************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 c1qal.phase.inp c1qal.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST c1qal.phase.out_freqs : haplotype frequency estimates c1qal.phase.out_pairs : most likely haplotype pairs for each individual c1qal.phase.out_recom : estimates of recombination parameters c1qal.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 20 Positions of loci: 152 315 501 554 704 786 951 1372 1701 2859 2904 3339 4128 4391 4510 4982 5296 5397 5614 5716 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file c1qal.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GAGTCTGAGACGGGGGGAAC 31.000000 2 GAGTCTGAGACGGGGGGAAT 2.000000 3 GAGTCTGAGACGTACGGGGC 1.000000 4 GAGTCTGAGACGTACGAGGC 5.000000 5 GAGTCTGAGACATGCAGGGC 3.000000 6 GAGTTTGAGACGTACGAGAC 1.000000 7 GAGTTTGAGACGTACGAGGC 3.000000 8 GAACCGGAGACGGGGGGAAC 1.000000 9 GAACCGGAGACATGCAGGGC 1.000000 10 GAACCGGAGGCATGCAGGGC 26.000000 11 GAACCGGAGGTATGCAGGGC 4.000000 12 GTGTCTGGGACGTACGGGGC 3.000000 13 GTGTCTAGGACGTACGGGAC 1.000000 14 GTGTCTAGGACGTACGGGGC 7.000000 15 AAGTCTGATACGGGGGGAAC 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (1,10) D003: (6,7) D004: (1,15) D005: (1,7) D006: (5,10) D007: (1,12) D008: (1,7) D009: (9,14) D010: (1,5) D011: (1,1) D012: (2,15) D013: (4,10) D014: (1,11) D015: (4,12) D016: (2,4) D033: (3,5) D034: (1,4) D035: (1,15) D036: (10,14) D037: (1,4) D038: (1,12) D039: (1,1) D040: (15,15) E001: (10,11) E002: (10,14) E003: (10,10) E004: (10,10) E005: (1,10) E006: (10,10) E007: (1,10) E008: (11,13) E009: (1,14) E010: (10,10) E011: (1,1) E012: (1,8) E013: (1,10) E014: (1,14) E015: (10,14) E016: (1,11) E017: (1,10) E018: (1,10) E019: (10,10) E020: (10,10) E021: (1,14) E022: (1,10) E023: (1,10) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C G G G G G G A A C 0 D002 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 D003 G A G T T T G A G A C G T A C G A G A C G A G T T T G A G A C G T A C G A G G C 0 D004 G A G T C T G A G A C G G G G G G A A C A A G T C T G A T A C G G G G G G A A C 0 D005 G A G T C T G A G A C G G G G G G A A C G A G T T T G A G A C G T A C G A G G C 0 D006 G A G T C T G A G A C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 D007 G A G T C T G A G A C G G G G G G A A C G T G T C T G G G A C G T A C G G G G C 0 D008 G A G T C T G A G A C G G G G G G A A C G A G T T T G A G A C G T A C G A G G C 0 D009 G A A C C G G A G A C A T G C A G G G C G T G T C T A G G A C G T A C G G G G C 0 D010 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C A T G C A G G G C 0 D011 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C G G G G G G A A C 0 D012 G A G T C T G A G A C G G G G G G A A (T) A A G T C T G A T A C G G G G G G A A (C) 0 D013 G A G T C T G A G A C G T A C G [A] G G C G A A C C G G A G G C A T G C A G G G C 0 D014 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G T A T G C A G G G C 0 D015 G A G T C T G A G A C G T A C G A G G C G T G T C T G G G A C G T A C G G G G C 0 D016 G A G T C T G A G A C G G G G G G A A (T) G A G T C T G A G A C G T A C G [A] G G (C) 0 D033 G A G T C T G A G A C G T A C G G G G C G A G T C T G A G A C A T G C A G G G C 0 D034 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C G T A C G A G G C 0 D035 G A G T C T G A G A C G G G G G G A A C A A G T C T G A T A C G G G G G G A A C 0 D036 G A A C C G G A G G C A T G C A G G G C G T G T C T A G G A C G T A C G G G G C 0 D037 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C G T A C G [A] G G C 0 D038 G A G T C T G A G A C G G G G G G A A C G T G T C T G G G A C G T A C G G G G C 0 D039 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C G G G G G G A A C 0 D040 A A G T C T G A T A C G G G G G G A A C A A G T C T G A T A C G G G G G G A A C 0 E001 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G T A T G C A G G G C 0 E002 G A A C C G G A G G C A T G C A G G G C G T G T C T A G G A C G T A C G G G G C 0 E003 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 E004 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 E005 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 E006 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 E007 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 E008 G A A C C G G A G G T A T G C A G G G C G T G T C T A G G A C G T A C G G [G] A C 0 E009 G A G T C T G A G A C G G G G G G A A C G T G T C T A G G A C G T A C G G G G C 0 E010 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 E011 G A G T C T G A G A C G G G G G G A A C G A G T C T G A G A C G G G G G G A A C 0 E012 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G A C G G G G G G A A C 0 E013 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 E014 G A G T C T G A G A C G G G G G G A A C G T G T C T A G G A C G T A C G G G G C 0 E015 G A A C C G G A G G C A T G C A G G G C G T G T C T A G G A C G T A C G G G G C 0 E016 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G T A T G C A G G G C 0 E017 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 E018 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 E019 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 E020 G A A C C G G A G G C A T G C A G G G C G A A C C G G A G G C A T G C A G G G C 0 E021 G A G T C T G A G A C G G G G G G A A C G T G T C T A G G A C G T A C G G G G C 0 E022 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G G C 0 E023 G A G T C T G A G A C G G G G G G A A C G A A C C G G A G G C A T G C A G G 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 T = T = = = ? ? G G = G G = A A = = = A C = G = = = ? ? A T = C A = G G = 0 D003 = = = = = = = = = = = = = = = = = = A ? = = = = = = = = = = = = = = = = = = G ? 