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

BEGIN COMMAND_LINE 
/usr/local/genome/lib/phase/PHASE2 -d1 ddit3.phase.inp ddit3.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
ddit3.phase.out_freqs : haplotype frequency estimates
ddit3.phase.out_pairs : most likely haplotype pairs for each individual
ddit3.phase.out_recom : estimates of recombination parameters
ddit3.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 95
Number of Loci: 4
Positions of loci: 2958 3591 4046 4354 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file ddit3.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1        AICC    2.000000
         2        AICT    2.000000
         3        AITC  142.000000
         4        ADTC   11.000000
         5        GICC    4.000000
         6        GICT   28.000000
         7        GITC    1.000000
END LIST_SUMMARY


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

BEGIN BESTPAIRS_SUMMARY
D001: (3,6)
D002: (3,3)
D003: (6,6)
D004: (3,3)
D005: (3,6)
D006: (4,4)
D007: (3,3)
D008: (4,6)
D009: (3,6)
D010: (3,4)
D011: (3,4)
D012: (3,3)
D013: (3,4)
D014: (3,3)
D015: (1,2)
DY01: (4,6)
DY02: (3,6)
DY03: (3,4)
DY04: (3,5)
DY05: (3,3)
DY06: (4,6)
DY07: (3,4)
DY08: (1,2)
DY09: (3,3)
DY10: (3,3)
DY11: (4,6)
DY12: (3,6)
E101: (3,3)
E102: (3,3)
E103: (3,3)
E104: (3,3)
E105: (3,3)
E106: (3,3)
E107: (3,3)
E108: (3,6)
E109: (3,3)
E110: (3,3)
E111: (3,3)
E112: (3,3)
E113: (3,3)
E114: (3,3)
E115: (3,3)
E116: (3,6)
E117: (3,3)
E118: (3,3)
E119: (3,3)
E120: (6,6)
E121: (3,6)
E122: (3,3)
H101: (3,3)
H102: (3,3)
H103: (3,3)
H104: (3,3)
H105: (3,3)
H106: (3,3)
H107: (3,3)
H108: (3,3)
H109: (3,3)
H110: (3,3)
H111: (3,6)
H112: (3,6)
H113: (3,6)
H114: (3,6)
H115: (3,3)
H116: (3,3)
H117: (3,3)
H118: (3,3)
H119: (3,3)
H120: (3,3)
H121: (3,6)
H122: (3,3)
X101: (3,3)
X102: (3,6)
X103: (3,3)
X104: (3,6)
X105: (5,6)
X106: (3,5)
X107: (3,3)
X108: (3,3)
X109: (3,6)
X110: (3,7)
X111: (3,6)
X112: (3,6)
X113: (3,3)
X114: (3,3)
X115: (3,3)
X116: (3,6)
X117: (3,5)
X118: (3,3)
X119: (3,3)
X120: (3,3)
X121: (3,3)
X122: (3,3)
X123: (3,3)
X124: (3,3)
END BESTPAIRS_SUMMARY


