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

BEGIN COMMAND_LINE 
/usr/local/genome/lib/phase/PHASE2 -d1 pax1x.phase.inp pax1x.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
pax1x.phase.out_freqs : haplotype frequency estimates
pax1x.phase.out_pairs : most likely haplotype pairs for each individual
pax1x.phase.out_recom : estimates of recombination parameters
pax1x.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 4
Positions of loci: 3907 5221 7769 8509 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file pax1x.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1        CTTT  154.000000
         2        CTTA    7.000000
         3        CTCA    1.000000
         4        CATA    2.000000
         5        ATTA    1.000000
         6        AATA    5.000000
         7        AACT    1.000000
         8        AACA    9.000000
END LIST_SUMMARY


Summary of best reconstruction
(numbers refer to the list of haplotypes given above)

BEGIN BESTPAIRS_SUMMARY
P001: (1,1)
P002: (1,1)
P003: (2,6)
P004: (1,1)
P005: (1,1)
P006: (1,1)
P007: (1,1)
P008: (1,1)
P009: (1,1)
P010: (1,1)
P011: (1,1)
P012: (1,1)
P013: (1,1)
P014: (1,1)
P015: (1,1)
P016: (1,7)
P017: (1,6)
P018: (1,1)
P019: (1,1)
P020: (1,1)
P021: (1,1)
P022: (1,2)
P023: (1,6)
P024: (1,1)
P025: (1,1)
P026: (1,1)
P027: (1,1)
P028: (1,1)
P029: (1,6)
P030: (1,1)
P031: (1,1)
P032: (1,1)
P033: (1,1)
P034: (1,1)
P035: (8,8)
P036: (1,8)
P037: (1,3)
P038: (1,2)
P039: (1,1)
P040: (1,1)
P041: (1,6)
P042: (1,1)
P043: (1,1)
P044: (1,1)
P045: (1,8)
P046: (1,1)
P047: (1,1)
P048: (1,1)
P049: (1,1)
P050: (1,1)
P051: (1,1)
P052: (1,1)
P053: (1,1)
P054: (1,1)
P055: (1,1)
P056: (1,1)
P057: (1,4)
P058: (1,1)
P059: (1,1)
P060: (1,1)
P061: (1,4)
P062: (1,1)
P063: (1,1)
P064: (1,2)
P065: (1,5)
P066: (1,8)
P067: (1,1)
P068: (1,1)
P069: (1,1)
P070: (1,1)
P071: (1,8)
P072: (8,8)
P073: (1,1)
P074: (1,1)
P075: (1,8)
P076: (1,1)
P077: (1,1)
P078: (1,1)
P079: (1,1)
P080: (1,2)
P081: (1,1)
P082: (1,1)
P083: (1,1)
P084: (1,1)
P085: (1,1)
P086: (1,1)
P087: (1,2)
P088: (1,1)
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 T T T 
C T T T 
0 P002
C T T T 
C T T T 
0 P003
 C   T  T A 
[A] [A] T A 
0 P004
C T T T 
C T T T 
0 P005
C T T T 
C T T T 
0 P006
C T T T 
C T T T 
0 P007
C T T T 
C T T T 
0 P008
C T T T 
C T T T 
0 P009
C T T T 
C T T T 
0 P010
C T T T 
C T T T 
0 P011
C T T T 
C T T T 
0 P012
C T T T 
C T T T 
0 P013
C T T T 
C T T T 
0 P014
C T T T 
C T T T 
0 P015
C T T T 
C T T T 
0 P016
C T T T 
A A C T 
0 P017
C T T T 
A A T A 
0 P018
C T T T 
C T T T 
0 P019
