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

BEGIN COMMAND_LINE 
/home/qyi/lib/phase/PHASE2 -d1 ilkn3.phase.inp ilkn3.phase.out 
END COMMAND_LINE 

BEGIN OUTFILE_LIST
ilkn3.phase.out_freqs : haplotype frequency estimates
ilkn3.phase.out_pairs : most likely haplotype pairs for each individual
ilkn3.phase.out_recom : estimates of recombination parameters
ilkn3.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST

BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 8
Positions of loci: 627 1219 1844 1990 2714 3406 5295 5947 
END INPUT_SUMMARY

List of haplotypes found in best reconstruction, with counts.
(See file ilkn3.phase.out_freqs for haplotype population frequency estimates)

BEGIN LIST_SUMMARY
         1    GTCCGCAC   24.000000
         2    GTCCGCAT   34.000000
         3    GTCCACAT    1.000000
         4    GTCTGCAC    1.000000
         5    GTCTGCAT    3.000000
         6    GTCTGCGT    1.000000
         7    GTCTACAC    1.000000
         8    GTCTACAT    3.000000
         9    GTTTGCAT    2.000000
        10    GTTTACAT   10.000000
        11    GCCTGGAC    1.000000
        12    GCCTGGAT    2.000000
        13    GCCTGGGC    5.000000
        14    ATTTACAT    6.000000
END LIST_SUMMARY


