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

BEGIN COMMAND_LINE 
/home/qyi/lib/phase/PHASE2 -d1 tradd.phase.inp tradd.phase.out 
END COMMAND_LINE 

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

BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 11
Positions of loci: 316 887 3878 4058 5609 5796 5799 7584 7826 8562 8845 
END INPUT_SUMMARY

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

BEGIN LIST_SUMMARY
         1 CCITCGCATCD    1.000000
         2 CCITGGCATCD   13.000000
         3 CCITGGCACCD    1.000000
         4 CCITGGCACCI    2.000000
         5 CCICGGAATCD    2.000000
         6 CCDTCGCATCD    5.000000
         7 CCDTCGCATCI    2.000000
         8 CCDTCGAATCD    1.000000
         9 CCDTGGCATCD    1.000000
        10 CCDTGGCATCI   49.000000
        11 CCDTGGCATAI    5.000000
        12 CCDCGGCATCI    1.000000
        13 CTITGCCATCD    6.000000
        14 TCITGGCTTCD    5.000000
END LIST_SUMMARY


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

BEGIN BESTPAIRS_SUMMARY
D001: (2,6)
D002: (2,10)
D003: (10,14)
D004: (6,8)
D005: (2,2)
D006: (4,6)
D007: (10,10)
D008: (6,10)
D009: (1,13)
D010: (2,13)
D011: (2,10)
D012: (10,13)
D013: (10,13)
D014: (10,13)
D015: (10,10)
D016: (6,14)
D033: (10,10)
D034: (2,2)
D035: (9,13)
D036: (2,5)
D037: (4,10)
D038: (10,14)
D039: (3,10)
D040: (14,14)
E001: (10,11)
E002: (5,12)
E003: (10,10)
E004: (10,11)
E005: (10,10)
E006: (10,10)
E007: (7,10)
E008: (11,11)
E009: (7,10)
E010: (10,10)
E011: (10,10)
E012: (10,10)
E013: (10,10)
E014: (10,10)
E015: (10,10)
E016: (10,10)
E017: (10,10)
E018: (2,10)
E019: (10,11)
E020: (2,10)
E021: (2,10)
E022: (10,10)
E023: (2,10)
END BESTPAIRS_SUMMARY


