************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 tunft.phase.inp tunft.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tunft.phase.out_freqs : haplotype frequency estimates tunft.phase.out_pairs : most likely haplotype pairs for each individual tunft.phase.out_recom : estimates of recombination parameters tunft.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 12 Positions of loci: 282 352 1009 1078 1440 1893 2642 4013 4040 4101 4366 4765 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tunft.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGGGAAAGTGGG 56.000000 2 GGGGAAAGTGGT 2.000000 3 GGGGAAAATGGG 3.000000 4 GGGGAGAGTGGG 1.000000 5 GGGGGGCGTGGG 5.000000 6 GGGAAAAGTGGT 5.000000 7 GAGAAAAGTGGT 1.000000 8 GAAGGGAGTGGG 1.000000 9 GAAGGGAGCGAG 3.000000 10 AGGGAAAGTGGG 6.000000 11 AGGGAAAGTAGG 11.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (1,5) D003: (1,1) D004: (1,10) D005: (1,5) D006: (1,6) D007: (5,11) D008: (1,1) D009: (1,1) D010: (1,10) D011: (1,3) D012: (2,7) D013: (5,11) D014: (1,1) D015: (1,1) D016: (1,11) D033: (1,10) D034: (1,11) D035: (10,11) D036: (1,1) D037: (5,8) D038: (1,3) D039: (1,3) D040: (1,4) E001: (1,6) E002: (1,11) E003: (1,10) E004: (1,9) E005: (1,1) E006: (1,11) E007: (1,1) E008: (1,11) E009: (1,10) E010: (1,1) E011: (1,11) E012: (1,1) E013: (2,6) E014: (1,9) E015: (1,1) E016: (1,1) E017: (1,11) E018: (1,6) E019: (1,1) E020: (1,1) E021: (1,9) E022: (1,6) E023: (1,11) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G G G G A A A G T G G G G G G G A A A G T G G G 0 D002 G G G G A A A G T G G G G G G G G G C G T G G G 0 D003 G G G G A A A G T G G G G G G G A A A G T G G G 0 D004 G G G G A A A G T G G G A G G G A A A G T G G G 0 D005 G G G G A A A G T G G G G G G G G G C G T G G G 0 D006 G G G G A A A G T G G G G G G A A A A G T G G T 0 D007 G G G G G G C G T G G G A G G G A A A G T A G G 0 D008 G G G G A A A G T G G G G G G G A A A G T G G G 0 D009 G G G G A A A G T G G G G G G G A A A G T G G G 0 D010 G G G G A A A G T G G G A G G G A A A G T G G G 0 D011 G G G G A A A G T G G G G G G G A A A A T G G G 0 D012 G (G) G G A A A G T G G T G (A) G A A A A G T G G T 0 D013 G G G G G G C G T G G G A G G G A A A G T A G G 0 D014 G G G G A A A G T G G G G G G G A A A G T G G G 0 D015 G G G G A A A G T G G G G G G G A A A G T G G G 0 D016 G G G G A A A G T G G G A G G G A A A G T A G G 0 D033 G G G G A A A G T G G G A G G G A A A G T G G G 0 D034 G G G G A A A G T G G G A G G G A A A G T A G G 0 D035 A G G G A A A G T G G G A G G G A A A G T A G G 0 D036 G G G G A A A G T G G G G G G G A A A G T G G G 0 D037 G G G G G G C G T G G G G A A G G G A G T G G G 0 D038 G G G G A A A G T G G G G G G G A A A A T G G G 0 D039 G G G G A A A G T G G G G G G G A A A A T G G G 0 D040 G G G G A A A G T G G G G G G G A G A G T G G G 0 E001 G G G G A A A G T G G G G G G A A A A G T G G T 0 E002 G G G G A A A G T G G G A G G G A A A G T A G G 0 E003 G G G G A A A G T G G G A G G G A A A G T G G G 0 E004 G G G G A A A G T G G G G A A G G G A G C G A G 0 E005 G G G G A A A G T G G G G G G G A A A G T G G G 0 E006 G G G G A A A G T G G G A G G G A A A G T A G G 0 E007 G G G G A A A G T G G G G G G G A A A G T G G G 0 E008 G G G G A A A G T G G G A G G G A A A G T A G G 0 E009 G G G G A A A G T G G G A G G G A A A G T G G G 0 E010 G G G G A A A G T G G G G G G G A A A G T G G G 0 E011 G G G G A A A G T G G G A G G G A A A G T A G G 0 E012 G G G G A A A G T G G G G G