************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 ilkn8.phase.inp ilkn8.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ilkn8.phase.out_freqs : haplotype frequency estimates ilkn8.phase.out_pairs : most likely haplotype pairs for each individual ilkn8.phase.out_recom : estimates of recombination parameters ilkn8.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 15 Positions of loci: 580 587 591 1479 1987 2968 3470 3821 4115 4501 4966 5326 5357 6174 6492 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ilkn8.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCTADTACGCDDCAA 6.000000 2 GCTADTACGTDDTAT 22.000000 3 GCTADTACTCDICAA 1.000000 4 GCTADTATGCDDCAA 12.000000 5 GCTAITACTCDICAA 4.000000 6 GCTGDTACTCDDCCA 1.000000 7 GCTGDCACTCDDCCA 3.000000 8 GGTADTACTCDDCAA 1.000000 9 GGTADTTCTCIDCAA 41.000000 10 TCAAITACGCDDCAA 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (4,9) D002: (2,5) D003: (3,4) D004: (5,9) D005: (4,9) D006: (5,10) D007: (1,9) D008: (4,10) D009: (7,9) D010: (1,9) D011: (2,4) D012: (4,9) D013: (4,6) D014: (2,5) D015: (9,9) D016: (4,10) D033: (1,9) D034: (1,4) D035: (1,1) D036: (4,7) D037: (4,7) D038: (2,9) D039: (2,2) D040: (4,8) E001: (2,9) E002: (9,9) E003: (9,9) E004: (2,9) E005: (9,9) E006: (9,9) E007: (9,9) E008: (2,9) E009: (2,9) E010: (2,2) E011: (2,2) E012: (2,9) E013: (9,9) E014: (9,9) E015: (2,9) E016: (9,9) E017: (2,2) E018: (2,9) E019: (2,9) E020: (2,9) E021: (2,9) E022: (9,9) E023: (9,9) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G C T A D T A T G C D D C A A G G T A D T T C T C I D C A A 0 D002 G C T A D T A C G T D D T A T G C T A I T A C T C D I C A A 0 D003 G C T A D T A C T C D I C A A G C T A D T A T G C D D C A A 0 D004 G C T A I T A C T C D I C A A G G T A D T T C T C I D C A A 0 D005 G C T A D T A T G C D D C A A G G T A D T T C T C I D C A A 0 D006 G C T A I T A C T C D I C A A T C A A I T A C G C D D C A A 0 D007 G C T A D T A C G C D D C A A G G T A D T T C T C I D C A A 0 D008 G C T A D T A T G C D D C A A T C A A I T A C G C D D C A A 0 D009 G C T G D C A C T C D D C C A G G T A D T T C T C I D C A A 0 D010 G C T A D T A C G C D D C A A G G T A D T T C T C I D C A A 0 D011 G C T A D T A C G T D D T A T G C T A D T A T G C D D C A A 0 D012 G C T A D T A T G C D D C A A G G T A D T T C T C I D C A A 0 D013 G C T A D T A T G C D D C A A G C T G D T A C T C D D C C A 0 D014 G C T A D T A C G T D D T A T G C T A I T A C T C D I C A A 0 D015 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 D016 G C T A D T A T G C D D C A A T C A A I T A C G C D D C A A 0 D033 G C T A D T A C G C D D C A A G G T A D T T C T C I D C A A 0 D034 G C T A D T A C G C D D C A A G C T A D T A T G C D D C A A 0 D035 G C T A D T A C G C D D C A A G C T A D T A C G C D D C A A 0 D036 G C T A D T A T G C D D C A A G C T G D C A C T C D D C C A 0 D037 G C T A D T A T G C D D C A A G C T G D C A C T C D D C C A 0 D038 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 D039 G C T A D T A C G T D D T A T G C T A D T A C G T D D T A T 0 D040 G (C) T A D T A (T) (G) C D D C A A G (G) T A D T A (C) (T) C D D C A A 0 E001 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E002 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E003 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E004 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E005 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E006 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E007 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E008 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E009 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E010 G C T A D T A C G T D D T A T G C T A D T A C G T D D T A T 0 E011 G C T A D T A C G T D D T A T G C T A D T A C G T D D T A T 0 E012 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E013 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E014 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E015 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E016 