************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 clspn.phase.inp clspn.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST clspn.phase.out_freqs : haplotype frequency estimates clspn.phase.out_pairs : most likely haplotype pairs for each individual clspn.phase.out_recom : estimates of recombination parameters clspn.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 94 Number of Loci: 9 Positions of loci: 9504 10710 17008 17341 17984 18241 19824 27297 31493 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file clspn.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGGDACGGT 11.000000 2 CGGDATGGT 66.000000 3 CAGDACGGT 3.000000 4 CAGDACAGC 91.000000 5 TGAIGCGAT 16.000000 6 TGAIGCGGT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,5) D002: (4,5) D003: (1,5) D004: (1,2) D005: (2,2) D006: (2,6) D007: (2,4) D008: (1,4) D009: (2,5) D010: (4,5) D011: (1,4) D012: (1,1) D013: (3,5) D014: (4,4) D015: (2,4) D016: (2,4) D033: (4,4) D034: (2,5) D035: (2,5) D036: (1,4) D037: (2,5) D038: (1,3) D039: (4,4) D040: (2,4) E001: (4,4) E002: (4,4) E003: (4,4) E004: (4,4) E005: (4,4) E006: (4,4) E007: (4,4) E008: (4,5) E009: (4,4) E010: (4,4) E011: (4,4) E012: (4,4) E013: (4,4) E014: (4,4) E015: (1,4) E016: (4,4) E017: (4,4) E018: (4,4) E019: (4,4) E020: (4,4) E021: (4,4) E022: (4,4) E023: (4,4) E024: (4,4) H101: (2,2) H102: (2,2) H103: (2,3) H104: (1,5) H105: (2,4) H106: (2,4) H107: (1,2) H108: (2,4) H109: (4,4) H110: (4,5) H111: (2,4) H112: (4,4) H113: (2,4) H114: (2,4) H115: (4,5) H116: (4,4) H117: (2,4) H118: (2,4) H119: (2,4) H120: (2,4) H121: (4,4) H122: (4,4) X125: (2,4) X126: (2,5) X127: (2,2) X128: (4,4) X129: (2,2) X130: (2,2) X131: (2,4) X132: (2,4) X133: (4,5) X134: (2,5) X135: (2,2) X136: (2,4) X137: (2,2) X138: (2,2) X139: (2,2) X140: (2,2) X141: (2,2) X142: (2,2) X143: (2,2) X144: (2,2) X145: (2,2) X146: (2,2) X147: (2,4) X148: (2,2) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C G G D A T G G T T G A I G C G A T 0 D002 C A G D A C A G C T G A I G C G A T 0 D003 C G G D A C G G T T G A I G C G A T 0 D004 C G G D A C G G T C G G D A T G G T 0 D005 C G G D A T G G T C G G D A T G G T 0 D006 C G G D A T G G T T G A I G C G G T 0 D007 C G G D A T G G T C A G D A C A G C 0 D008 C G G D A C G G T C A G D A C A G C 0 D009 C G G D A T G G T T G A I G C G A T 0 D010 C A G D A C A G C T G A I G C G A T 0 D011 C G G D A C G G T C A G D A C A G C 0 D012 C G G D A C G G T C G G D A C G G T 0 D013 C A G D A C G G T T G A I G C G A T 0 D014 C A G D A C A G C C A G D A C A G C 0 D015 C G G D A T G G T C A G D A C A G C 0 D016 C G G D A T G G T C A G D A C A G C 0 D033 C A G D A C A G C C A G D A C A G C 0 D034 C G G D A T G G T T G A I G C G A T 0 D035 C G G D A T G G T T G A I G C G A T 0 D036 C G G D A C G G T C A G D A C A G C 0 D037 C G G D A T G G T T G A I G C G A T 0 D038 C G G D A C G G T C A G D A C G G T 0 D039 C A G D A C A G C C A G D A C A G C 0 D040 C G G D A T G G T C A G D A C A G C 0 E001 C A G D A C A G C C A G D A C A G C 0 E002 C A G D A C A G C C A G D A C A G C 0 E003 C A G D A C A G C C A G D A C A G C 0 E004 C A G D A C A G C C A G D A C A G C 0 E005 C A G D A C A G C C A G D A C A G C 0 E006 C A G D A C A G C C A G D A C A G C 0 E007 C A G D A C A G C C A G D A C A G C 0 E008 C A G D A C A G C T G A I G C G A T 0 E009 C A G D A C A G C C A G D A C A G C 0 E010 C A G D A C A G C C A G D A C A G C 0 E011 C A G D A C A G C C A G D A C A G C 0 E012 C A G D A C A G C C A G D A C A G C 0 E013 C A G D A C A G C C A G D A C A G C 0 E014 C A G D A C A G C C A G D A C A G C 0 E015 C G G D A C G G T C A G D A C A G C 0 E016 C A G D A C A G C C A G D A C A G C 0 E017 C A G D A C A G C C A G D A C A G C 0 E018 C A G D A C A G C C A G D A C A G C 0 E019 C A G D A C A G C C A G D A C A G C 0 E020 C A G D A C A G C C A G D A C A G C 0 E021 C A G D A C A G C C A G D A C A G C 0 E022 C A G D A C A G C C A G D A C A G C 0 E023 C A G D A C A G C C A G D A C A G C 0 E024 C A G D A C A G C C A G D A C A G C 0 H101 C G G D A T G G T C G G D A T G G T 0 H102 C G G D A T G G T C G G D A T G G T 0 H103 C G G D A T G G T C A G D A C G G T 0 H104 C