************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 csft3.phase.inp csft3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST csft3.phase.out_freqs : haplotype frequency estimates csft3.phase.out_pairs : most likely haplotype pairs for each individual csft3.phase.out_recom : estimates of recombination parameters csft3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 17 Positions of loci: 28 321 379 789 1158 1607 1980 2504 2584 2617 3370 3456 3666 4050 4215 4480 5168 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file csft3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACCCGGGACCCGCCCCG 1.000000 2 ACCCGGGACCCGCCTCG 39.000000 3 ACCCGGGACCCGCCTCT 2.000000 4 GCCCGGCACCCGTCCCT 3.000000 5 GCCCGGCGCTCGCCCCT 6.000000 6 GCCCGGGACCCGCCTCG 3.000000 7 GCCCACCACCCGCCCGT 1.000000 8 GCCCACCACCCACCCCT 1.000000 9 GCCCACCACCCACCCGT 14.000000 10 GTCCGGCACCCGCTCCT 8.000000 11 GTCCGGCATCCGCTCCT 7.000000 12 GTCCAGCACCCGCTCCT 1.000000 13 GTCTGGCACCCGCTCCT 2.000000 14 GTCTGGCACCAGCTCCT 3.000000 15 GTTCGGCACCCGCTCCT 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,5) D002: (2,4) D003: (11,14) D004: (2,2) D005: (5,10) D006: (8,11) D007: (9,10) D008: (11,14) D009: (15,15) D010: (2,2) D011: (5,10) D012: (6,11) D013: (2,10) D014: (2,15) D015: (1,2) D016: (4,11) D033: (2,2) D034: (4,12) D035: (2,2) D036: (2,2) D037: (6,6) D038: (2,13) D039: (5,13) D040: (2,14) E001: (2,2) E002: (9,10) E003: (2,9) E004: (3,3) E005: (2,2) E006: (5,5) E007: (2,9) E008: (7,9) E009: (9,9) E010: (2,2) E011: (2,9) E012: (9,10) E013: (2,2) E014: (2,2) E015: (2,9) E016: (2,10) E017: (2,2) E018: (9,10) E019: (9,9) E020: (9,11) E021: (2,2) E022: (2,2) E023: (2,11) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A C C C G G G A C C C G C C T C G G C C C G G C G C T C G C C C C T 0 D002 A C C C G G G A C C C G C C T C G G C C C G G C A C C C G T C C C T 0 D003 G T C C G G C A T C C G C T C C T G T C T G G C A C C A G C T C C T 0 D004 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 D005 G C C C G G C G C T C G C C C C T G T [C] C G G C A C C C G C T C C T 0 D006 G C C C A C C A C C C A C C C C T G T C C G G C A T C C G C T C C T 0 D007 G C C C A C C A C C C A C C C G T G T C C G G C A C C C G C T C C T 0 D008 G T C C G G C A T C C G C T C C T G T C T G G C A C C A G C T C C T 0 D009 G T T C G G C A C C C G C T C C T G T T C G G C A C C C G C T C C T 0 D010 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 D011 G C C C G G C G C T C G C C C C T G T C C G G C A [C] C C G C T C C T 0 D012 G C C C G G G A C C C G C C T C G G T C C G G C A T C C G C T C C T 0 D013 A C C C G G G A C C C G C C T C G G T C C G G C A C C C G C T C C T 0 D014 A C C C G G G A C C C G C C T C G G T T C G G C A C C C G C T C C T 0 D015 A C C C G G G A C C C G C C C C G A C C C G G G A C C C G C C T C G 0 D016 G C C C G G C A C C C G T C C C T G T C C G G C A T C C G C T C C T 0 D033 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 D034 G C C C (G) G C A C C C G T C C C T G T C C (A) G C A C C C G C T C C T 0 D035 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 D036 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 D037 G C C C G G G A C C C G C C T C G G C C C G G G A C C C G C C T C G 0 D038 A C C C G G G A C C C G C C T C G G T C T G G C A C C C G C T C C T 0 D039 G C C C G G C G C T C G C C C C T G T C T G G C A C C C G C T C C T 0 D040 A C C C G G G A C C C G C C T C G G T C T G G C A C C A G C T C C T 0 E001 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E002 G C C C A C C A C C C A C C C G T G T C C G G C A C C C G C T C C T 0 E003 A C C C G G G A C C C G C C T C G G C C C A C C A C C C A C C C G T 0 E004 A C C C G G G A C C C G C C T C T A C C C G G G A C C C G C C T C T 0 E005 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E006 G C C C G G C G C T C G C C C C T G C C C G G C G C T C G C C C C T 0 E007 A C C C G G G A C C C G C C T C G G C C C A C C A C C C A C C C G T 0 E008 G C C C A C C A C C C G C C C G T G C C C A C C A C C C A C C C G T 0 E009 G C C C A C C A C C C A C C C G T G C C C A C C A C C C A C C C G T 0 E010 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E011 A C C C G G G A C C C G C C T C G G C C C A C C A C C C A C C C G T 0 E012 G C C C A C C A C C C A C C C G T G T C C G G C A C C C G C T C C T 0 E013 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E014 