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

BEGIN BESTPAIRS1
0 D001
C C I T G G C A T C D 
C C D T C G C A T C D 
0 D002
C C I T G G C A T C D 
C C D T G G C A T C I 
0 D003
C C D T G G C A T C I 
T C I T G G C T T C D 
0 D004
C C D T [C] G C A T C D 
C C D T [C] G A A T C D 
0 D005
C C I T G G C A T C D 
C C I T G G C A T C D 
0 D006
C C (I) T G G C A C C (I) 
C C (D) T C G C A T C (D) 
0 D007
C C D T G G C A T C I 
C C D T G G C A T C I 
0 D008
C C D T C G C A T C D 
C C D T G G C A T C I 
0 D009
C C I T (C) G C A T C D 
C T I T (G) C C A T C D 
0 D010
C C I T G G C A T C D 
C T I T G C C A T C D 
0 D011
C C I T G G C A T C D 
C C D T G G C A T C I 
0 D012
C C D T G G C A T C I 
C T I T G C C A T C D 
0 D013
C C D T G G C A T C I 
C T I T G C C A T C D 
0 D014
C C D T G G C A T C I 
C T I T G C C A T C D 
0 D015
C C D T  G  G C A T C I 
C C D T [G] G C A T C I 
0 D016
C C D T C G C A T C D 
T C I T G G C T T C D 
0 D033
C C D T G G C A T C I 
C C D T G G C A T C I 
0 D034
C C I T G G C A T C D 
C C I T G G C A T C D 
0 D035
C C D T G G C A T C D 
C T I T G C C A T C D 
0 D036
C C I T G G C A T C D 
C C I C G G A A T C D 
0 D037
C C I T G G C A C C I 
C C D T G G C A T C I 
0 D038
C C D T G G C A T C I 
T C I T G G C T T C D 
0 D039
C C I T G G C A (C) C (D) 
C C D T G G C A (T) C (I) 
0 D040
T C I T G G C T T C D 
T C I T G G C T T C D 
0 E001
C C D T G G C A T C I 
C C D T G G C A T A I 
0 E002
C C I C G G A A T C D 
C C D C G G C A T C I 
0 E003
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E004
C C D T G G C A T C I 
C C D T G G C A T A I 
0 E005
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E006
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E007
C C D T C G C A T C I 
C C D T G G C A T C I 
0 E008
C C D T G G C A T A I 
C C D T G G C A T A I 
0 E009
C C D T C G C A T C I 
C C D T G G C A T C I 
0 E010
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E011
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E012
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E013
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E014
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E015
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E016
C C D T  G  G C A T C I 
C C D T [G] G C A T C I 
0 E017
C C D T  G  G C A T C I 
C C D T [G] G C A T C I 
0 E018
C C I T G G C A T C D 
C C D T G G C A T C I 
0 E019
C C D T G G C A T C I 
C C D T G G C A T A I 
0 E020
C C I T G G C A T C D 
C C D T G G C A T C I 
0 E021
C C I T G G C A T C D 
C C D T G G C A T C I 
0 E022
C C D T G G C A T C I 
C C D T G G C A T C I 
0 E023
C C I T G G C A T C D 
C C D T G G C A T C I 
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
= = I ? G = = = = = = 
= = D ? C = = = = = = 
0 D002
= = I ? ? ? ? ? ? = D 
= = D ? ? ? ? ? ? = I 
0 D003
C = D = = = = A = = I 
T = I = = = = T = = D 
0 D004
= = = = ? = C = = = = 
= = = = ? = A = = = = 
0 D005
= = = = = = = ? ? = = 
= = = = = = = ? ? = = 
0 D006
= = (I) = G = = = C = (I) 
= = (D) = C = = = T = (D) 
0 D007
= = = = = = = = = = = 
= = = = = = = = = = = 
0 D008
= = = = C = = = = = D 
= = = = G = = = = = I 
0 D009
= C = = (C) G = = = = = 
= T = = (G) C = = = = = 
0 D010
= C = = = G = = = = = 
= T = = = C = = = = = 
0 D011
= = I = = = = = = = D 
= = D = = = = = = = I 
0 D012
= C D ? = G = = = = I 
= T I ? = C = = = = D 
0 D013
= C D = = G = = = = I 
= T I = = C = = = = D 
0 D014
= C D = = G = = ? = I 
= T I = = C = = ? = D 
0 D015
= = = = ? = = = = = = 
= = = = ? = = = = = = 
0 D016
C = D = C = = A = = = 
T = I = G = = T = = = 
0 D033
= = = = ? = = = ? = = 
= = = = ? = = = ? = = 
0 D034
= = ? = = ? ? ? ? = = 
= = ? = = ? ? ? ? = = 
0 D035
= C D = = G = = = = = 
= T I = = C = = = = = 
0 D036
= = = T = = C = = = = 
= = = C = = A = = = = 
0 D037
= = I ? ? = = = C = = 
= = D ? ? = = = T = = 
0 D038
C = D = = = = A = = I 
T = I = = = = T = = D 
0 D039
= = I = = ? ? = (C) = (D) 
= = D = = ? ? = (T) = (I) 
0 D040
= = = = ? ? ? = = = = 
= = = = ? ? ? = = = = 
0 E001
= = = = = = = = = C = 
= = = = = = = = = A = 
0 E002
= = I = = = A = ? = D 
= = D = = = C = ? = I 
0 E003
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E004
= = = = = = = = = C = 
= = = = = = = = = A = 
0 E005
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E006
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E007
= = ? ? C = = = = = = 
= = ? ? G = = = = = = 
0 E008
= = = = ? = = ? ? = = 
= = = = ? = = ? ? = = 
0 E009
= = = ? C = = = = = = 
= = = ? G = = = = = = 
0 E010
= = = ? = = = ? = = = 
= = = ? = = = ? = = = 
0 E011
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E012
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E013
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E014
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E015
= = ? ? = = = = = = = 
= = ? ? = = = = = = = 
0 E016
= = = = ? ? ? = ? = = 
= = = = ? ? ? = ? = = 
0 E017
? = = = ? = = = = = = 
? = = = ? = = = = = = 
0 E018
= = I ? = = = ? = = D 
= = D ? = = = ? = = I 
0 E019
= = = = = = = = = C = 
= = = = = = = = = A = 
0 E020
= = I = = = = = = = D 
= = D = = = = = = = I 
0 E021
= = I = = = = ? = = D 
= = D = = = = ? = = I 
0 E022
= = = = = = = = = = = 
= = = = = = = = = = = 
0 E023
= = I = = = = = = = D 
= = D = = = = = = = I 
END BESTPAIRS2


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

BEGIN PHASEPROBS
= = 0.97 ? 1.00 = = = = = = 
= = 0.98 ? ? ? ? ? ? = 1.00 
1.00 = 1.00 = = = = 1.00 = = 1.00 
= = = = ? = 1.00 = = = = 
= = = = = = = ? ? = = 
= = 0.88 = 0.97 = = = 0.98 = 0.83 
= = = = = = = = = = = 
= = = = 0.97 = = = = = 1.00 
= 1.00 = = 0.62 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 0.90 = = 1.00 = = = = = 
= = = 1.00 = = 1.00 = = = = 
= = 0.94 ? ? = = = 1.00 = = 
1.00 = 1.00 = = = = 1.00 = = 1.00 
= = 1.00 = = ? ? = 0.78 = 0.66 
= = = = ? ? ? = = = = 
= = = = = = = = = 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