************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ustf1.phase.inp ustf1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ustf1.phase.out_freqs : haplotype frequency estimates ustf1.phase.out_pairs : most likely haplotype pairs for each individual ustf1.phase.out_recom : estimates of recombination parameters ustf1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 25 Positions of loci: 1927 2005 2208 2284 2669 2943 3051 3342 3533 3894 4064 4938 5299 5337 5863 5880 5892 6349 6974 7131 7851 8082 8119 9328 9331 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ustf1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TCAGCTTGGGCGCCGCGCGC 1 TGCC 28.000000 2 TCAGCTTGGGCGCCGCGCGC 1 TGCT 2.000000 3 TCAGCTTGGGCGCCGCGCGC 1 TGGC 2.000000 4 TTGGCCCAGACCCCGTGCGC 2 GGCC 2.000000 5 TTGGCCCAGACCCCGTGCGC 4 GCCC 1.000000 6 TTGGCCCAGACCCTGTGCGC 2 GGCC 10.000000 7 TTGGCCCAGACCCTGTGCGC 2 GCCC 3.000000 8 TTGGCCCAGACCCTGTGCGC 2 GCCT 1.000000 9 CTGGGCCAAATGGCACACGT 2 GGCC 1.000000 10 CTGGGCCAAATGGCACACGT 2 GGGC 16.000000 11 CTGCGCCAAACGCCGCGTAC 2 GGCC 5.000000 12 CTGCGCCAAACGCCACGCGC 2 GGCC 23.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (1,1) D003: (1,12) D004: (2,10) D005: (1,11) D006: (1,6) D007: (1,12) D008: (10,11) D009: (6,8) D010: (11,12) D011: (1,1) D012: (1,9) D013: (1,6) D014: (1,6) D015: (1,1) D016: (1,10) D033: (1,1) D034: (5,11) D035: (1,12) D036: (1,1) D037: (1,2) D038: (1,6) D039: (11,12) D040: (1,3) E001: (10,12) E002: (1,10) E003: (10,12) E004: (10,12) E005: (10,12) E006: (1,7) E007: (12,12) E008: (4,12) E009: (12,12) E010: (7,10) E011: (6,7) E012: (1,10) E013: (10,12) E014: (6,12) E015: (12,12) E016: (1,12) E017: (12,12) E018: (3,12) E019: (6,10) E020: (10,10) E021: (10,12) E022: (6,10) E023: (4,6) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C C 0 D002 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C C 0 D003 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 D004 T C A G C T T G G G C G C C G C G C G C 1 T G C T C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 D005 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G C G C C A A A C G C C G C G T A C 2 G G C C 0 D006 T C A G C T T G G G C G C C G C G C G C 1 T G C C T T G G C C C A G A C C C T G T G C G C 2 G G C C 0 D007 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 D008 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C G C G T A C 2 G G C C 0 D009 T T G G C C C A G A C C C T G T G C G C 2 G (G) C C T T G G C C C A G A C C C T G T G C G C 2 G (C) C T 0 D010 C T G C G C C A A A C G C C G C G T A C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 D011 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C C 0 D012 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G G G C C A A A T G G C A C A C G T 2 G G C C 0 D013 T C A G C T T G G G C G C C G C G C G C 1 T G C C T T G G C C C A G A C C C T G T G C G C 2 G G C C 0 D014 T C A G C T T G G G C G C C G C G C G C 1 T G C C T T G G C C C A G A C C C T G T G C G C 2 G G C C 0 D015 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C C 0 D016 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 D033 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C C 0 D034 T T G G C C C A G A C C C C G T G C G C (4) G (C) C C C T G C G C C A A A C G C C G C G T A C (2) G (G) C C 0 D035 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 D036 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C C 0 D037 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G C T 0 D038 T C A G C T T G G G C G C C G C G C G C 1 T G C C T T G G C C C A G A C C C T G T G C G C 2 G G C C 0 D039 C T G C G C C A A A C G C C G C G T A C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 D040 T C A G C T T G G G C G C C G C G C G C 1 T G C C T C A G C T T G G G C G C C G C G C G C 1 T G G C 0 E001 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E002 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 E003 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E004 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E005 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E006 T C A G C T T G G G C G C C G C G C G C 1 T G C C T T G G C C C A G A C C C T G T G C G C 2 G C C C 0 E007 C T G C G C C A A A C G C C A C G C G C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E008 T T G G C C C A G A C C C C G T G C G C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E009 C T G C G C C A A A C G C C A C G C G C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E010 T T G G C C C A G A C C C T G T G C G C 2 G C C C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 E011 T T G G C C C A G A C C C T G T G C G C 2 G G C C T T G G C C C A G A C C C T G T G C G C 2 G C C C 0 E012 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 E013 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E014 T T G G C C C A G A C C C T G T G C G C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E015 C T G C G C C A A A C G C C A C G C G C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E016 T C A G C T T G G G C G C C G C G C G C 1 T G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E017 C T G C G C C A A A C G C C A C G C G C 2 G G C C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E018 T C A G C T T G G G C G C C G C G C G C 1 T G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E019 T T G G C C C A G A C C C T G T G C G C 2 G G C C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 E020 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 E021 C T G G G C C A A A T G G C A C A C G T 2 G G