************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 bfppd.phase.inp bfppd.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST bfppd.phase.out_freqs : haplotype frequency estimates bfppd.phase.out_pairs : most likely haplotype pairs for each individual bfppd.phase.out_recom : estimates of recombination parameters bfppd.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 23 Positions of loci: 697 1646 1801 1802 2557 2766 3684 4022 4573 4607 5162 5180 6484 6527 7202 7454 7541 7580 8311 8497 8690 9099 9878 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file bfppd.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CTCGAGAATTTDACACTTCCIGA 8.000000 2 CTCGAGAATTTDACACTTCCIGC 1.000000 3 CTCGAGAATTTDACGCTTCCIGA 1.000000 4 CTCGGGAATTTDACACTTCCDGC 5.000000 5 CTCGGGAATTTDGCACTTCCIGA 7.000000 6 CTCGGGAATTTDGCACTTTCIGA 2.000000 7 CTCGGGAATTTDGCGCTTCTIGA 1.000000 8 CTCGGGAGTTTDACGCTTCCIGC 2.000000 9 CTCGGGAGTTTDACGCTTCTIGC 9.000000 10 CTCGGGAGTTTDACGCTTCTDGC 1.000000 11 CTCGGGAGTTCDACGCTTCCIAC 18.000000 12 CTCGGGAGTTCDACGCTTCCDAC 1.000000 13 CTCGGGAGTATDACGCTTCTIGC 4.000000 14 CTCAGGAGCTTIACACTTCCIGC 1.000000 15 CTCAGGAGCTTIACACCCTCIGC 10.000000 16 CTCAGGGGCTTIACACCCTCIGC 4.000000 17 CTTGGGAGTTTDACACTTCCIGC 1.000000 18 CTTGGGAGTTTDACGCTTCCIGC 11.000000 19 CACGGAAGTTTDATGTTTCCIGC 4.000000 20 TTCAGGAGCTTIACACCCTCIGC 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,18) D002: (9,18) D003: (1,20) D004: (4,18) D005: (13,13) D006: (6,14) D007: (4,5) D008: (17,18) D009: (15,20) D010: (4,13) D011: (4,15) D012: (9,11) D013: (9,15) D014: (4,9) D015: (15,18) D016: (7,11) D033: (9,9) D034: (9,16) D035: (5,15) D036: (16,20) D037: (2,18) D038: (8,18) D039: (6,15) D040: (13,15) E001: (16,19) E002: (5,11) E003: (1,15) E004: (8,11) E005: (1,16) E006: (1,5) E007: (11,18) E008: (9,11) E009: (11,19) E010: (15,18) E011: (5,11) E012: (11,18) E013: (11,19) E014: (10,15) E015: (11,11) E016: (3,11) E017: (5,18) E018: (1,19) E019: (11,11) E020: (1,11) E021: (9,11) E022: (11,12) E023: (1,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C T C G A G A A T T T D A C A C T T C C I G A C T T G G G A G T T T D A C G C T T C C I G C 0 D002 C T C G G G A G T T T D A C G C T T C T I G C C T T G G G A G T T T D A C G C T T C C I G C 0 D003 C T C G A G A A T T T D A C A C T T C C I G A T T C A G G A G C T T I A C A C C C T C I G C 0 D004 C T C G G G A A T T T D A C A C T T C C D G C C T T G G G A G T T T D A C G C T T C C I G C 0 D005 C T C G G G A G T A T D A C G C T T C T I G C C T C G G G A G T A T D A C G C T T C T I G C 0 D006 C T C G G G A A T T T D G C A C T T (T) C I G A C T C A G G A G C T T I A C A C T T (C) C I G C 0 D007 C T C G G G A A T T T D A C A C T T C C D G C C T C G G G A A T T T D G C A C T T C C I G A 0 D008 C T T G G G A G T T T D A C A C T T C C I G C C T T G G G A G T T T D A C G C T T C C I G C 0 D009 C T C A G G A G C T T I A C A C C C T C I G C T T C A G G A G C T T I A C A C C C T C I G C 0 D010 C T C G G G A A T T T D A C A C T T C C D G C C T C G G G A G T A T D A C G C T T C T I G C 0 D011 C T C G G G A A T T T D A C A C T T C C D G C C T C A G G A G C