C T T T 
C T T T 
0 P020
C T T T 
C T T T 
0 P021
C T T T 
C T T T 
0 P022
C T T T 
C T T A 
0 P023
C T T T 
A A T A 
0 P024
C T T T 
C T T T 
0 P025
C T T T 
C T T T 
0 P026
C T T T 
C T T T 
0 P027
C T T T 
C T T T 
0 P028
C T T T 
C T T T 
0 P029
C T T T 
A A T A 
0 P030
C T T T 
C T T T 
0 P031
C T T T 
C T T T 
0 P032
C T T T 
C T T T 
0 P033
C T T T 
C T T T 
0 P034
C T T T 
C T T T 
0 P035
A A C A 
A A C A 
0 P036
C T T T 
A A C A 
0 P037
C T T T 
C T C A 
0 P038
C T T T 
C T T A 
0 P039
C T T T 
C T T T 
0 P040
C T T T 
C T T T 
0 P041
C T T T 
A A T A 
0 P042
C T T T 
C T T T 
0 P043
C T T T 
C T T T 
0 P044
C T T T 
C T T T 
0 P045
C T T T 
A A C A 
0 P046
C T T T 
C T T T 
0 P047
C T T T 
C T T T 
0 P048
C T T T 
C T T T 
0 P049
C T T T 
C T T T 
0 P050
C T T T 
C T T T 
0 P051
C T T T 
C T T T 
0 P052
C T T T 
C T T T 
0 P053
C T T T 
C T T T 
0 P054
C T T T 
C T T T 
0 P055
C T T T 
C T T T 
0 P056
C T T T 
C T T T 
0 P057
C T T T 
C A T A 
0 P058
C T T T 
C T T T 
0 P059
C T T T 
C T T T 
0 P060
C T T T 
C T T T 
0 P061
C T T T 
C A T A 
0 P062
C T T T 
C T T T 
0 P063
C T T T 
C T T T 
0 P064
C T T T 
C T T A 
0 P065
(C) T T T 
(A) T T A 
0 P066
C T T T 
A A C A 
0 P067
C T T T 
C T T T 
0 P068
C T T T 
C T T T 
0 P069
C T T T 
C T T T 
0 P070
C T T T 
C T T T 
0 P071
C T T T 
A A C A 
0 P072
A A C A 
A A C A 
0 P073
C T T T 
C T T T 
0 P074
C T T T 
C T T T 
0 P075
C T T T 
A A C A 
0 P076
C T T T 
C T T T 
0 P077
C T T T 
C T T T 
0 P078
C T T T 
C T T T 
0 P079
C T T T 
C T T T 
0 P080
C T T T 
C T T A 
0 P081
C T T T 
C T T T 
0 P082
C T T T 
C T T T 
0 P083
C T T T 
C T T T 
0 P084
C T T T 
C T T T 
0 P085
C T T T 
C T T T 
0 P086
C T T T 
C T T T 
0 P087
 C   T  T T 
[C] [T] T A 
0 P088
C T T T 
C T T T 
0 P089
C T T T 
C T T A 
0 P090
C T T T 
C T 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
= ? = = 
= ? = = 
0 P002
= ? = = 
= ? = = 
0 P003
? ? = = 
? ? = = 
0 P004
? ? = = 
? ? = = 
0 P005
? ? = = 
? ? = = 
0 P006
? ? = = 
? ? = = 
0 P007
= ? = = 
= ? = = 
0 P008
= ? = = 
= ? = = 
0 P009
= = = = 
= = = = 
0 P010
= = = = 
= = = = 
0 P011
= = = = 
= = = = 
0 P012
= = = = 
= = = = 
0 P013
= = = = 
= = = = 
0 P014
? = = = 
? = = = 
0 P015
= ? = = 
= ? = = 
0 P016
C ? T = 
A ? C = 
0 P017
C T = T 
A A = A 
0 P018
= = = = 
= = = = 
0 P019
= = = = 
= = = = 
0 P020
= = = = 
= = = = 
0 P021
= = = = 
= = = = 
0 P022
= = = T 
= = = A 
0 P023
C T = T 
A A = A 
0 P024
= = = = 
= = = = 
0 P025
= = = = 
= = = = 
0 P026
= = = = 
= = = = 
0 P027
= = = = 
= = = = 
0 P028
= = = = 
= = = = 
0 P029
C T = T 
A A = A 
