************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 fbsbp.phase.inp fbsbp.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fbsbp.phase.out_freqs : haplotype frequency estimates fbsbp.phase.out_pairs : most likely haplotype pairs for each individual fbsbp.phase.out_recom : estimates of recombination parameters fbsbp.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 19 Positions of loci: 120 1762 1800 2019 3305 3917 4058 4146 4670 4769 4789 5416 5418 5484 5543 6547 6723 8246 8562 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fbsbp.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CAGTAGIGACGATAAGCGC 7.000000 2 CAGTAGIGATAATAGGCAC 1.000000 3 CAATAGIGACGATAAGCGC 3.000000 4 CAATAGICATAATAGCCAC 39.000000 5 CAATAGDGATAATAAGAAC 4.000000 6 CAATAGDGATACTAAGAAC 4.000000 7 CAATTGICATAATAGCCAC 3.000000 8 CGACAAIGATAATGAGCGC 14.000000 9 CGACAAIGATAATGGGCGC 1.000000 10 TAATAGICTTAATAGCCAC 4.000000 11 TAATAGICTTAACAGCCAG 14.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (3,4) D003: (6,11) D004: (3,4) D005: (4,4) D006: (1,11) D007: (4,4) D008: (4,11) D009: (4,4) D010: (4,11) D011: (4,4) D012: (1,11) D013: (4,11) D014: (4,11) D015: (10,11) D016: (8,8) D033: (8,10) D034: (4,11) D035: (2,4) D036: (1,3) D037: (1,4) D038: (8,10) D039: (11,11) D040: (10,11) E001: (6,8) E002: (4,8) E003: (7,8) E004: (4,4) E005: (4,4) E006: (4,8) E007: (4,4) E008: (4,4) E009: (5,8) E010: (4,4) E011: (1,8) E012: (4,11) E013: (4,4) E014: (4,8) E015: (4,11) E016: (5,9) E017: (4,6) E018: (4,8) E019: (7,8) E020: (5,7) E021: (4,4) E022: (4,6) E023: (5,8) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C A G T A G I G A C G A T A A G C G C C A G T A G I G A C G A T A A G C G C 0 D002 C A A T A G I G A C G A T A A G C G C C A A T A G I C A T A A T A G C C A C 0 D003 C A A T A G D G A T A C T A A G A A C T A A T A G I C T T A A C A G C C A G 0 D004 C A A T A G I G A C G A T A A G C G C C A A T A G I C A T A A T A G C C A C 0 D005 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 D006 C A G T A G I G A C G A T A A G C G C T A A T A G I C T T A A C A G C C A G 0 D007 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 D008 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 D009 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 D010 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 D011 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 D012 C A G T A G I G A C G A T A A G C G C T A A T A G I C T T A A C A G C C A G 0 D013 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 D014 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 D015 T A A T A G I C T T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 D016 C G A C A A I G A T A A T G A G C G C C G A C A A I G A T A A T G A G C G C 0 D033 C G A C A A I G A T A A T G A G C G C T A A T A G I C T T A A T A G C C A C 0 D034 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 D035 C A G T A G I G A T A A T [A] [G] (G) C A C C A A T A G I C A T A A T A G (C) C A C 0 D036 C A G T A G I G A C G A T A A G C G C C A A T A G I G A C G A T A A G C G C 0 D037 C A G T A G I G A C G A T A A G C G C C A A T A G I C A T A A T A G C C A C 0 D038 C G A C A A I G A T A A T G A G C G C T A A T A G I C T T A A T A G C C A C 0 D039 T A A T A G I C T T A A C A G C C A G T A A T A G I C T T A A C A G C C A G 0 D040 T A A T A G I C T T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 E001 C A A T A G D G A T A C T A A G A A C C G A C A A I G A T A A T G A G C G C 0 E002 C A A T A G I C A T A A T A G C C A C C G A C A A I G A T A A T G A G C G C 0 E003 C A A T (T) G I C A T A A T A G C C A C C G A C (A) A I G A T A A T G A G C G C 0 E004 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E005 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E006 C A A T A G I C A T A A T A G C C A C C G A C A A I G A T A A T G A G C G C 0 E007 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E008 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E009 C A A T A G D G A T A A T A A G A A C C G A C A A I G A T A A T G A G C G C 0 E010 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E011 C A G T A G I G A C G A T A A G C G C C G A C A A I G A T A A T G A G C G C 0 E012 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 E013 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E014 C A A T A G I C A T A A T A G C C A C C G A C A A I G A T A A T G A G C G C 0 E015 C A A T A G I C A T A A T A G C C A C T A A T A G I C T T A A C A G C C A G 0 E016 C A A T A G D G A T A A T A (A) G A A