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E017 G C T A D T A C G T D D T A T G C T A D T A C G T D D T A T 0 E018 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E019 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E020 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E021 G C T A D T A C G T D D T A T G G T A D T T C T C I D C A A 0 E022 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 0 E023 G G T A D T T C T C I D C A A G G T A D T T C T C I D C A A 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 = = ? = A T G = D = = = = = G = = ? = T C T = I = = = = 0 D002 = = = = D = = = G T = D T = T = = = = I = = = T C = I C = A 0 D003 = = = = = = = C T = = I = = = = = = = = = = T G = = D = = = 0 D004 = C = = I = A = = = D I = = = = G = = D = T = = = I D = = = 0 D005 = C ? = = = A T G ? ? = = = = = G ? = = = T C T ? ? = = = = 0 D006 G = T = = = = = T = = I = ? = T = A = = = = = G = = D = ? = 0 D007 = C = = = = A = G = D = = = = = G = = = = T = T = I = = = = 0 D008 G = T = ? ? = T = = = = = = = T = A = ? ? = C = = = = = = = 0 D009 = C = G ? C A = = ? D = = C = = G = A ? T T = = ? I = = A = 0 D010 = C = = = = A = G = D = = = = = G = = = = T = T = I = = = = 0 D011 = = = = = = = C = T = = T = T = = = = = = = T = C = = C = A 0 D012 = C = = = = A T G = ? = = = = = G = = = = T C T = ? = = = = 0 D013 = = = A = = = T G = = = = A = = = = G = = = C T = = = = C = 0 D014 = = = = D = = = G T = D T = T = = = = I = = = T C = I C = A 0 D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D016 G = T = D = = T = = = = = = = T = A = I = = C = = = = = = = 0 D033 = C = = ? = A = G = ? = = = = = G = = ? = T = T = ? = = = = 0 D034 = = = = = = = C = = = = = = = = = = = = = = T = = = = = = = 0 D035 = = = = = = = = = ? ? = = = = = = = = = = = = = ? ? = = = = 0 D036 = = = A = T = T G = = = = A = = = = G = C = C T = = = = C = 0 D037 = = = A = T = T G = = = = A = = = = G = C = C T = = = = C = 0 D038 = C = = = = A = G T D = T = T = G = = = = T = T C I = C = A 0 D039 = = = = = = = = = = ? = = = = = = = = = = = = = = ? = = = = 0 D040 = (C) = = = = = (T) (G) = = = = = = = (G) = = = = = (C) (T) = = = = = = 0 E001 = C = = = = A = G ? ? = T = T = G = = = = T = T ? ? = C = A 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 = C = = = = A = G T D = T = T = G = = = = T = T C I = C = A 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E008 = C = = = = A = G T ? = T = T = G = = = = T = T C ? = C = A 0 E009 = C = = = = A = G T D = T = T = G = = = = T = T C I = C = A 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 = = = = = = = = = ? = = = = = = = = = = = = = = ? = = = = = 0 E012 = C = = = = A = G T ? = T = T = G = = = = T = T C ? = C = A 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 = C = = = = A = G T D = T = T = G = = = = T = T C I = C = A 0 E016 = = = = = = = = = = ? = = = = = = = = = = = = = = ? = = = = 0 E017 = = = = = = = = = = ? ? ? = = = = = = = = = = = = ? ? ? = = 0 E018 = C = = = ? A = G T D = T = T = G = = = ? T = T C I = C = A 0 E019 = C = = = = ? ? G T ? ? ? = T = G = = = = ? ? T C ? ? ? = A 0 E020 = C = = = = A = G T D = T = T = G = = = = T = T C I = C = A 0 E021 = C = = = = A = G T D ? ? = T = G = = = = T = T C I ? ? = A 0 E022 = = = = ? = = = = = = = = = = = = = = ? = = = = = = = = = = 0 E023 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = 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 ? 1.00 1.00 = = ? 1.00 = = 1.00 = = 1.00 = = = = 1.00 = 1.00 = 1.00 = = = = = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = ? = = = = = = = 1.00 = = = 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 = = = = = = = = = = ? = = = = = 0.88 = = = = = 0.89 0.89 = = = = = = = 1.00 = = = = 1.00 = 1.00 ? ? = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 ? = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 ? = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = ? = = = = = = = = = = = = = = ? ? ? = = = 1.00 = = = ? 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = ? ? 1.00 1.00 ? ? ? = 1.00 = 1.00 = = = = 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