************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 mc1rp.phase.inp mc1rp.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mc1rp.phase.out_freqs : haplotype frequency estimates mc1rp.phase.out_pairs : most likely haplotype pairs for each individual mc1rp.phase.out_recom : estimates of recombination parameters mc1rp.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 25 Positions of loci: 318 404 1581 1598 2132 2414 2422 2648 2783 3221 3266 3485 3888 3984 4161 4188 4296 4652 4676 4804 4821 5245 6027 6133 6590 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mc1rp.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CACAICCCGCGAGGCCTGAGAACGC 5.000000 2 CACAICCCGCGTGGCCTGGACGCAC 7.000000 3 CATAICCCGCGAGACCTGGGCGCAC 2.000000 4 CATAICCCGTGAGGCCTGGGCGCAC 9.000000 5 CGTAICCCGCGAGACCTGGGCGCAC 1.000000 6 CGTADCCCGTGAGGCCTAGGCACAC 4.000000 7 CGTADCCCGTATGGCCTAGACACAC 13.000000 8 CGTADCCCGTATGGCCTAGACAGAC 3.000000 9 CGTADCCCGTATGGCCCAGACACAC 3.000000 10 CGTADCCCGTATGGCTTAGACACAC 4.000000 11 CGTADCTCGTATGGCCTAGACACAC 6.000000 12 CGTGDCCCGTGAGGCCTAGACACAC 1.000000 13 TGCGITCCACGAGGCCTAGACACAA 3.000000 14 TGCGITCTACGAGGCCTAGACACAC 23.000000 15 TGCGITCTACGAGGTCTAGACACAC 5.000000 16 TGCGITCTACGATGCCTAGACACAC 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,4) D002: (4,4) D003: (2,11) D004: (4,7) D005: (13,14) D006: (7,14) D007: (1,11) D008: (7,9) D009: (2,14) D010: (8,13) D011: (4,14) D012: (6,7) D013: (8,11) D014: (1,1) D015: (2,11) D016: (1,7) D033: (2,7) D034: (4,11) D035: (9,9) D036: (1,14) D037: (2,13) D038: (4,8) D039: (2,14) D040: (4,11) E001: (10,14) E002: (14,16) E003: (3,3) E004: (7,14) E005: (14,15) E006: (7,10) E007: (14,15) E008: (7,16) E009: (6,15) E010: (5,6) E011: (10,14) E012: (7,16) E013: (7,14) E014: (14,16) E015: (7,14) E016: (14,15) E017: (14,16) E018: (12,14) E019: (14,14) E020: (6,15) E021: (10,14) E022: (4,14) E023: (7,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C A C A I C C C G C G T G G C C T G G A C G C A C C A T A I C C C G T G A G G C C T G G G C G C A C 0 D002 C A T A I C C C G T G A G G C C T G G G C G C A C C A T A I C C C G T G A G G C C T G G G C G C A C 0 D003 C A C A I C C C G C G T G G C C T G G A C G C A C C G T A D C T C G T A T G G C C T A G A C A C A C 0 D004 C A T A I C C C G T G A G G C C T G G G C G C A C C G T A D C [C] C G T A T G G C C T A G A C A C A C 0 D005 T G C G I T C C A C G A G G C C T A G A C A C A A T G C G I T C T A C G A G G C C T A G A C A C A C 0 D006 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 D007 C A C A I C C C G C G A G G C C T G A G A A C G C C G T A D C T C G T A T G G C C T A G A C A C A C 0 D008 C G T A D C C C G T A T G G C C T A G A C A C A C C G T A D C C C G T A T G G C C C A G A C A C A C 0 D009 C A C A I C C C G C G T G G C C T G G A C G C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 D010 C G T A D C C C G T A T G G C C T A G A C A G A C T G C G I T C C A C G A G G C C T A G A C A C A A 0 D011 C A T A I C C C G T G A G G C C T G G G C G C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 D012 C G T A D C C C G T G A G G C C T A G G C A C A C C G T A D C C C G T A T G G C C T A G A C A C A C 0 D013 C G T A D C C C G T A T G G C C T A G A C A G A C C G T A D C T C G T A T G G C C T A G A C A C A C 0 D014 C A C A I C C C G C G A G G C C T G A G A A C G C C A C A I C C C G C G A G G C C T G A G A A C G C 0 D015 C A C A I C C C G C G T G G C C T G G A C G C A C C G T A D C T C G T A T G G C C T A G A C A C A C 0 D016 C A C A I C C C G C G A G G C C T G A G A A C G C C G T A D C C C G T A T G G C C T A G A C A C A C 0 D033 C A C A I C C C G C G T G G C C T G G A C G C A C C G T A D C [C] C G T A T G G C C T A G A C A C A C 0 D034 C A T A I C C C G T G A G G C C T G G G C G C A C C G T A D C T C G T A T G G C C T A G A C A C A C 0 D035 C G T A D C C C G T A T G G C C C A G A C A C A C C G T A D C C C G T A T G G C C C A G A C A C A C 0 D036 C A C A I C C C G C G A G G C C T G A G A A C G C T G C G I T C T A C G A G G C C T A G A C A C