0 D004 G = = = = = = = G ? ? = = = = = = = = ? A = = = = = = = T ? ? = = = = = = = = ? 0 D005 = = = = C = = = = = = = G G G = G A A ? = = = = T = = = = = = = T A C = A G G ? 0 D006 = = G T = T = = = A = = = = = = = = ? ? = = A C = G = = = G = = = = = = = = ? ? 0 D007 = A = = = = = A = = = = G G G = = A ? ? = T = = = = = G = = = = T A C = = G ? ? 0 D008 = = = = C = = = = = = = G G G = G A A ? = = = = T = = = = = = = T A C = A G G ? 0 D009 = A A C = G G A = = = A = G = A = = = = = T G T = T A G = = = G = A = G = = = = 0 D010 = = = = = = = = = = = G G = G G = ? A = = = = = = = = = = = = A T = C A = ? G = 0 D011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D012 G = = = = = = = G = = = = = = = = = = (T) A = = = = = = = T = = = = = = = = = = (C) 0 D013 = = G T = T = = = A = G = A = G ? ? = = = = A C = G = = = G = A = G = A ? ? = = 0 D014 = = G T = T = = = A C G G = G ? ? ? ? ? = = A C = G = = = G T A T = C ? ? ? ? ? 0 D015 = A = = = = = A = = = = = = = = A = = = = T = = = = = G = = = = = = = = G = = = 0 D016 = = = = = = = = = = = = G G G = ? ? A (T) = = = = = = = = = = = = T A C = ? ? G (C) 0 D033 = = = = = = = = = = = G = A = G = = = = = = = = = = = = = = = A = G = A = = = = 0 D034 = = = = = = = = = = = = G G G = G A A = = = = = = = = = = = = = T A C = A G G = 0 D035 G = = = = = = = G = = = = = = = = = = = A = = = = = = = T = = = = = = = = = = = 0 D036 = A A C = G G A = G = A = G = A ? = = = = T G T = T A G = A = G = A = G ? = = = 0 D037 = = = = = = = = = = = = G G G = ? ? A = = = = = = = = = = = = = T A C = ? ? G = 0 D038 = A = = = = = A = = = = G G G = = ? A = = T = = = = = G = = = = T A C = = ? G = 0 D039 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D040 = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = 0 E001 = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = T = = = = = = = = = 0 E002 = A A C = G G A = G = A = G = A ? ? = = = T G T = T A G = A = G = A = G ? ? = = 0 E003 = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = 0 E004 = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = 0 E005 = = G T = T = = = A = G G = G G ? ? A = = = A C = G = = = G = A T = C A ? ? G = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 = = G T = T = = = A = G G = G G = ? A = = = A C = G = = = G = A T = C A = ? G = 0 E008 = A A C = G G A = G T A = G = A ? ? G = = T G T = T A G = A C G = A = G ? ? A = 0 E009 = A = = = = G A = = = = G G G = = A A = = T = = = = A G = = = = T A C = = G G = 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 = = G T = T = = = = = = = = = = = = = = = = A C = G = = = = = = = = = = = = = = 0 E013 = = G T = T = ? = A = G G = G G ? ? A = = = A C = G = ? = G = A T = C A ? ? G = 0 E014 = A = = = = G A = = = = G G G = = A A = = T = = = = A G = = = = T A C = = G G = 0 E015 = A A C = G G A = G = A = G = A = = = = = T G T = T A G = A = G = A = G = = = = 0 E016 = = G T = T = = = A C G G = G G ? ? A = = = A C = G = = = G T A T = C A ? ? G = 0 E017 = = G T = T = = = A = G G = G G = A A = = = A C = G = = = G = A T = C A = G G = 0 E018 = = G T = T = = = ? ? G G = G G = A A = = = A C = G = = = ? ? A T = C A = G G = 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E020 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E021 = A = = = = G A = = = = G G G = = A A = = T = = = = A G = = = = T A C = = G G = 0 E022 = = G T = T = = = A = G G = G G = A A = = = A C = G = = = G = A T = C A = G G = 0 E023 = = G T = T = = = A = G G = G G ? ? A = = = A C = G = = = G = A T = C A ? ? 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 ? ? = = = = = = = = ? = = = = 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 ? ? = = = = 0.99 = = = = = = = 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 = = = = = = = = = = 0.87 = = 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 0.89 = = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = 1.00 1.00 = ? 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 ? ? 1.00 = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = ? = 1.00 = 1.00 1.00 = 1.00 1.00 ? ? 1.00 = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 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 = = = = 1.00 1.00 1.00 = = 1.00 1.00 = = = 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = 1.00 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