************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 ilk24.phase.inp ilk24.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ilk24.phase.out_freqs : haplotype frequency estimates ilk24.phase.out_pairs : most likely haplotype pairs for each individual ilk24.phase.out_recom : estimates of recombination parameters ilk24.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 24 Positions of loci: 634 806 1619 1889 2049 2461 3260 3530 3625 4069 4243 4332 4585 4602 4943 6016 6282 6748 6998 8314 8321 10727 10894 11077 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ilk24.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TTIACDCCCTAIGCCCCAITAGGG 26.000000 2 TTIACDCCCTAIGCCCCAITTAAA 2.000000 3 TTIACDCCCTAIGCCTCADTAAAA 1.000000 4 TTIACDCCTCGDACCTCGDTAAAA 5.000000 5 TTIACDTCTCGDGTCTTADTAAAA 26.000000 6 TTIACDTCTCGDGTCTTADAAAAA 4.000000 7 TTIACICCTCGDACCTCGDTAAAA 4.000000 8 TTIATDCCCTAIGCCCCAITTAAA 5.000000 9 TTIGCICCTCGDACCTCGDTAAAA 6.000000 10 TTDACDTCTCGDGTCTTADTAAAA 6.000000 11 CTIACDCCCCADGCCTCAITAGAG 1.000000 12 CTIACDCCTCGDGCCTCADTAAAA 2.000000 13 CTIACDCCTCGDGCATCADTAAAA 2.000000 14 CGIACDCATCGDGCCTCADTAGGG 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,8) D002: (4,9) D003: (9,14) D004: (5,7) D005: (4,7) D006: (3,5) D007: (1,8) D008: (6,12) D009: (6,9) D010: (10,14) D011: (12,13) D012: (5,11) D013: (1,9) D014: (1,13) D015: (4,5) D016: (6,14) D033: (1,5) D034: (4,7) D035: (4,9) D036: (5,5) D037: (5,9) D038: (2,14) D039: (6,7) D040: (8,8) E001: (1,5) E002: (1,5) E003: (1,5) E004: (1,5) E005: (5,10) E006: (1,5) E007: (5,10) E008: (1,5) E009: (1,5) E010: (1,10) E011: (1,5) E012: (1,1) E013: (1,5) E014: (1,8) E015: (5,10) E016: (1,5) E017: (1,5) E018: (5,5) E019: (1,10) E020: (1,5) E021: (1,5) E022: (1,2) E023: (1,1) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T T I A C D C C C T A I G C C C C A I T A G G G T T I A T D C C C T A I G C C C C A I T T A A A 0 D002 T T I A C D C C T C G D A C C T C G D T A A A A T T I G C I C C T C G D A C C T C G D T A A A A 0 D003 T T I G C I C C T C G D A C C T C G D T A A A A C G I A C D C A T C G D G C C T C A D T A G G G 0 D004 T T I A C D T C T C G D G T C T T A D T A A A A T T I A C I C C T C G D A C C T C G D T A A A A 0 D005 T T I A C D C C T C G D A C C T C G D T A A A A T T I A C I C C T C G D A C C T C G D T A A A A 0 D006 T T I A C D C C C T A I G C C T C A D T A A A A T T I A C D T C T C G D G T C T T A D T A A A A 0 D007 T T I A C D C C C T A I G C C C C A I T A G G G T T I A T D C C C T A I G C C C C A I T T A A A 0 D008 T T I A C D T C T C G D G T C T T A D A A A A A C T I A C D C C T C G D G C C T C A D T A A A A 0 D009 T T I A C D T C T C G D G T C T T A D (A) A A A A T T I [G] C I C C T C G D A C C T C G D (T) A A A A 0 D010 T T D A C D T C T C G D G T C T T A D T A A A A C G I A C D C A T C G D G C C T C A D T A G G G 0 D011 C T I A C D C C T C G D G C C T C A D T A A A A C T I A C D C C T C G D G C A T C A D T A A A A 0 D012 (T) T I A C D T C (T) C (G) D G T C T T A D T A A A A (C) T I A C D C C (C) C (A) D G C C T C A I T A G A G 0 D013 T T I A C D C C C T A I G C C C C A I T A G G G T T I G C I C C T C G D A C C T C G D T A A A A 0 D014 T T I A C D C C C T A I G C C C C A I T A G G G C T I A C D C C T C G D G C A T C A D T A A A A 0 D015 T T I A C D C C T C G D A C C T C G D T A A A A T T I A C D T C T C G D G T C T T A D T A A A A 0 D016 T T I A C D T C T C G D G T C T T A D A A A A A C G I A C D C A T C G D G C C T C A D T A G G G 0 D033 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 D034 T T I A C D C C T C G D A C C T C G D T A A A A T T I A C I C C T C G D A C C T C G D T A A A A 0 D035 T T I A C D C C T C G D A C C T C G D T A A A A T T I G C I C C T C G D A C C T C G D T A A A A 0 D036 T T I A C D T C T C G D G T C T T A D T A A A A T T I A C D T