A C 0 D037 C A C A I C C C G C G T G G C C T G G A C G C A C T G C G I T C C A C G A G G C C T A G A C A C A A 0 D038 C A T A I C C C G T G A G G C C T G G G C G C A C C G T A D C C C G T A T G G C C T A G A C A G A C 0 D039 C A C A I C C C G C G T G G C C T G G A C G C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 D040 C A T A I C C C G T G A G G C C T G G G C G C A C C G T A D C T C G T A T G G C C T A G A C A C A C 0 E001 C G T A D C C C G T A T G G C T T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E002 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A T G C C T A G A C A C A C 0 E003 C A T A I C C C G C G A G A C C T G G G C G C A C C A T A I C C C G C G A G A C C T G G G C G C A C 0 E004 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E005 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A G G T C T A G A C A C A C 0 E006 C G T A D C C C G T A T G G C C T A G A C A C A C C G T A D C C C G T A T G G C T T A G A C A C A C 0 E007 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A G G T C T A G A C A C A C 0 E008 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A T G C C T A G A C A C A C 0 E009 C G T A D C C C G T G A G G C C T A G G C A C A C T G C G I T C T A C G A G G T C T A G A C A C A C 0 E010 C G T A I C C C G C G A G A C C T G G G C G C A C C G T A D C C C G T G A G G C C T A G G C A C A C 0 E011 C G T A D C C C G T A T G G C T T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E012 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A T G C C T A G A C A C A C 0 E013 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E014 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A T G C C T A G A C A C A C 0 E015 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E016 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A G G T C T A G A C A C A C 0 E017 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A T G C C T A G A C A C A C 0 E018 C G T G D C C C G T G A G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E019 T G C G I T C T A C G A G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E020 C G T A D C C C G T G A G G C C T A G G C A C A C T G C G I T C T A C G A G G T C T A G A C A C A C 0 E021 C G T A D C C C G T A T G G C T T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E022 C A T A I C C C G T G A G G C C T G G G C G C A C T G C G I T C T A C G A G G C C T A G A C A C A C 0 E023 C G T A D C C C G T A T G G C C T A G A C A C A C T G C G I T C T A C G A G G C C T A G A C A C A 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 = = C = = ? ? = = C = T = = = = = = = A = ? = = = = = T = = ? ? = = T = A = = = = = = = G = ? = = = 0 D002 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 D003 ? ? C = I = C = = C G = ? ? = = = G = = = G = = = ? ? T = D = T = = T A = ? ? = = = A = = = A = = = 0 D004 = A = = I ? ? = = ? ? ? = = = = = G = G = G ? ? = = G = = D ? ? = = ? ? ? = = = = = A = A = A ? ? = 0 D005 = ? = = = = = C = = = = = = = = = = = = = = = = A = ? = = = = = T = = = = = = = = = = = = = = = = C 0 D006 C = T A D C = C G T A T ? ? = = = = = = = = = = = T = C G I T = T A C G A ? ? = = = = = = = = = = = 0 D007 ? ? C = I = C = = C G A = = = = = G ? G A = = G = ? ? T = D = T = = T A T = = = = = A ? A C = = A = 0 D008 = = = = = = = = = = = = = = = = T = = = = = = ? = = = = = = = = = = = = = = = = = C = = = = = = ? = 0 D009 C A = A = C = C G = = T = = = = = G = = = G = = = T G = G = T = T A = = A = = = = = A = = = A = = = 0 D010 C = T A D C = = G T A T = = = = = = = = = = G = C T = C G I T = = A C G A = = = = = = = = = = C = A 0 D011 C A T A = C = C G T = = = = = = = G = G = G = = = T G C G = T = T A C = = = = = = = A = A = A = = = 0 D012 = = = = = = = = = = G A = = = = = = = G = = = = = = = = = = = = = = = A T = = = = = = = A = = = = = 0 D013 = = = = = = C = = = = = = = = = = = = = = = G = = = = = = = = T = = = = = = = = = = = = = = = C = = 0 D014 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? 