C C G A C A A I G A T A A T G (G) G C G C 0 E017 C A A T A G I C A T A A T A G C C A C C A A T A G D G A T A C T A A G A A C 0 E018 C A A T A G I C A T A A T A G C C A C C G A C A A I G A T A A T G A G C G C 0 E019 C A A T (T) G I C A T A A T A G C C A C C G A C (A) A I G A T A A T G A G C G C 0 E020 C A A T A G D G A T A A T A A G A A C C A A T T G I C A T A A T A G C C A C 0 E021 C A A T A G I C A T A A T A G C C A C C A A T A G I C A T A A T A G C C A C 0 E022 C A A T A G I C A T A A T A G C C A C C A A T A G D G A T A C T A A G A A C 0 E023 C A A T A G D G A T A A T A A G A A C C G A C A A I G A T A A T G A G C G 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 = = = = ? = = = = = = = = = = ? ? = = = = = = ? = = = = = = = = = = ? ? = = 0 D002 = = = = = = = G ? ? ? = = = A ? ? G = = = = = = = = C ? ? ? = = = G ? ? A = 0 D003 C = = = = = D G A = = C T = A G A = C T = = = = = I C T = = A C = G C C = G 0 D004 = = = = = = ? G = C G = = = A G = G = = = = = = = ? C = T A = = = G C = A = 0 D005 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = 0 D006 C = G = = = = G A C G = T = A G = G C T = A = = = = C T T A = C = G C = A G 0 D007 = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = ? ? = = = = 0 D008 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 D009 ? = = = = = = = ? ? ? = = = = = = = = ? = = = = = = = ? ? ? = = = = = = = = 0 D010 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 D011 = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = ? ? = = = = 0 D012 C = G = = = = G A C G = T ? ? G = G C T = A = = = = C T T A = C ? ? C = A G 0 D013 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 D014 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 D015 = = = = = = = = = = = = T = = = = = C = = = = = = = = = = = = C = = = = = G 0 D016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D033 C G = C = A = G A = = = = G A G = ? = T A = T = G = C T = = = = A G C = ? = 0 D034 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 D035 = = G = = = = G = = = = = ? ? (G) = = = = = A = = = = C = = = = = ? ? (C) = = = 0 D036 = = G = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = 0 D037 = = G = = = = G = C G = = = A G = G = = = A = = = = C = T A = = = G C = A = 0 D038 C G = C = A = G A = = = = G A G = G = T A = T = G = C T = = = = A G C = A = 0 D039 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D040 = = = = = = = = = = = = T = = = = = C = = = = = = = = = = = = C = = = = = G 0 E001 = A = T = G D = = = = C = A = = A A = = G = C = A I = = = = A = G = = C G = 0 E002 = A = T = G = C = = = = = A G C = A = = G = C = A = G = = = = = G A G = G = 0 E003 = A = T (T) G = C = = = = = A G ? = A = = G = C (A) A = G = = = = = G A ? = G = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = A = T = G = C = = = = = A G C = A = = G = C = A = G = = = = = G A G = G = 0 E007 ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = A = T = G D = = = = = = A = ? ? A = = G = C = A I = = = = = = G = ? ? G = 0 E010 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = 0 E011 = A G T = G = = = C G = = A = ? ? = = = G A C = A = = = T A = = G = ? ? = = 0 E012 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = A = T = G = C = = = = = ? ? C = A = = G = C = A = G = = = = = ? ? G = G = 0 E015 C = = = = = = = A = = = T = = = = = C T = = = = = = = T = = = C = = = = = G 0 E016 = A = T = ? D ? ? ? ? = = A (A) = A A = = G = C = ? I ? ? ? ? = = G (G) = C G = 0 E017 ? = = = = = I C = = = A = = G ? ? = = ? = = = = = D G = = = C = = A ? ? = = 0 E018 = A = T = G = C ? = = = = A G C = A = = G = C = A = G ? = = = = G A G = G = 0 E019 = A = T (T) G = C = = = = = A G C = A = = G = C (A) A = G = = = = = G A G = G = 0 E020 = = = = A = D G ? = = = = = A G A = = = = = = T = I C ? = = = = = G C C = = 0 E021 = = = = = = ? ? = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = 0 E022 = = = = = = I C = = = A = = G C C = = = = = = = = D G = = = C = = A G A = = 0 E023 = A = T = G D = = = = = = A = = A A = = G = C = A I = = = = = = G = = C 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 = 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 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 = = = = = ? ? 0.71 = = = = = 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 0.87 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 0.51 = 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 0.88 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 1.00 = = = = = 0.92 = 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 = END PHASEPROBS