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

BEGIN BESTPAIRS1
0 D001
(A) I T C 
(G) I C T 
0 D002
A I T C 
A I T C 
0 D003
G I C T 
G I C T 
0 D004
A I T C 
A I T C 
0 D005
(A) I T C 
(G) I C T 
0 D006
A D T C 
A D T C 
0 D007
A I T C 
A I T C 
0 D008
(A) (D) T C 
(G) (I) C T 
0 D009
(A) I T C 
(G) I C T 
0 D010
A I T C 
A D T C 
0 D011
A I T C 
A D T C 
0 D012
[A] I T C 
 A  I T C 
0 D013
A I T C 
A D T C 
0 D014
A I  T  C 
A I [T] C 
0 D015
A I C C 
A I C T 
0 DY01
(A) (D) T C 
(G) (I) C T 
0 DY02
(A) I T C 
(G) I C T 
0 DY03
A I T C 
A D T C 
0 DY04
(A) I T C 
(G) I C C 
0 DY05
A I T C 
A I T C 
0 DY06
(A) (D) T C 
(G) (I) C T 
0 DY07
A I T C 
A D T C 
0 DY08
A I C C 
A I C T 
0 DY09
A I T C 
A I T C 
0 DY10
A I T C 
A I T C 
0 DY11
(A) (D) T C 
(G) (I) C T 
0 DY12
(A) I T C 
(G) I C T 
0 E101
A I T C 
A I T C 
0 E102
A I T C 
A I T C 
0 E103
A I T C 
A I T C 
0 E104
[A] I T C 
 A  I T C 
0 E105
A I T C 
A I T C 
0 E106
A I T C 
A I T C 
0 E107
A I  T  C 
A I [T] C 
0 E108
(A) I T C 
(G) I C T 
0 E109
A I T C 
A I T C 
0 E110
A I T C 
A I T C 
0 E111
A I T C 
A I T C 
0 E112
A I T C 
A I T C 
0 E113
A I  T  C 
A I [T] C 
0 E114
A I T C 
A I T C 
0 E115
A I T C 
A I T C 
0 E116
(A) I T C 
(G) I C T 
0 E117
A I T C 
A I T C 
0 E118
A I T C 
A I T C 
0 E119
A I T C 
A I T C 
0 E120
G I C T 
G I C T 
0 E121
(A) I T C 
(G) I C T 
0 E122
A I T C 
A I T C 
0 H101
A I T C 
A I T C 
0 H102
A I T C 
A I T C 
0 H103
A I T C 
A I T C 
0 H104
A I T C 
A I T C 
0 H105
A I T C 
A I T C 
0 H106
A I T C 
A I T C 
0 H107
A I T C 
A I T C 
0 H108
A I T C 
A I T C 
0 H109
A I T C 
A I T C 
0 H110
A I T C 
A I T C 
0 H111
(A) I T C 
(G) I C T 
0 H112
(A) I T C 
(G) I C T 
0 H113
(A) I T C 
(G) I C T 
0 H114
(A) I T C 
(G) I C T 
0 H115
A I T C 
A I T C 
0 H116
A I T C 
A I T C 
0 H117
A I T C 
A I T C 
0 H118
A I T C 
A I T C 
0 H119
A I T C 
A I T C 
0 H120
A I T C 
A I T C 
0 H121
(A) I T C 
(G) I C T 
0 H122
A I T C 
A I T C 
0 X101
A I T C 
A I T C 
0 X102
(A) I T C 
(G) I C T 
0 X103
A I T C 
A I T C 
0 X104
(A) I T C 
(G) I C T 
0 X105
G I C C 
G I C T 
0 X106
(A) I T C 
(G) I C C 
0 X107
A I T C 
A I T C 
0 X108
A I T C 
A I T C 
0 X109
(A) I T C 
(G) I C T 
0 X110
A I T C 
G I T C 
0 X111
(A) I T C 
(G) I C T 
0 X112
(A) I T C 
(G) I C T 
0 X113
A I T C 
A I T C 
0 X114
A I T C 
A I T C 
0 X115
A I T C 
A I T C 
0 X116
(A) I T C 
(G) I C T 
0 X117
(A) I T C 
(G) I C C 
0 X118
A I T C 
A I T C 
0 X119
A I T C 
A I T C 
0 X120
A I T C 
A I T C 
0 X121
A I T C 
A I T C 
0 X122
A I T C 
A I T C 
0 X123
A I T C 
A I T C 
0 X124
A I T C 
A I 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 D001
(A) = T C 
(G) = C T 
0 D002
= = = = 
= = = = 
0 D003
= = = = 
= = = = 
0 D004
= = = = 
= = = = 
0 D005
(A) = T C 
(G) = C T 
0 D006
= = = = 
= = = = 
0 D007
= = = = 
= = = = 
0 D008
(A) (D) T C 
(G) (I) C T 
0 D009
(A) = T C 
(G) = C T 
0 D010
= I = = 
= D = = 
0 D011
= I = = 
= D = = 
0 D012
? = = = 
? = = = 
0 D013
? I = = 
? D = = 
0 D014
= = ? = 
= = ? = 
0 D015
? = = C 
? = = T 
0 DY01
(A) (D) T C 
(G) (I) C T 
0 DY02
(A) = T C 
(G) = C T 
0 DY03
= I = = 
= D = = 
0 DY04
(A) = T = 
(G) = C = 
0 DY05
= = = = 
= = = = 
0 DY06
(A) (D) T C 
(G) (I) C T 
0 DY07
= I = = 
= D = = 
0 DY08
? = = C 
? = = T 
0 DY09
= = = ? 
= = = ? 
0 DY10
= = = = 
= = = = 
0 DY11
(A) (D) T C 
(G) (I) C T 
0 DY12
(A) = T C 
(G) = C T 
0 E101
= = = = 
= = = = 
0 E102
= = = = 
= = = = 
0 E103
= = = = 
= = = = 
0 E104
? = = = 
? = = = 
0 E105
= = = = 
= = = = 
0 E106
= = = = 
= = = = 
0 E107
= = ? = 
= = ? = 
0 E108
(A) = T C 
(G) = C T 
0 E109
= = = = 
= = = = 
0 E110
= = = = 
= = = = 
0 E111
= = = = 
= = = = 
0 E112
= = = = 
= = = = 
0 E113
= = ? ? 
= = ? ? 
0 E114
= = = = 
= = = = 
0 E115
= = = = 
= = = = 
0 E116
(A) = T C 
(G) = C T 
0 E117
= = = = 
= = = = 
0 E118
= = = = 
= = = = 
0 E119
= = = = 
= = = = 
0 E120
= = = = 
= = = = 
0 E121
(A) = T C 
(G) = C T 
0 E122
= = = = 
= = = = 
0 H101
= = = = 
= = = = 
0 H102
= = = = 
= = = = 
0 H103
= = = = 
= = = = 
0 H104
= = = = 
= = = = 
0 H105
= = = = 
= = = = 
0 H106
= = = = 
= = = = 
0 H107
? = ? = 
? = ? = 
0 H108
= = = = 
= = = = 
0 H109
= = = = 
= = = = 
0 H110
= = = = 
= = = = 
0 H111
(A) = T C 
(G) = C T 
0 H112
(A) = T C 
(G) = C T 
0 H113
(A) = T C 
(G) = C T 
0 H114
(A) = T C 
(G) = C T 
0 H115
= = = = 
= = = = 
0 H116
= = = = 
= = = = 
0 H117
= = = = 
= = = = 
0 H118
= = = = 
= = = = 
0 H119
= = = = 
= = = = 
0 H120
= = = = 
= = = = 
0 H121
(A) = T C 
(G) = C T 
0 H122
= = = = 
= = = = 
0 X101
= = = = 
= = = = 
0 X102
(A) = T C 
(G) = C T 
0 X103
= = = = 
= = = = 
0 X104
(A) = T C 
(G) = C T 
0 X105
= = = C 
= = = T 
0 X106
(A) = T = 
(G) = C = 
0 X107
= = = = 
= = = = 
0 X108
= = ? = 
= = ? = 
0 X109
(A) = T C 
(G) = C T 
0 X110
A = = = 
G = = = 
0 X111
(A) = T C 
(G) = C T 
0 X112
(A) = T C 
(G) = C T 
0 X113
= = = = 
= = = = 
0 X114
= = = = 
= = = = 
0 X115
= = = = 
= = = = 
0 X116
(A) = T C 
(G) = C T 
0 X117
(A) = T = 
(G) = C = 
0 X118
= = = = 
= = = = 
0 X119
= = = = 
= = = = 
0 X120
= = = = 
= = = = 
0 X121
= = = = 
= = = = 
0 X122
= = = = 
= = = = 
0 X123
= = = = 
= = = = 
0 X124
= = = = 
= = = = 
END BESTPAIRS2