T T I A C A C C C T C I G C 0 D012 C T C G G G A G T T T D A C G C T T C T I G C C T C G G G A G T T C D A C G C T T C C I A C 0 D013 C T C G G G A G T T T D A C G C T T C T I G C C T C A G G A G C T T I A C A C C C T C I G C 0 D014 C T C G G G A A T T T D A C A C T T C C D G C C T C G G G A G T T T D A C G C T T C [T] I G C 0 D015 C T C A G G A G C T T I A C A C C C T C I G C C T T G G G A G T T T D A C G C T T C C I G C 0 D016 C T C G G G A A T T T D G C G C T T C (T) I G (A) C T C G G G A G T T C D A C G C T T C (C) I A (C) 0 D033 C T C G G G A G T T T D A C G C T T C T I G C C T C G G G A G T T T D A C G C T T C T I G C 0 D034 C T C G G G A G T T T D A C G C T T C T I G C C T C A G G G G C T T I A C A C C C T C I G C 0 D035 C T C G G G A A T T T D G C A C T T C C I G A C T C A G G A G C T T I A C A C C C T C I G C 0 D036 C T C A G G G G C T T I A C A C C C T C I G C T T C A G G A G C T T I A C A C C C T C I G C 0 D037 C T C G A G A A T T T D A C A C T T C C I G C C T T G G G A G T T T D A C G C T T C C I G C 0 D038 C T C G G G A G T T T D A C G C T T C C I G C C T T G G G A G T T T D A C G C T T C C I G C 0 D039 C T C G G G A A T T T D G C A C T T T C I G A C T C A G G A G C T T I A C A C C C T C I G C 0 D040 C T C G G G A G T A T D A C G C T T C T I G C C T C A G G A G C T T I A C A C C C T C I G C 0 E001 C T C A G G G G C T T I A C A C C C T C I G C C A C G G A A G T T T D A T G T T T C C I G C 0 E002 C T C G G G A A T T T D G C A C T T C C I G A C T C G G G A G T T C D A C G C T T C C I A C 0 E003 C T C G A G A A T T T D A C A C T T C C I G A C T C A G G A G C T T I A C A C C C T C I G C 0 E004 C T C G G G A G T T T D A C G C T T C C I G C C T C G G G A G T T C D A C G C T T C C I A C 0 E005 C T C G A G A A T T T D A C A C T T C C I G A C T C A G G G G C T T I A C A C C C T C I G C 0 E006 C T C G A G A A T T T D A C A C T T C C I G A C T C G G G A A T T T D G C A C T T C C I G A 0 E007 C T C G G G A G T T C D A C G C T T C C I A C C T T G G G A G T T T D A C G C T T C C I G C 0 E008 C T C G G G A G T T T D A C G C T T C T I G C C T C G G G A G T T C D A C G C T T C C I A C 0 E009 C T C G G G A G T T C D A C G C T T C C I A C C A C G G A A G T T T D A T G T T T C C I G C 0 E010 C T C A G G A G C T T I A C A C C C T C I G C C T [T] G G G A G T T T D A C G C T T C C I G C 0 E011 C T C G G G A A T T T D G C A C T T C C I G A C T C G G G A G T T C D A C G C T T C C I A C 0 E012 C T C G G G A G T T C D A C G C T T C C I A C C T [T] G G G A G T T T D A C G C T T C C I G C 0 E013 C T C G G G A G T T C D A C G C T T C C I A C C A C G G A A G T T T D A T G T T T C C I G C 0 E014 C T C G G G A G T T T D A C G C T T C T (D) G C C T C A G G [A] G C T T I A C A C C C T C (I) G C 0 E015 C T C G G G A G T T C D A C G C T T C C I A C C T C G G G A G T T C D A C G C T T C C I A C 0 E016 C T C G A G A A T T T D A C G C T T C C I G A C T C G G G A G T T C D A C G C T T C C I A C 0 E017 C T C G G G A A T T T D G C A C T T C C I G A C T T G G G A G T T T D A C G C T T C C I G C 0 E018 C T C G A G A A T T T D A C A C T T C C I G A C A C G G A A G T T T D A T G T T T C C I G C 0 E019 