*************************************************************
****                                                     ****
****            Output from PHASE v2.0                   ****
****  Code by M Stephens, with contributions from N Li   ****
****                                                     ****
*************************************************************

BEGIN COMMAND_LINE 
/usr/local/genome/lib/phase/PHASE2 -d1 fauxx.phase.inp fauxx.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
fauxx.phase.out_freqs : haplotype frequency estimates
fauxx.phase.out_pairs : most likely haplotype pairs for each individual
fauxx.phase.out_recom : estimates of recombination parameters
fauxx.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 2
Positions of loci: 1936 3792 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file fauxx.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1          CA   91.000000
         2          GC   89.000000
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: (1,2)
P005: (1,2)
P006: (1,2)
P007: (2,2)
P008: (2,2)
P009: (2,2)
P010: (2,2)
P011: (2,2)
P012: (1,2)
P013: (1,2)
P014: (1,2)
P015: (1,2)
P016: (2,2)
P017: (1,1)
P018: (1,2)
P019: (1,2)
P020: (2,2)
P021: (1,2)
P022: (1,1)
P023: (1,2)
P024: (1,2)
P025: (1,1)
P026: (1,2)
P027: (1,1)
P028: (1,2)
P029: (1,1)
P030: (1,2)
P031: (1,2)
P032: (1,1)
P033: (2,2)
P034: (1,2)
P035: (1,2)
P036: (2,2)
P037: (1,2)
P038: (2,2)
P039: (1,2)
P040: (1,2)
P041: (2,2)
P042: (1,1)
P043: (1,2)
P044: (2,2)
P045: (1,2)
P046: (1,2)
P047: (1,2)
P048: (1,1)
P049: (2,2)
P050: (1,2)
P051: (1,2)
P052: (1,1)
P053: (1,1)
P054: (1,2)
P055: (2,2)
P056: (1,1)
P057: (1,2)
P058: (2,2)
P059: (1,1)
P060: (1,2)
P061: (2,2)
P062: (1,2)
P063: (1,2)
P064: (1,2)
P065: (1,1)
P066: (1,1)
P067: (1,1)
P068: (1,2)
P069: (1,2)
P070: (1,2)
P071: (1,2)
P072: (1,1)
P073: (2,2)
P074: (1,2)
P075: (1,2)
P076: (2,2)
P077: (1,1)
P078: (1,2)
P079: (1,1)
P080: (1,2)
P081: (1,2)
P082: (1,1)
P083: (1,2)
P084: (1,2)
P085: (2,2)
P086: (1,1)
P087: (1,1)
P088: (1,2)
P089: (1,2)
P090: (1,1)
END BESTPAIRS_SUMMARY


Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:

