = =
0 P011
= = = = =
= = = = =
0 P012
= A = = =
= G = = =
0 P013
= A = = =
= G = = =
0 P014
= = = = =
= = = = =
0 P015
= = = = =
= = = = =
0 P016
= = = = =
= = = = =
0 P017
= ? ? = =
= ? ? = =
0 P018
= = = = =
= = = = =
0 P019
= A = = =
= G = = =
0 P020
= A = = =
= G = = =
0 P021
= A = = =
= G = = =
0 P022
= = = = =
= = = = =
0 P023
= = = = =
= = = = =
0 P024
= = = = =
= = = = =
0 P025
= = = = =
= = = = =
0 P026
= A = = =
= G = = =
0 P027
= = = = =
= = = = =
0 P028
= ? = = =
= ? = = =
0 P029
= = = = =
= = = = =
0 P030
= = = = =
= = = = =
0 P031
= = = = =
= = = = =
0 P032
= = = = =
= = = = =
0 P033
= = = = =
= = = = =
0 P034
= = = = =
= = = = =
0 P035
= A = = =
= G = = =
0 P036
= = = = =
= = = = =
0 P037
= = = = =
= = = = =
0 P038
= = = = =
= = = = =
0 P039
= A = = =
= G = = =
0 P040
T = ? T C
A = ? C T
0 P041
= = ? = =
= = ? = =
0 P042
= = = = =
= = = = =
0 P043
= A = = =
= G = = =
0 P044
= A = = =
= G = = =
0 P045
= = = = =
= = = = =
0 P046
= ? = = =
= ? = = =
0 P047
T G C T C
A A T C T
0 P048
= ? = = =
= ? = = =
0 P049
= A = = =
= G = = =
0 P050
= A = = =
= G = = =
0 P051
= = = = =
= = = = =
0 P052
= = = = =
= = = = =
0 P053
= A = ? =
= G = ? =
0 P054
= = ? = =
= = ? = =
0 P055
? = = = =
? = = = =
0 P056
T = C = C
A = T = T
0 P057
= A = = =
= G = = =
0 P058
= = = = =
= = = = =
0 P059
= A = = =
= G = = =
0 P060
= = = = =
= = = = =
0 P061
T = C = C
A = T = T
0 P062
= = = = =
= = = = =
0 P063
? = = = =
? = = = =
0 P064
T = = = =
A = = = =
0 P065
= A ? = T
= G ? = C
0 P066
= A = = =
= G = = =
0 P067
= = = = =
= = = = =
0 P068
= A = = =
= G = = =
0 P069
= A = = =
= G = = =
0 P070
= = = = =
= = = = =
0 P071
= = = = =
= = = = =
0 P072
= A = = =
= G = = =
0 P073
= = = = =
= = = = =
0 P074
= A = = =
= G = = =
0 P075
= = = = =
= = = = =
0 P076
= ? = = =
= ? = = =
0 P077
= A = = =
= G = = =
0 P078
= A = = =
= G = = =
0 P079
T = C T C
A = T C T
0 P080
= A T C T
= G C T C
0 P081
T = C T C
A = T C T
0 P082
= A = = =
= G = = =
0 P083
= A = = =
= G = = =
0 P084
= = = = =
= = = = =
0 P085
= = = = =
= = = = =
0 P086
= = = = =
= = = = =
0 P087
T = C T C
A = T C T
0 P088
? ? C T C
? ? T C T
0 P089
= = ? T C
= = ? C T
0 P090
= A = = =
= 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
= 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
= ? = = =
= 1.00 = = =
= 1.00 = = =
= = = = =
= = = = =
= 1.00 = ? =
= = ? = =
? = = = =
1.00 = 1.00 = 1.00
= 1.00 = = =
= = = = =
= 1.00 = = =
= = = = =
1.00 = 1.00 = 1.00
= = = = =
? = = = =
1.00 = = = =
= 0.91 ? = 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 = = =
= 1.00 = = =
= = = = =
= = = = =
= = = = =
1.00 = 1.00 1.00 1.00
? ? 1.00 1.00 1.00
= = ? 1.00 1.00
= 1.00 = = =
END PHASEPROBS