C T C G D G T C T T A D T A A A A 0 D037 T T I A C D T C T C G D G T C T T A D T A A A A T T I G C I C C T C G D A C C T C G D T A A A A 0 D038 T T I A C D C C C T A I G C C C C A I T T A A A C G I A C D C A T C G D G C C T C A D T A G G G 0 D039 T T I A C D T C T C G D G T C T T A D (A) A A A A T T I A C I C C T C G D A C C T C G D (T) A A A A 0 D040 T T I A T D C C C T A I G C C C C A I T T A A A T T I A T D C C C T A I G C C C C A I T T A A A 0 E001 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E002 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E003 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E004 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E005 T T I A C D T C T C G D G T C T T A D T A A A A T T D A C D T C T C G D G T C T T A D T A A A A 0 E006 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E007 T T I A C D T C T C G D G T C T T A D T A A A A T T D A C D T C T C G D G T C T T A D T A A A A 0 E008 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E009 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E010 T T I A C D C C C T A I G C C C C A I T A G G G T T D A C D T C T C G D G T C T T A D T A A A A 0 E011 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E012 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D C C C T A I G C C C C A I T A G G G 0 E013 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E014 T T I A C D C C C T A I G C C C C A I T A G G G T T I A T D C C C T A I G C C C C A I T T A A A 0 E015 T T I A C D T C T C G D G T C T T A D T A A A A T T D A C D T C T C G D G T C T T A D T A A A A 0 E016 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E017 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E018 T T I A C D T C T C G D G T C T T A D T A A A A T T I A C D T C T C G D G T C T T A D T A A A A 0 E019 T T I A C D C C C T A I G C C C C A I T A G G G T T D A C D T C T C G D G T C T T A D T A A A A 0 E020 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E021 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D T C T C G D G T C T T A D T A A A A 0 E022 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D C C C T A I G C C C C A I T T A A A 0 E023 T T I A C D C C C T A I G C C C C A I T A G G G T T I A C D C C C T A I G C C C C A I T A G G 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 ? ? = = C ? = ? = = = = = = = = = = = = A G G ? ? ? = = T ? = ? = = = = = = = = = = = = T A A ? 0 D002 = = = A = D = = = = = = = = = = = ? = = = = ? ? = = = G = I = = = = = = = = = = = ? = = = = ? ? 0 D003 T T = G = I = C = = = = A = = = = G = = = A A ? C G = A = D = A = = = = G = = = = A = = = G G ? 0 D004 = = ? = = D T = = = = = G T = = T A = = = = = = = = ? = = I C = = = = = A C = = C G = = = = = = 0 D005 = = = = = D = ? = = = = = = = = = ? = = = = = ? = = = = = I = ? = = = = = = = = = ? = = = = = ? 0 D006 = = = = = = C = C ? ? ? = C = = C = = = = = = ? = = = = = = T = T ? ? ? = T = = T = = = = = = ? 0 D007 = = = = C = = = = = = = = = = = = = = = A G G ? = = = = T = = = = = = = = = = = = = = = T A A ? 0 D008 ? ? ? ? ? ? ? = = = = = = T = = T = = A = = = ? ? ? ? ? ? ? ? = = = = = = C = = C = = T = = = ? 0 D009 = = = ? ? D T = = = = = G T ? = T ? = (A) = = ? ? = = = ? ? I C = = = = = A C ? = C ? = (T) = = ? ? 0 D010 T T D = = ? T C = = = = = T = = T = = = = A A A C G I = = ? C A = = = = = C = = C = = = = G G G 0 D011 = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = 0 D012 (T) = = = = = T = (T) = (G) = = T = = T = D = = A = A (C) = = = = = C = (C) = (A) = = C = = C = I = = G = G 0 D013 = = = A = D = = C T A I G = = C = A I = = G G G = = = G = I = = T C G D A = = T = G D = = A A A 0 D014 T = = = = = = = C T A I = = C C = = I = = G G ? C = = = = = = = T C G D = = A T = = D = = A A ? 0 D015 = = = = = = C = = = = = A C ? = C G = = = = = ? = = = = = = T = = = = = G T ? = T A = = = = = ? 