G G A A A G T G G G 0 E013 G G G G A A A G T G G T G G G A A A A G T G G T 0 E014 G G G G A A A G T G G G G A A G G G A G C G A G 0 E015 G G G G A A A G T G G G G G G G A A A G T G G G 0 E016 G G G G A A A G T G G G G G G G A A A G T G G G 0 E017 G G G G A A A G T G G G A G G G A A A G T A G G 0 E018 G G G G A A A G T G G G G G G [A] A A A G T G G T 0 E019 G G G G A A A G T G G G G G G G A A A G T G G G 0 E020 G G G G A A A G T G G G G G G G A A A G T G G G 0 E021 G G G G A A A G T G G G G A A G G G A G C G A G 0 E022 G G G G A A A G T G G G G G G A A A A G T G G T 0 E023 G G G G A A A G T G G G A G G G A A A G T A G G 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 = = = = A A A = = = = = = = = = G G C = = = = = 0 D003 = = = = = = = = = = = = = = = = = = = = = = = = 0 D004 G = = = = = = = = = = = A = = = = = = = = = = = 0 D005 = = = = A A A = = = ? ? = = = = G G C = = = ? ? 0 D006 = = = G = = = = = = = G = = = A = = = = = = = T 0 D007 G = = = G G C = = G = = A = = = A A A = = A = = 0 D008 = = = = = = = = = = = = = = = = = = = = = = = = 0 D009 ? = = = ? = = = = = = = ? = = = ? = = = = = = = 0 D010 G = = = = = = = = = = = A = = = = = = = = = = = 0 D011 = = = = = = = G = = = = = = = = = = = A = = = = 0 D012 = (G) = G ? = = = = = = = = (A) = A ? = = = = = = = 0 D013 G = = = G G C = = G = = A = = = A A A = = A = = 0 D014 = = = = = = ? ? ? = = = = = = = = = ? ? ? = = = 0 D015 = = = = = = = = = = = = = = = = = = = = = = = = 0 D016 G = = = = = = = = G = = A = = = = = = = = A = = 0 D033 G = = = = = = = = = = = A = = = = = = = = = = = 0 D034 G = = = = = = = = G = = A = = = = = = = = A = = 0 D035 = = = = = = = = = G = = = = = = = = = = = A = = 0 D036 = = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = G G = ? = C = = = = = = A A = ? = A = = = = = 0 D038 = = = = = = = G = = = = = = = = = = = A = = = = 0 D039 = = = = = = = G = = = = = = = = = = = A = = = = 0 D040 = = = = ? A = = = = = ? = = = = ? G = = = = = ? 0 E001 ? ? = G ? = = = = = = G ? ? = A ? = = = = = = T 0 E002 G = = = = = = = = G = = A = = = = = = = = A = = 0 E003 G = = = ? = = = = = = = A = = = ? = = = = = = = 0 E004 = G G = A A = = T = G = = A A = G G = = C = A = 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 G = = = = = = = = G = = A = = = = = = = = A = = 0 E007 = = = = = = = = = = = = = = = = = = = = = = = = 0 E008 G = = = = = = = = G = = A = = = = = = = = A = = 0 E009 G = = = ? = = = = = = = A = = = ? = = = = = = = 0 E010 = = = = = = = ? = = = = = = = = = = = ? = = = = 0 E011 G = = = = = = = = G = = A = = = = = = = = A = = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = G = = = = = = = = = = = A = = = = = = = = 0 E014 = G G = A A = = T = G = = A A = G G = = C = A = 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 = = = = = = = = = = ? ? = = = = = = = = = = ? ? 0 E017 G = = = = = = = = G = = A = = = = = = = = A = = 0 E018 = = = ? = = = = = = = G = = = ? = = = = = = = T 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = 0 E020 = = = = = = = ? ? = = ? = = = = = = = ? ? = = ? 0 E021 = G G = A A = = T = G = = A A = G G = = C = A = 0 E022 = = = G = = = = = = = G = = = A = = = = = = = T 0 E023 G = = = = = = = = G = = A = = = = = = = = 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 1.00 1.00 = = = ? ? = = = 1.00 = = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = ? = = = ? = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = = 0.52 = 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 = = END PHASEPROBS