BEGIN BESTPAIRS1
0 P001
C A 
G C 
0 P002
G C 
G C 
0 P003
G C 
G C 
0 P004
C A 
G C 
0 P005
C A 
G C 
0 P006
C A 
G C 
0 P007
G C 
G C 
0 P008
G C 
G C 
0 P009
G C 
G C 
0 P010
G C 
G C 
0 P011
G C 
G C 
0 P012
C A 
G C 
0 P013
C A 
G C 
0 P014
C A 
G C 
0 P015
C A 
G C 
0 P016
G C 
G C 
0 P017
C A 
C A 
0 P018
C A 
G C 
0 P019
C A 
G C 
0 P020
G C 
G C 
0 P021
C A 
G C 
0 P022
C A 
C A 
0 P023
C A 
G C 
0 P024
C A 
G C 
0 P025
C A 
C A 
0 P026
C A 
G C 
0 P027
C A 
C A 
0 P028
C A 
G C 
0 P029
C A 
C A 
0 P030
C A 
G C 
0 P031
C A 
G C 
0 P032
C A 
C A 
0 P033
G C 
G C 
0 P034
C A 
G C 
0 P035
C A 
G C 
0 P036
G C 
G C 
0 P037
C A 
G C 
0 P038
G C 
G C 
0 P039
C A 
G C 
0 P040
C A 
G C 
0 P041
G C 
G C 
0 P042
C A 
C A 
0 P043
C A 
G C 
0 P044
G C 
G C 
0 P045
C A 
G C 
0 P046
C A 
G C 
0 P047
C A 
G C 
0 P048
C A 
C A 
0 P049
G C 
G C 
0 P050
C A 
G C 
0 P051
C A 
G C 
0 P052
C A 
C A 
0 P053
C A 
C A 
0 P054
C A 
G C 
0 P055
G C 
G C 
0 P056
C A 
C A 
0 P057
C A 
G C 
0 P058
G C 
G C 
0 P059
C A 
C A 
0 P060
C A 
G C 
0 P061
G C 
G C 
0 P062
C A 
G C 
0 P063
C A 
G C 
0 P064
C A 
G C 
0 P065
C A 
C A 
0 P066
C A 
C A 
0 P067
C A 
C A 
0 P068
C A 
G C 
0 P069
C A 
G C 
0 P070
C A 
G C 
0 P071
C A 
G C 
0 P072
C A 
C A 
0 P073
G C 
G C 
0 P074
C A 
G C 
0 P075
C A 
G C 
0 P076
G C 
G C 
0 P077
C A 
C A 
0 P078
C A 
G C 
0 P079
C A 
C A 
0 P080
C A 
G C 
0 P081
C A 
G C 
0 P082
C A 
C A 
0 P083
C A 
G C 
0 P084
C A 
G C 
0 P085
G C 
G C 
0 P086
C A 
C A 
0 P087
C A 
C A 
0 P088
C A 
G C 
0 P089
C A 
G C 
0 P090
C A 
C 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
C ? 
G ? 
0 P002
? = 
? = 
0 P003
= = 
= = 
0 P004
? A 
? C 
0 P005
C A 
G C 
0 P006
C ? 
G ? 
0 P007
= = 
= = 
0 P008
= = 
= = 
0 P009
= = 
= = 
0 P010
= = 
= = 
0 P011
= ? 
= ? 
0 P012
C A 
G C 
0 P013
C A 
G C 
0 P014
C A 
G C 
0 P015
C A 
G C 
0 P016
= = 
= = 
0 P017
= = 
= = 
0 P018
C A 
G C 
0 P019
C A 
G C 
0 P020
= = 
= = 
0 P021
C A 
G C 
0 P022
= ? 
= ? 
0 P023
C A 
G C 
0 P024
C A 
G C 
0 P025
= ? 
= ? 
0 P026
C A 
G C 
0 P027
= = 
= = 
0 P028
C A 
G C 
0 P029
= = 
= = 
0 P030
C A 
G C 
0 P031
C A 
G C 
0 P032
= = 
= = 
0 P033
= = 
= = 
0 P034
C A 
G C 
0 P035
? A 
? C 
0 P036
= = 
= = 
0 P037
C A 
G C 
0 P038
= = 
= = 
0 P039
C A 
G C 
0 P040
C A 
G C 
0 P041
= = 
= = 
0 P042
= = 
= = 
0 P043
C A 
G C 
0 P044
= ? 
= ? 
0 P045
C A 
G C 
0 P046
C A 
G C 
0 P047
C A 
G C 
0 P048
= = 
= = 
0 P049
= = 
= = 
0 P050
C A 
G C 
0 P051
C A 
G C 
0 P052
= = 
= = 
0 P053
= = 
= = 
0 P054
C A 
G C 
0 P055
= = 
= = 
0 P056
= = 
= = 
0 P057
C A 
G C 
0 P058
= = 
= = 
0 P059
= = 
= = 
0 P060
C A 
G C 
0 P061
= = 
= = 
0 P062
C A 
G C 
0 P063
C A 
G C 
0 P064
C A 
G C 
0 P065
= = 
= = 
0 P066
= = 
= = 
0 P067
= = 
= = 
0 P068
C A 
G C 
0 P069
C A 
G C 
0 P070
C A 
G C 
0 P071
C A 
G C 
0 P072
= = 
= = 
0 P073
= = 
= = 
0 P074
C A 
G C 
0 P075
C A 
G C 
0 P076
= = 
= = 
0 P077
= = 
= = 
0 P078
C A 
G C 
0 P079
= = 
= = 
0 P080
C A 
G C 
0 P081
C A 
G C 
0 P082
= = 
= = 
0 P083
C A 
G C 
0 P084
C A 
G C 
0 P085
= = 
= = 
0 P086
= = 
= = 
0 P087
= = 
= = 
0 P088
C A 
G C 
0 P089
C A 
G 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 
= = 
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