0 D016 T T = = = = T C = = = = = T ? = T = = A = A A ? C G = = = = C A = = = = = C ? = C = = T = G G ? 0 D033 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 D034 = = = = = D = = = = = = = = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = = = = = = 0 D035 = = = A = D = = = = = = = = = = = = = = = = = ? = = = G = I = = = = = = = = = = = = = = = = = ? 0 D036 = = = = = = = = = = = = = = = = ? = = ? = = = = = = = = = = = = = = = = = = = = ? = = ? = = = = 0 D037 = = ? A = ? T = = = = = G T = = T A = = = = = = = = ? G = ? C = = = = = A C = = C G = = = = = = 0 D038 T T = = = = = C C T A I = = = C = = I = T A A A C G = = = = = A T C G D = = = T = = D = A G G G 0 D039 = = = = = D T = = = = = G T = = T A = (A) = = = ? = = = = = I C = = = = = A C = = C G = (T) = = = ? 0 D040 ? = = = = = = = = = = = = = ? = = = = = = = = ? ? = = = = = = = = = = = = = ? = = = = = = = = ? 0 E001 ? ? = = = = ? = C T A I = C = C C = I = = G G G ? ? = = = = ? = T C G D = T = T T = D = = A A A 0 E002 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 E003 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 E004 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 E005 = = I = = = = = = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = C = C T A I = C = C C = I = ? G G G = = = = = = T = T C G D = T = T T = D = ? A A A 0 E007 = = I = = = = = = = = = = = ? = = = = = = = = ? = = D = = = = = = = = = = = ? = = = = = = = = ? 0 E008 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 E009 ? ? = = = = C ? ? T A I = C = C C = I = = G G G ? ? = = = = T ? ? C G D = T = T T = D = = A A A 0 E010 = = I = = = C ? C T A I = C = C C = ? = = G G G = = D = = = T ? T C G D = T = T T = ? = = A A A 0 E011 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = ? ? ? = ? = C T A I = C = C C = I = = G G G = = ? ? ? = ? = T C G D = T = T T = D = = A A A 0 E014 = = = = C = = = = = = = = = = = = = = = A G G ? = = = = T = = = = = = = = = = = = = = = T A A ? 0 E015 = = I = = = = = = = = = = = = = = = = = = = = ? = = D = = = = = = = = = = = = = = = = = = = = ? 0 E016 = = ? = = = C = C T A I ? ? = C C = ? = = G G ? = = ? = = = T = T C G D ? ? = T T = ? = = A A ? 0 E017 ? ? = = = = ? ? ? T A I = C = C C ? ? = = G G ? ? ? = = = = ? ? ? C G D = T = T T ? ? = = A A ? 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 = = I = = = C = C T A I = C = C C = I = = G G G = = D = = = T = T C G D = T = T T = D = = A A A 0 E020 = = = = = = C = C T A I = C = C C = I = = G G G = = = = = = T = T C G D = T = T T = D = = A A A 0 E021 = = ? = = = C = C T A I = C = C C = I = = G G G = = ? = = = T = T C G D = T = T T = D = = A A A 0 E022 = = = = = = = = = = = = = = = = = = = = A G G G = = = = = = = = = = = = = = = = = = = = T A A A 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 ? = = = 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 = = 0.96 = = = ? = = = ? ? 0.99 1.00 = = = = = 1.00 1.00 ? = 1.00 ? = 0.90 = = ? ? 1.00 1.00 1.00 = = ? 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = 1.00 = = = = = = = = = 0.87 = = = = = 1.00 = 0.76 = 0.76 = = 1.00 = = 1.00 = 1.00 = = 1.00 = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 = = 1.00 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 = = = = = = = = = = = = = = = = = = = = = 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 = 0.98 0.98 0.98 0.98 = = = = = 0.99 1.00 = = = = = 1.00 1.00 = = 1.00 1.00 = 0.90 = = = ? ? = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = ? = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = ? 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = ? = = = = = = = = ? = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 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 ? = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = = = = ? = ? = = = = = = = = = END PHASEPROBS