0 P030
= = = = 
= = = = 
0 P031
= = = = 
= = = = 
0 P032
= = = = 
= = = = 
0 P033
= = = = 
= = = = 
0 P034
= = = = 
= = = = 
0 P035
= = = = 
= = = = 
0 P036
C T T T 
A A C A 
0 P037
= = T T 
= = C A 
0 P038
= = = T 
= = = A 
0 P039
= = = = 
= = = = 
0 P040
= = = = 
= = = = 
0 P041
C T = T 
A A = A 
0 P042
= = = = 
= = = = 
0 P043
= = = = 
= = = = 
0 P044
= = = = 
= = = = 
0 P045
C T T T 
A A C A 
0 P046
= = = = 
= = = = 
0 P047
= = = = 
= = = = 
0 P048
= = = = 
= = = = 
0 P049
= = = = 
= = = = 
0 P050
= = = = 
= = = = 
0 P051
= = = = 
= = = = 
0 P052
= = = = 
= = = = 
0 P053
= = = = 
= = = = 
0 P054
= = = = 
= = = = 
0 P055
= = = = 
= = = = 
0 P056
= = = = 
= = = = 
0 P057
= T = T 
= A = A 
0 P058
= = = = 
= = = = 
0 P059
= = = = 
= = = = 
0 P060
= = = = 
= = = = 
0 P061
= T = T 
= A = A 
0 P062
= = = = 
= = = = 
0 P063
= = = = 
= = = = 
0 P064
= = = T 
= = = A 
0 P065
(C) = = T 
(A) = = A 
0 P066
C T T T 
A A C A 
0 P067
= = = = 
= = = = 
0 P068
= = = = 
= = = = 
0 P069
= = = = 
= = = = 
0 P070
= = = = 
= = = = 
0 P071
C T T T 
A A C A 
0 P072
= = = = 
= = = = 
0 P073
= ? = = 
= ? = = 
0 P074
= = = = 
= = = = 
0 P075
C T T T 
A A C A 
0 P076
= = = = 
= = = = 
0 P077
= = = = 
= = = = 
0 P078
= = = = 
= = = = 
0 P079
? = = = 
? = = = 
0 P080
= ? = T 
= ? = A 
0 P081
= ? = = 
= ? = = 
0 P082
= = = = 
= = = = 
0 P083
= = = = 
= = = = 
0 P084
= = = = 
= = = = 
0 P085
= = = = 
= = = = 
0 P086
= = = = 
= = = = 
0 P087
? ? = T 
? ? = A 
0 P088
= ? = = 
= ? = = 
0 P089
= ? = T 
= ? = A 
0 P090
= ? = = 
= ? = = 
END BESTPAIRS2


Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?

BEGIN PHASEPROBS
= ? = = 
= ? = = 
? ? = = 
? ? = = 
? ? = = 
? ? = = 
= ? = = 
= ? = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
? = = = 
= ? = = 
0.97 ? 0.99 = 
1.00 1.00 = 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = = 1.00 
0.99 1.00 = 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
1.00 1.00 = 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
1.00 1.00 1.00 0.99 
= = 0.93 1.00 
= = = 1.00 
= = = = 
= = = = 
0.99 1.00 = 0.99 
= = = = 
= = = = 
= = = = 
1.00 1.00 1.00 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= 0.97 = 1.00 
= = = = 
= = = = 
= = = = 
= 0.98 = 1.00 
= = = = 
= = = = 
= = = 1.00 
0.55 = = 1.00 
1.00 1.00 1.00 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
1.00 1.00 1.00 0.99 
= = = = 
= ? = = 
= = = = 
1.00 1.00 1.00 0.99 
= = = = 
= = = = 
= = = = 
? = = = 
= ? = 1.00 
= ? = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
? ? = 1.00 
= ? = = 
= ? = 1.00 
= ? = = 
END PHASEPROBS