************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 vitrn.phase.inp vitrn.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST vitrn.phase.out_freqs : haplotype frequency estimates vitrn.phase.out_pairs : most likely haplotype pairs for each individual vitrn.phase.out_recom : estimates of recombination parameters vitrn.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 18 Positions of loci: 384 925 967 1037 2006 2011 2656 3627 3827 4005 4192 4361 4534 4772 4873 5232 5259 5278 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file vitrn.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGTGGTCCCTTDTCAAGG 5.000000 2 GGTGGTCCCTTDTCAGCG 2.000000 3 GGTGGTCTCTTDTCAAGG 36.000000 4 GGTGGTCTCTTDTCAAGA 4.000000 5 GGTGGTTCCTTDTCAGCG 28.000000 6 GGTGGTTTCTTDTCAGCG 1.000000 7 GGCTACCCTCCDTCAAGG 1.000000 8 GCTGGTCTCTTDTCAAGG 3.000000 9 TGCTGCCCTCCDCCAAGG 1.000000 10 TGCTACCCCTTITTGAGG 3.000000 11 TGCTACCCTCCDTCAAGG 9.000000 12 TGCTACCCTCCDCCAAGG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,5) D002: (6,11) D003: (4,12) D004: (5,10) D005: (8,11) D006: (1,3) D007: (4,5) D008: (3,5) D009: (2,11) D010: (3,3) D011: (3,8) D012: (9,11) D013: (1,3) D014: (5,5) D015: (3,11) D016: (3,11) D033: (2,11) D034: (3,10) D035: (1,10) D036: (3,4) D037: (3,8) D038: (3,7) D039: (3,3) D040: (3,4) E001: (5,5) E002: (3,3) E003: (3,5) E004: (3,5) E005: (3,5) E006: (3,5) E007: (3,5) E008: (3,3) E009: (3,5) E010: (1,5) E011: (5,5) E012: (3,3) E013: (5,5) E014: (1,5) E015: (3,5) E016: (3,5) E017: (5,5) E018: (3,3) E019: (5,11) E020: (3,5) E021: (3,5) E022: (3,11) E023: (3,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 D002 G G T G G T T (T) C T T D T C A G C G T G C T A C C (C) T C C D T C A A G G 0 D003 G G T G G T C T C T T D (T) C A A G A T G C T A C C C T C C D (C) C A A G G 0 D004 G G T G G T T C C T T D T C A G C G T G C T A C C C C T T I T T G A G G 0 D005 G C T G G T C T C T T D T C A A G G T G C T A C C C T C C D T C A A G G 0 D006 G G T G G T C C C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 D007 G G T G G T C T C T T D T C A A G A G G T G G T T C C T T D T C A G C G 0 D008 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 D009 G G T G G T C C C T T D T C A G C G T G C T A C C C T C C D T C A A G G 0 D010 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 D011 G G T G G T C T C T T D T C A A G G G C T G G T C T C T T D T C A A G G 0 D012 T G C T (G) C C C T C C D C C A A G G T G C T (A) C C C T C C D T C A A G G 0 D013 G G T G G T C C C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 D014 G G T G G T T C C T T D T C A G C G G G T G G T T C C T T D T C A G C G 0 D015 G G T G G T C T C T T D T C A A G G T G C T A C C C T C C D T C A A G G 0 D016 G G T G G T C T C T T D T C A A G G T G C T A C C C T C C D T C A A G G 0 D033 G G T G G T C C C T T D T C A G C G [T] G C T A C C C T C C D T C A A G G 0 D034 G G T G G T C T C T T D T C A A G G T G C T A C C C C T T I T T G A G G 0 D035 G G T G G T C C C T T D T C A A G G T G C T A C C C C T T I T T G A G G 0 D036 G G T G G T C [T] C T T D T C A A G G G G T G G T C T C T T D T C A A G A 0 D037 G G T G G T C T C T T D T C A A G G G C T G G T C T C T T D T C A A G G 0 D038 G G T G G T C T C T T D T C A A G G G G C T A C C C T C C D T C A A G G 0 D039 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 D040 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G A 0 E001 G G T G G T T C C T T D T C A G C G G G T G G T T C C T T D T C A G C G 0 E002 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 E003 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E004 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E005 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E006 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E007 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E008 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 E009 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E010 G G T G G T C C C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E011 G G T G G T T C C T T D T C A G C G G G T G G T T C C T T D T C A G C G 0 E012 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 E013 G G T G G T T C C T T D T C A G C G G G T G G T T C C T T D T C A G C G 0 E014 G G T G G T C C C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E015 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E016 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E017 