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

BEGIN BESTPAIRS_SUMMARY
D001: (1,2)
D002: (2,2)
D003: (1,11)
D004: (1,4)
D005: (2,8)
D006: (1,2)
D007: (1,2)
D008: (2,12)
D009: (5,13)
D010: (7,13)
D011: (2,8)
D012: (2,2)
D013: (2,14)
D014: (2,14)
D015: (12,13)
D016: (2,14)
D033: (2,5)
D034: (13,13)
D035: (2,2)
D036: (2,6)
D037: (2,10)
D038: (1,8)
D039: (5,10)
D040: (2,10)
E001: (1,10)
E002: (2,9)
E003: (1,2)
E004: (1,2)
E005: (10,14)
E006: (2,2)
E007: (1,2)
E008: (2,10)
E009: (10,14)
E010: (1,2)
E011: (1,1)
E012: (3,14)
E013: (2,9)
E014: (1,2)
E015: (1,1)
E016: (1,2)
E017: (1,10)
E018: (1,10)
E019: (1,1)
E020: (1,2)
E021: (1,2)
E022: (1,2)
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
G T C C G C A C 
G T C C G C A T 
0 D002
G T C C G C A T 
G T C C G C A T 
0 D003
G T C C G C A C 
G C C T G G A C 
0 D004
G T C C G C A C 
G T C T G C A C 
0 D005
G T C (C) G C A T 
G T C (T) A C A T 
0 D006
G T C C G C A C 
G T C C G C A T 
0 D007
G T C C G C A C 
G T C C G C A T 
0 D008
G T C C G C A T 
G C C T G G A T 
0 D009
G T C T G C A T 
G C C T G G G C 
0 D010
G T C T A C A C 
G C C T G G G C 
0 D011
G T C (C) G C A T 
G T C (T) A C A T 
0 D012
G T C C G C A T 
G T C C G C A T 
0 D013
G T C C G C A T 
A T T T A C A T 
0 D014
G T C C G C A T 
A T T T A C A T 
0 D015
G C C T G G  A  T 
G C C T G G [G] C 
0 D016
G T C C G C A T 
A T T T A C A T 
0 D033
G T C C G C A T 
G T C T G C A T 
0 D034
G C C T G G G C 
G C C T G G G C 
0 D035
G T C C G C A T 
G T C C G C A T 
0 D036
G T C (C) G C A T 
G T C (T) G C G T 
0 D037
G T C C G C A T 
G T T T A C A T 
0 D038
G T C C G C A (C) 
G T C T A C A (T) 
0 D039
G T (C) T G C A [T] 
G T (T) T A C A [T] 
0 D040
G T C C  G  C A T 
G T T T [A] C A T 
0 E001
G T C C G C A (C) 
G T T T A C A (T) 
0 E002
G T C C G C A [T] 
G T T T G C A [T] 
0 E003
G T C C G C A C 
G T C C G C A T 
0 E004
G T C C G C A C 
G T C C G C A T 
0 E005
G T T T A C A T 
A T T T A C A T 
0 E006
G T C C G C A T 
G T C C G C A T 
0 E007
G T C C G C A C 
G T C C G C A T 
0 E008
G T C C G C A T 
G T T T A C A T 
0 E009
G T T T A C A T 
A T T T A C A T 
0 E010
G T C C G C A C 
G T C C G C A T 
0 E011
G T C C G C A C 
G T C C G C A C 
0 E012
G T C C A C A T 
A T T T A C A T 
0 E013
G T C C G C A T 
G T T T G C A T 
0 E014
G T C C G C A C 
G T C C G C A T 
0 E015
G T C C G C A C 
G T C C G C A C 
0 E016
G T C C G C A C 
G T C C G C A T 
0 E017
G T C C G C A (C) 
G T T T A C A (T) 
0 E018
G T C C G C A (C) 
G T T T A C A (T) 
0 E019
G T C C G C A C 
G T C C G C A C 
0 E020
G T C C G C A C 
G T C C G C A T 
0 E021
G T C C G C A C 
G T C C G C A T 
0 E022
G T C C G C A C 
G T C C G C A T 
0 E023
G T C C G C A T 
G T T T A C A 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 D001
= = = = = = = C 
= = = = = = = T 
0 D002
= = = = = = = = 
= = = = = = = = 
0 D003
= T = C = C = = 
= C = T = G = = 
0 D004
= = = C = = = = 
= = = T = = = = 
0 D005
= = = (C) G = = = 
= = = (T) A = = = 
0 D006
= = = = = = = C 
= = = = = = = T 
0 D007
= = = = = = = C 
= = = = = = = T 
0 D008
= T = C = C = = 
= C = T = G = = 
0 D009
= T = = = C A T 
= C = = = G G C 
0 D010
= T = = A C A = 
= C = = G G G = 
0 D011
= = = (C) G = = = 
= = = (T) A = = = 
0 D012
= = = = = = = = 
= = = = = = = = 
0 D013
G = C C G = ? = 
A = T T A = ? = 
0 D014
G = C C G = = = 
A = T T A = = = 
0 D015
= = = = = = ? T 
= = = = = = ? C 
0 D016
G = C C G = ? = 
A = T T A = ? = 
0 D033
= = = C = = = = 
= = = T = = = = 
0 D034
= = = = = = = = 
= = = = = = = = 
0 D035
= = = = = = = = 
= = = = = = = = 
0 D036
= = = (C) ? = A = 
= = = (T) ? = G = 
0 D037
= ? C C G = = = 
= ? T T A = = = 
0 D038
= = = C G = = (C) 
= = = T A = = (T) 
0 D039
= = (C) = G = = ? 
= = (T) = A = = ? 
0 D040
= = C C ? = = = 
= = T T ? = = = 
0 E001
= = C C G = = (C) 
= = T T A = = (T) 
0 E002
= = C C = = = ? 
= = T T = = = ? 
0 E003
= = = = = = = C 
= = = = = = = T 
0 E004
= = = = = = = C 
= = = = = = = T 
0 E005
G = = = = = = = 
A = = = = = = = 
0 E006
= = = = = = = = 
= = = = = = = = 
0 E007
= = = = = = ? C 
= = = = = = ? T 
0 E008
= = C C G = = = 
= = T T A = = = 
0 E009
G = = = = = ? = 
A = = = = = ? = 
0 E010
= = = = = = = C 
= = = = = = = T 
0 E011
= = = = = = ? = 
= = = = = = ? = 
0 E012
G = C C = = ? = 
A = T T = = ? = 
0 E013
= = C C = = = = 
= = T T = = = = 
0 E014
= = = = = = = C 
= = = = = = = T 
0 E015
= = = = = = = = 
= = = = = = = = 
0 E016
= = = = = = = C 
= = = = = = = T 
0 E017
= = C C G = = (C) 
= = T T A = = (T) 
0 E018
= = C C G = = (C) 
= = T T A = = (T) 
0 E019
= = = = = ? = = 
= = = = = ? = = 
0 E020
= = = = = = = C 
= = = = = = = T 
0 E021
= = = = = = = C 
= = = = = = = T 
0 E022
= = = = = ? = C 
= = = = = ? = T 
0 E023
= = C C G = ? = 
= = T T A = ? = 
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 = = = = 
= = = 0.90 1.00 = = = 
= = = = = = = 1.00 
= = = = = = = 1.00 
= 1.00 = 1.00 = 1.00 = = 
= 0.99 = = = 0.99 0.94 0.98 
= 1.00 = = 0.98 1.00 0.98 = 
= = = 0.89 1.00 = = = 
= = = = = = = = 
0.99 = 1.00 1.00 1.00 = ? = 
0.99 = 1.00 1.00 1.00 = = = 
= = = = = = ? 0.98 
0.99 = 1.00 1.00 1.00 = ? = 
= = = 1.00 = = = = 
= = = = = = = = 
= = = = = = = = 
= = = 0.51 ? = 1.00 = 
= ? 1.00 1.00 0.99 = = = 
= = = 0.97 0.99 = = 0.58 
= = 0.77 = 1.00 = = ? 
= = 0.99 0.99 ? = = = 
= = 1.00 1.00 1.00 = = 0.86 
= = 0.99 1.00 = = = ? 
= = = = = = = 1.00 
= = = = = = = 1.00 
1.00 = = = = = = = 
= = = = = = = = 
= = = = = = ? 1.00 
= = 1.00 1.00 0.99 = = = 
1.00 = = = = = ? = 
= = = = = = = 1.00 
= = = = = = ? = 
0.99 = 1.00 0.97 = = ? = 
= = 0.99 1.00 = = = = 
= = = = = = = 1.00 
= = = = = = = = 
= = = = = = = 1.00 
= = 1.00 1.00 1.00 = = 0.87 
= = 1.00 1.00 1.00 = = 0.87 
= = = = = ? = = 
= = = = = = = 1.00 
= = = = = = = 1.00 
= = = = = ? = 1.00 
= = 1.00 1.00 0.99 = ? = 
END PHASEPROBS