0 D015 = A C = I = C = = C G = = = = = = G = = = G = = = = G T = D = T = = T A = = = = = = A = = = A = = = 0 D016 = A C = I = = = = C G A = = = = = G A G A = = G = = G T = D = = = = T A T = = = = = A G A C = = A = 0 D033 = A C = I ? ? ? ? C G = = = = = = G = = = G = = = = G T = D ? ? ? ? T A = = = = = = A = = = A = = = 0 D034 = A = = I = C = = = G A = = = = = G = G = G = = = = G = = D = T = = = A T = = = = = A = A = A = = = 0 D035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D036 C ? = A = C = C G = = = = = = = = G A G A = = G = T ? = G = T = T A = = = = = = = = A G A C = = A = 0 D037 C ? = A = C = = G = = T = = = = = G = = = G = = C T ? = G = T = = A = = A = = = = = A = = = A = = A 0 D038 = A = = I = = = = = G A = = = = = G = G = G C = = = G = = D = = = = = A T = = = = = A = A = A G = = 0 D039 C A = A = C = C G = = T = = = = = G = = = G = = = T G = G = T = T A = = A = = = = = A = = = A = = = 0 D040 = A = = I = C = = = G A = = = = = G = G = G = = = = G = = D = T = = = A T = = = = = A = A = A = = = 0 E001 C = T A D C = C G T A T = = = T = = = = = = = = ? T = C G I T = T A C G A = = = C = = = = = = = = ? 0 E002 = = = = = = = ? = = = = G = = = = = = = = = = = = = = = = = = = ? = = = = T = = = = = = = = = = = = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 C = T A D C = C G T A T = = = = = = = = = = = = = T = C G I T = T A C G A = = = = = = = = = = = = = 0 E005 = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = C = = = = = = = ? = = = = = = = = = = = = = = = = T = = = = = = = ? = 0 E007 = = = = = = = ? = = = = = = C = = = = = = = = = = = = = = = = = ? = = = = = = T = = = = = = = = = = 0 E008 C = T A D C = C G T A T G = = = = = = = = = = = = T = C G I T = T A C G A T = = = = = = = = = = = = 0 E009 C = T A D C = C G T = = = = C = = = = G = = = = = T = C G I T = T A C = = = = T = = = = A = = = = = 0 E010 = = = = I = = = = C = = = A = = = G = = = G ? = = = = = = D = = = = T = = = G = = = A = = = A ? = = 0 E011 C = T A D C = C G T A T = ? = T = = = = = = = = = T = C G I T = T A C G A = ? = C = = = = = = = = = 0 E012 C ? T A D C = C G T A T G = = = = = = = = = = = = T ? C G I T = T A C G A T = = = = = = = = = = = = 0 E013 C = T A D C = C G T A T = = = = = = = = = = = = = T = C G I T = T A C G A = = = = = = = = = = = = = 0 E014 = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = 0 E015 C = T A D C = C G T A T = = = = = = = = = = = = = T = C G I T = T A C G A = = = = = = = = = = = = = 0 E016 = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 E017 ? ? = = = = = = = = = = G = = = = = = = = = = = = ? ? = = = = = = = = = = T = = = = = = = = = = = = 0 E018 C = T = D C = C G T = = = = = = = = = = = = = = = T = C = I T = T A C = = = = = = = = = = = = = = = 0 E019 = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = 0 E020 C ? ? A D C = C G T = = = = C = = = = G = = = = = T ? ? G I T = T A C = = = = T = = = = A = = = = = 0 E021 C = T A D C = C G T A T = = = T = = = = = = = = = T = C G I T = T A C G A = = = C = = = = = = = = = 0 E022 C A T A = C = C G T = = = = = = = G = G = G = = = T G C G = T = T A C = = = = = = = A = A = A = = = 0 E023 C ? T A D C = C G T A T = = = = = = = = = = = = = T ? C G I T = T A C G 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 ? ? = = ? = = = = = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? ? = = = = = = = = = = = ? ? 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = 1.00 ? 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = ? = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = 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 = = = = = = = = = = = 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 0.99 = = 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 = = = 0.97 = = = = = = = = ? = = = = = = = ? = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = 0.95 = = = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 = = = 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 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 = = = = 0.94 = = = = 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 = = = = = = = = = = = = = END PHASEPROBS