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

BEGIN PHASEPROBS
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
0.56 = 0.99 0.99 
= = = = 
= = = = 
0.55 0.53 0.99 0.99 
0.56 = 0.99 0.99 
= 1.00 = = 
= 1.00 = = 
? = = = 
? 1.00 = = 
= = ? = 
? = = 1.00 
0.55 0.52 0.99 0.99 
0.56 = 0.99 0.99 
= 1.00 = = 
0.54 = 1.00 = 
= = = = 
0.55 0.53 0.99 0.99 
= 1.00 = = 
? = = 1.00 
= = = ? 
= = = = 
0.55 0.53 0.99 0.99 
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
? = = = 
= = = = 
= = = = 
= = ? = 
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = ? ? 
= = = = 
= = = = 
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
? = ? = 
= = = = 
= = = = 
= = = = 
0.56 = 0.99 0.99 
0.56 = 0.99 0.99 
0.56 = 0.99 0.99 
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
0.56 = 0.99 0.99 
= = = = 
= = = = 
0.56 = 0.99 0.99 
= = = = 
0.56 = 0.99 0.99 
= = = 1.00 
0.54 = 1.00 = 
= = = = 
= = ? = 
0.56 = 0.99 0.99 
1.00 = = = 
0.56 = 0.99 0.99 
0.56 = 0.99 0.99 
= = = = 
= = = = 
= = = = 
0.56 = 0.99 0.99 
0.54 = 1.00 = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
= = = = 
END PHASEPROBS