G G T G G T T C C T T D T C A G C G G G T G G T T C C T T D T C A G C G 0 E018 G G T G G T C T C T T D T C A A G G G G T G G T C T C T T D T C A A G G 0 E019 G G T G G T T C C T T D T C A G C G T G C T A C C C T C C D T C A A G G 0 E020 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E021 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 0 E022 G G T G G T C T C T T D T C A A G G T G C T A C C C T C C D T C A A G G 0 E023 G G T G G T C T C T T D T C A A G G G G T G G T T C C T T D T C A G C G 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 = = = = = = ? T = = = = = = = A G = = = = = = = ? C = = = = = = = G C = 0 D002 G = T G G T T (T) C T T = = = = G C = T = C T A C C (C) T C C = = = = A G = 0 D003 G = T G G T = T C T T = (T) = = = = A T = C T A C = C T C C = (C) = = = = G 0 D004 G = T G G T T = = = ? D = C A G C = T = C T A C C = = = ? I = T G A G = 0 D005 G C T G G T = T C T T = = = = = = = T G C T A C = C T C C = = = = = = = 0 D006 = = = = = = = C = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 D007 = = = = = = C T = = = = = = = A G A = = = = = = T C = = = = = = = G C G 0 D008 = = = = = = C T = = = = ? ? = A G = = = = = = = T C = = = = ? ? = G C = 0 D009 G = T G G T = = C T T = = = = G C = T = C T A C = = T C C = = = = A G = 0 D010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D011 = G = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = 0 D012 = = = = (G) = = = = = = = C = = = = = = = = = (A) = = = = = = = T = = = = = 0 D013 = = = = = = = C = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 D014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D015 G = T G G T = T C T T = = = ? ? ? ? T = C T A C = C T C C = = = ? ? ? ? 0 D016 G = T G G T = T C T T = = = = = = = T = C T A C = C T C C = = = = = = = 0 D033 ? = T G G T = = C T T = = = = G C = ? = C T A C = = T C C = = = = A G = 0 D034 G = T G G T = T = = ? D ? ? A ? ? ? T = C T A C = C = = ? I ? ? G ? ? ? 0 D035 ? = T G G T = = = = ? D = C A = = = ? = C T A C = = = = ? I = T G = = = 0 D036 = = = = = = = ? = = = = = = = = = G = = = = = = = ? = = = = = = = = = A 0 D037 ? G = = = = = = = = = = ? ? = ? ? ? ? C = = = = = = = = = = ? ? = ? ? ? 0 D038 = = T G G T = T C T T = ? ? = = = = = = C T A C = C T C C = ? ? = = = = 0 D039 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D040 = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = A 0 E001 ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E003 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 0 E004 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 0 E005 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 0 E006 = = = = = = C T = = ? = = = = A G = = = = = = = T C = = ? = = = = G C = 0 E007 = = = = = = C T = = = = = = ? A G = = = = = = = T C = = = = = = ? G C = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 0 E010 = = = = = = C = = = = = = = = A G = = = = = = = T = = = = = = = = G C = 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = = = = C = = = = = = = = A G = = = = = = = T = = = = = = = = G C = 0 E015 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 0 E016 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 0 E017 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 G = T G G T T = C T T = = = = G C = T = C T A C C = T C C = = = = A G = 0 E020 ? = = = = = C T = = = = = = = A G = ? = = = = = T C = = = = = = = G C = 0 E021 = = = = = = C T = = = = = ? = A G = = = = = = = T C = = = = = ? = G C = 0 E022 G = T G G T = T C T T = = = = = = = T = C T A C = C T C C = = = = = = = 0 E023 = = = = = = C T = = = = = = = A G = = = = = = = T C = = = = = = = G C = 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 0.99 0.51 1.00 1.00 1.00 = = = = 0.99 0.99 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 0.70 = = = = 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 0.96 1.00 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 = = = = 0.97 0.97 = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = 0.57 = = = = = = = 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 = 0.99 1.00 1.00 1.00 = = = = = = = ? = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = = = 0.97 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 1.00 = = = = = = = 1.00 1.00 = = = = = = = 1.00 1.00 = = = = = = = 1.00 1.00 = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = ? = = = = = 1.00 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 = END PHASEPROBS