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E015 A C C C G G G A C C C G C C T C G G C C C A C C A C C C A C C C G T 0 E016 A C C C G G G A C C C G C C T C G G T C C G G C A C C C G C T C C T 0 E017 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E018 G C C C A C C A C C C A C C C G T G T [C] C G G C A C C C G C T C C T 0 E019 G C C C A C C A C C C A C C C G T G C C C A C C A C C C A C C C G T 0 E020 G C C C A C C A C C C A C C C G T G T C C G G C A T C C G C T C C T 0 E021 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E022 A C C C G G G A C C C G C C T C G A C C C G G G A C C C G C C T C G 0 E023 A C C C G G G A C C C G C C T C G G T C C G G C A T C C G C T C C T 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 A ? ? = ? = G A = C = = = ? T = G G ? ? = ? = C G = T = = = ? C = T 0 D002 A = = ? = = G = = = = = C = T = G G = = ? = = C = = = = = T = C = T 0 D003 = = = C = = = = T = C = = = = = = = = = T = = = = C = A = = = = = = 0 D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D005 = ? ? = = = ? G = T = = = C = = = = ? ? = = = ? A = C = = = T = = = 0 D006 = C = = A C = = C = = A = C = = = = T = = G G = = T = = G = T = = = 0 D007 = C = = ? C = = = = = A = C = G = = T = = ? G = = = = = G = T = C = 0 D008 = = = C = = = = T = C = = = = = = = = = T = = = = C = A = = = = = = 0 D009 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = ? ? = = = 0 D010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D011 = C = = ? = = G ? ? = = = ? = = = = T = = ? = = A ? ? = = = ? = = = 0 D012 = C = = = = G = C = = = = C T = G = T = = = = C = T = = = = T C = T 0 D013 A C = = = = G = = = = = ? C T = G G T = = = = C = = = = = ? T C = T 0 D014 A C C = = = G = = = = = = C T = G G T T = = = C = = = = = = T C = T 0 D015 = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = T = = 0 D016 = C = = = = = = C = = = T C = = = = T = = = = = = T = = = C T = = = 0 D033 = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 D034 = C = = (G) = = = = = = = T C = = = = T = = (A) = = = = = = = C T = = = 0 D035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D038 A C = C = = G = = = = = = C T = G G T = T = = C = = = = = = T C = T 0 D039 = C = C = = = G = T = = = C = = = = T = T = = = A = C = = = T = = = 0 D040 A C = C = = G = = = C = = C T = G G T = T = = C = = = A = = T C = T 0 E001 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 = C = = A C = = = = = A = C = G ? = T = = G G = = = = = G = T = C ? 0 E003 A = = = G G G = = = = G = = T C G G = = = A C C = = = = A = = C G T 0 E004 = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 E005 = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 A = = = G G G = = = = G = = T C G G = = = A C C = = = = A = = C G T 0 E008 = = = = = = = = = = = G = = = = = = = = = = = = = = = = A = = = = = 0 E009 = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 E010 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = 0 E011 ? = = = G G G = = = = G = = T C G ? = = = A C C = = = = A = = C G T 0 E012 = C = = A C = = = = = A = C = G = = T = = G G = = = = = G = T = C = 0 E013 ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 A = ? ? G G G = = = = G = = T C G G = ? ? A C C = = = = A = = C G T 0 E016 A C = = ? = G ? = = = = = C T = G G T = = ? = C ? = = = = = T C = T 0 E017 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E018 = ? ? = A C = = = = = A = ? = G = = ? ? = G G = = = = = G = ? = C = 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E020 = C = = A C = = C = = A = C = G = = T = = G G = = T = = G = T = C = 0 E021 = ? ? = = = = ? = = = = = = = = = = ? ? = = = = ? = = = = = = = = = 0 E022 = ? ? = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = 0 E023 ? ? ? ? ? = G = C = = = = C T ? G ? ? ? ? ? = C = T = = = = T 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 = 1.00 = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = ? = = 1.00 ? ? = = = ? = = = = 1.00 = = = = 1.00 = 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 = = 0.57 = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 0.98 = = 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 = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = ? = 1.00 ? = = = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = ? ? = 1.00 1.00 = = = = = 1.00 = ? = 1.00 = = = = = = = = = = = = = = = = = = = 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