G C C T G C G C C A A A C G C C A C G C G C 2 G G C C 0 E022 T T G G C C C A G A C C C T G T G C G C 2 G G C C C T G G G C C A A A T G G C A C A C G T 2 G G G C 0 E023 T T G G C C C A G A C C C C G T G C G C 2 G G C C T T G G C C C A G A C C C T G T G C G C 2 G G C 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 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 D003 T C A G C T T G G G = = = = G = = = = = 1 T = = = C T G C G C C A A A = = = = A = = = = = 2 G = = = 0 D004 T C A = C T T G G G C = C = G = G = = C 1 T = C T C T G = G C C A A A T = G = A = A = = T 2 G = G C 0 D005 T C A G C T T G G G = = = = = = = C G = 1 T = = = C T G C G C C A A A = = = = = = = T A = 2 G = = = 0 D006 = C A = = T T G = G = G = C = C = = = = 1 T = = = = T G = = C C A = A = C = T = T = = = = 2 G = = = 0 D007 T C A G C T T G G G = = = = G = = = = = 1 T = = = C T G C G C C A A A = = = = A = = = = = 2 G = = = 0 D008 ? = = G = = = = = = T = G = A = A C G T = = = ? ? ? = = C = = = = = = C = C = G = G T A C = = = ? ? 0 D009 = = = = = = = = = = = ? = = = = = = = = = = (G) = C = = = = = = = = = = = ? = = = = = = = = = = (C) = T 0 D010 = = = = = = = = = = = = = = G = = T A = = = = = = = = = = = = = = = = = = = = A = = C G = = = = = = 0 D011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D012 T C A = C T T G G G C = C = G = G = = C 1 T = = = C T G = G C C A A A T = G = A = A = = T 2 G = = = 0 D013 = C A = = T T G = G = G = C = C = = = = 1 T = = = = T G = = C C A = A = C = T = T = = = = 2 G = = = 0 D014 = C A = = T T G = G = G = C = C = = = = 1 T = = = = T G = = C C A = A = C = T = T = = = = 2 G = = = 0 D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D016 T C A = C T T G G G C = C = G = G = = C 1 T = C = C T G = G C C A A A T = G = A = A = = T 2 G = G = 0 D033 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D034 T = = G C = = = G = = C = = = T = C G = (4) = (C) = = C = = C G = = = A = = G = = = C = T A = (2) = (G) = = 0 D035 T C A G C T T G G G = = = = G = = = = = 1 T = = ? C T G C G C C A A A = = = = A = = = = = 2 G = = ? 0 D036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = T 0 D038 = C A = = T T G = G = G = C = C = = = = 1 T = = = = T G = = C C A = A = C = T = T = = = = 2 G = = = 0 D039 = = = = = = = = = = = = = = G = = T ? = = = = = = = = = = = = = = = = = = = = A = = C ? = = = = = = 0 D040 = = = = = = = = = = = = = = = ? ? = = = = = = C = = = = = = = = = = = = = = = = ? ? = = = = = = G = 0 E001 = ? ? ? = = = = = = T = G = = = A = = T = = = G = = ? ? ? = = = = = = C = C = = = G = = C = = = C = 0 E002 T C A = C T T G G G C = C = G = G = = C 1 T = C = C T G = G C C A A A T = G = A = A = = T 2 G = G = 0 E003 = = = G = = = = = = T = G = = = A = = T = = = G = = = = C = = = = = = C = C = = = G = = C = = = C = 0 E004 = = = G = = = = = = T = G = = = A = = T = = = G = = = = C = = = = = = C = C = = = G = = C = = = C = 0 E005 = = = G = = = = = = T = G = = = A = = T = = = G = = = = C = = = = = = C = C = = = G = = C = = = C = 0 E006 = C A = = T T G = G = G = C = C = = = = 1 T G = = = T G = = C C A = A = C = T = T = = = = 2 G C = = 0 E007 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E008 T = = G C = = = G = = C = = G T = = = = = = = = = C = = C G = = = A = = G = = A C = = = = = = = = = 0 E009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 T = = = C = = = G = C C C T G T G = = C = = C C = C = = = G = = = A = T G G C A C A = = T = = G G = 0 E011 = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = C = = 0 E012 T C A = C T T G G G C = C = G = G = = C 1 T = C = C T G = G C C A A A T = G = A = A = = T 2 G = G = 0 E013 = = = G = = = = = = T = G = = = A = = T = = = G = = = = C = = = = = = C = C = = = G = = C = = = C = 0 E014 T = = G C = = = G = = C = T G T = = = = = = = = = C = = C G = = = A = = G = C A C = = = = = = = = = 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 T C ? ? C T T G G G = = = = G = = = = = 1 T = = = C T ? ? G C C A A A = = = = A = = = = = 2 G = = = 0 E017 = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = 0 E018 T C ? ? C T T G G G = = = = G = = ? = = 1 T = G = C T ? ? G C C A A A = = = = A = = ? = = 2 G = C = 0 E019 T = = = C = = = G = C C C T G T G = = C = = = C = C = = = G = = = A = T G G C A C A = = T = = = G = 0 E020 = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = 0 E021 = = = G = = = = = = T = G = = = A = = T = = = G = = = = C = = = = = = C = C = = = G = = C = = = C = 0 E022 T = = = C = = = G = C C C T G T G = = C = = = C = C = = = G = = = A = T G G C A C A = = T = = = G = 0 E023 = ? ? ? = = = = = = = = = C = = = = = = = = = = = = ? ? ? = = = = = = = = = T = = = = = = = = = = = 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 0.94 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = = = = 1.00 1.00 = = = ? = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = ? ? = = = = = = = = = = = ? = = = = = = = = = = 0.50 = 1.00 = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 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 = 0.58 = 0.73 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = = = = 1.00 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 = = 1.00 ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = 1.00 = = ? ? ? = = = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 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 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = 1.00 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 = 0.94 = 1.00 = = = 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = = = 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