C T C G G G A G T T C D A C G C T T C C I A C C T C G G G A G T T C D A C G C T T C C I A C 0 E020 C T C G A G A A T T T D A C A C T T C C I G A C T C G G G A G T T C D A C G C T T C C I A C 0 E021 C T C G G G A G T T T D A C G C T T C T I G C C T C G G G A G T T C D A C G C T T C C I A C 0 E022 C T C G G G A G T T C D A C G C T T C C I A C C T C G G G A G T T C D A C G C T T C C D A C 0 E023 C T C G A G A A T T T D A C A C T T C C I G A C T C G G G A A T T T D G C A C T T C C I G 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 D001 = = C = A = = A = = = = = = A = = = = = = = A = = T = G = = G = = = = = = G = = = = = = = C 0 D002 = = C = = = = = = = = = = = = = = = = T = = = = = T = = = = = = = = = = = = = = = = C = = = 0 D003 C = = G A = = A T = = D = = = = T T C = = = A T = = A G = = G C = = I = = = = C C T = = = C 0 D004 = = C = = = = A = = = = = = A = = = = = D = = = = T = = = = G = = = = = = G = = = = = I = = 0 D005 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = 0 D006 = = = G = = = A T = = D G = = = = = (T) = = = A = = = A = = = G C = = I A = = = = = (C) = = = C 0 D007 = = = = = = = = = = = = A = = = = = = = D = C = = = = = = = = = = = = G = = = = = = = I = A 0 D008 = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = 0 D009 C = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = 0 D010 = = = = ? = = A = T = = = = A = = = = C D = = = = = = ? = = G = A = = = = G = = = = T I = = 0 D011 = = = G = = = A T = = D = = = = T T C = D = = = = = A = = = G C = = I = = = = C C T = I = = 0 D012 = = = = = = = = = = T = = = = = = = = T = G = = = = = = = = = = = C = = = = = = = = C = A = 0 D013 = = = G = = = = T = = D = = G = T T C T = = = = = = A = = = = C = = I = = A = C C T C = = = 0 D014 = = = = = = = A = = = = = ? A = = = = ? D = = = = = = = = = G = = = = = ? G = = = = ? I = = 0 D015 = = C A = = = = C = = I = = A = C C T = = = = = = T G = = = = T = = D = = G = T T C = = = = 0 D016 = = = = = = = A = = T = G = = ? = = = (T) ? G (A) = = = = = = = G = = C = A = = ? = = = (C) ? A (C) 0 D033 = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = 0 D034 = = = G = = A = T = = D = = G = T T C T = = = = = = A = = G = C = = I = = A = C C T C = = = 0 D035 = = = G = = = A T = = D G = = = T T C = = = A = = = A = = = G C = = I A = = = C C T = = = C 0 D036 C = = = = = G = = = = = = = = = = = = = = = = T = = = = = A = = = = = = = = = = = = = = = = 0 D037 = = C = A = = A = = = = = = A = = = = = = = = = = T = G = = G = = = = = = G = = = = = = = = 0 D038 = = C = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = 0 D039 = = = G = = = A T = = D G = = = T T = ? = = A = = = A = = = G C = = I A = = = C C = ? = = C 0 D040 = = = G = = = = T A = D = = ? = T T C T ? = = = = = A = = = = C T = I = = ? = C C T C ? = = 0 E001 = T = A = G G = C = = I = C A C C C T = = = = = A = G = A A = T = = D = T G T T T C = = = = 0 E002 = = = = = = = A = = T = G = A = ? ? = = = G A = = = = = = = G = = C = A = G = ? ? = = = A C 0 E003 = = = G A = = A T = = D = = = = T T C = = = A = = = A G = = G C = = I = = = = C C T = = = C 0 E004 = = = = = = = = = = T = = = = = = = = = ? G = = = = = = = = = = = C = = = = = = = = = ? A = 0 E005 = = = G A = A A T = = D = = = = T T C = = = A = = = A G = G G C = = I = = = = C C T = = = C 0 E006 = = = = A = = = = = = = A = = = = = = = = = = = = = = G = = = = = = = G = = = = = = = = = = 0 E007 = = C = = = = = = = C = = = = = = = = = = A = = = T = = = = = = = T = = = = = = = = = = G = 0 E008 = = = = = = = = = = T = = = = = = = = T ? G = = = = = = = = = = = C = = = = = = = = C ? A = 0 E009 = ? ? ? = G ? ? = = C = = C = C ? = = = = A = = ? ? ? = A ? ? = = T = = T = T ? = = = = G = 0 E010 = ? ? ? = = = = C = = I = = A = C C T = = = = = ? ? ? = = = = T = = D = = G = T T C = = = = 0 E011 = ? ? ? = = = A = = T = G = A = ? = = = = G A = ? ? ? = = = G = = C = A = G = ? = = = = A C 0 E012 = ? ? ? = = = = = = C = = = = = = = = = = A = = ? ? ? = = = = = = T = = = = = = = = = = G = 0 E013 = ? ? ? = G ? = = = C = = C = C ? ? = = = A = = ? ? ? = A ? = = = T = = T = T ? ? = = = G = 0 E014 = ? ? ? = = ? ? T = = D = = G = ? ? C T (D) = = = ? ? ? = = ? ? C = = I = = A = ? ? T C (I) = = 0 E015 = ? ? ? = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = 0 E016 = ? ? ? A = = A = = T = = = = ? ? = = = = G A = ? ? ? G = = G = = C = = = = ? ? = = = = A C 0 E017 = = C = = = = A = = = = G = A = = = = = = = A = = T = = = = G = = = = A = G = = = = = = = C 0 E018 = T = = A G = A = = = = = C A C = = = = ? ? ? = A = = G A = G = = = = = T G T = = = = ? ? ? 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E020 = = = = A = = A = = T = = = A = = = = = ? G A = = = = G = = G = = C = = = G = = = = = ? A C 0 E021 = = = = = = = = = = T = = = = = = = = T = G = = = = = = = = = = = C = = = = = = = = C = A = 0 E022 = ? ? ? = = = = = = = = = = = = = = = = I = = = ? ? ? = = = = = = = = = = = = = = = = D = = 0 E023 = = = = A = = = = = = = A = = = = = = = = = = = = = = G = = = = = = = G = = = = = = = = = = 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 = = = = = = 0.98 = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = 0.99 = = 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 = = = = = 0.83 = = = 0.95 = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 1.00 = 0.99 = = = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 = = = 1.00 1.00 = = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = 1.00 = = = = = = = = 0.99 = 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 = = = = = = = = = = = 0.99 = = 1.00 = 0.99 = = ? = = = 0.77 ? 1.00 0.85 = = = = = = = = = = = = = = = = ? ? = = = = = = = = 1.00 = = 0.99 = 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 0.98 = = = = = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = 1.00 = = = = = = 0.97 = = = = = = = = = = 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 0.98 = 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 = 0.99 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 0.53 = = = ? ? ? = = = = = = = = = = = = = = = = = = = = ? ? ? 1.00 = = 1.00 = = 0.99 = = = = ? ? = = = = 0.99 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 = = = = = = = = 0.99 = 1.00 = = ? ? ? = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = = = = = = 1.00 = = = = = = = = = = END PHASEPROBS