G G D A C G G T T G A I G C G A T 0 H105 C G G D A T G G T C A G D A C A G C 0 H106 C G G D A T G G T C A G D A C A G C 0 H107 C G G D A C G G T C G G D A T G G T 0 H108 C G G D A T G G T C A G D A C A G C 0 H109 C A G D A C A G C C A G D A C A G C 0 H110 C A G D A C A G C T G A I G C G A T 0 H111 C G G D A T G G T C A G D A C A G C 0 H112 C A G D A C A G C C A G D A C A G C 0 H113 C G G D A T G G T C A G D A C A G C 0 H114 C G G D A T G G T C A G D A C A G C 0 H115 C A G D A C A G C T G A I G C G A T 0 H116 C A G D A C A G C C A G D A C A G C 0 H117 C G G D A T G G T C A G D A C A G C 0 H118 C G G D A T G G T C A G D A C A G C 0 H119 C G G D A T G G T C A G D A C A G C 0 H120 C G G D A T G G T C A G D A C A G C 0 H121 C A G D A C A G C C A G D A C A G C 0 H122 C A G D A C A G C C A G D A C A G C 0 X125 C G G D A T G G T C A G D A C A G C 0 X126 C G G D A T G G T T G A I G C G A T 0 X127 C G G D A T G G T C G G D A T G G T 0 X128 C A G D A C A G C C A G D A C A G C 0 X129 C G G D A T G G T C G G D A T G G T 0 X130 C G G D A T G G T C G G D A T G G T 0 X131 C G G D A T G G T C A G D A C A G C 0 X132 C G G D A T G G T C A G D A C A G C 0 X133 C A G D A C A G C T G A I G C G A T 0 X134 C G G D A T G G T T G A I G C G A T 0 X135 C G G D A T G G T C G G D A T G G T 0 X136 C G G D A T G G T C A G D A C A G C 0 X137 C G G D A T G G T C G G D A T G G T 0 X138 C G G D A T G G T C G G D A T G G T 0 X139 C G G D A T G G T C G G D A T G G T 0 X140 C G G D A T G G T C G G D A T G G T 0 X141 C G G D A T G G T C G G D A T G G T 0 X142 C G G D A T G G T C G G D A T G G T 0 X143 C G G D A T G G T C G G D A T G G T 0 X144 C G G D A T G G T C G G D A T G G T 0 X145 C G G D A T G G T C G G D A T G G T 0 X146 C G G D A T G G T C G G D A T G G T 0 X147 C G G D A T G G T C A G D A C A G C 0 X148 C G G D A T G G T C G G D A T G G 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 C = G ? A T = G = T = A ? G C = A = 0 D002 C A G D A = A G C T G A I G = G A T 0 D003 C = G D A = = G = T = A I G = = A = 0 D004 = = = = = C = = = = = = = = T = = = 0 D005 = = = = = = = = = = = = = = = = = = 0 D006 C = ? ? A T = = = T = ? ? G C = = = 0 D007 = G = = = T G = T = A = = = C A = C 0 D008 = G = = = = ? = ? = A = = = = ? = ? 0 D009 C = G D A T = G = T = A I G C = A = 0 D010 C A G ? A = A G C T G A ? G = G A T 0 D011 = G = = = = G = T = A = = = = A = C 0 D012 = = = = = = = = = = = = = = = = = = 0 D013 C A G D A = = G = T G A I G = = A = 0 D014 = = = = = = = = = = = = = = = = = = 0 D015 = G = = = T G = T = A = = = C A = C 0 D016 = G = = = T G = T = A = = = C A = C 0 D033 = = = = = = = = = = = = = = = = = = 0 D034 C = G D A T = G = T = A I G C = A = 0 D035 C = G D A T = G = T = A I G C = A = 0 D036 = G = = = = G = T = A = = = = A = C 0 D037 C = G D A T = G = T = A I G C = A = 0 D038 = G = = = = = = = = A = = = = = = = 0 D039 = = = = = = = = = = = = = = = = = = 0 D040 = G = = = T G = ? = A = = = C A = ? 0 E001 = = = ? = = = = = = = = ? = = = = = 0 E002 = = = ? = = = = = = = = ? = = = = = 0 E003 = = = = = = = = = = = = = = = = = = 0 E004 = = = = = = = = = = = = = = = = = = 0 E005 = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = 0 E007 ? = = = = = = = = ? = = = = = = = = 0 E008 C A G D A = A G C T G A I G = G A T 0 E009 = = = = = = = = = = = = = = = = = = 0 E010 = = = = = = = = = = = = = = = = = = 0 E011 = = = = = = = = = = = = = = = = = = 0 E012 = = = = = = = = = = = = = = = = = = 0 E013 = = = = = = = = = = = = = = = = = = 0 E014 = = = = = = = = = = = = = = = = = = 0 E015 = G = = = = G = T = A = = = = A = C 0 E016 = = = = = = = = = = = = = = = = = = 0 E017 = = = ? = = = = = = = = ? = = = = = 0 E018 = = = = = = = = = = = = = = = = = = 0 E019 = = = = = = = = = = = = = = = = = = 0 E020 = = = = = = = = = = = = = = = = = = 0 E021 = = = = = = = = = = = = = = = = = = 0 E022 = = = = = = = = = = = = = = = = = = 0 E023 = = = = = = = = = = = = = = = = = = 0 E024 = = = = = = = = = = = = = = = = = = 0 H101 = = = ? = = = = = = = = ? = = = = = 0 H102 = = = = = = = = = = = = = = = = = = 0 H103 = G = = = T = = = = A = = = C = = = 0 H104 C = G D A = = G = T = A I G = = A = 0 H105 = G = = = T G = T = A = = = C A = C 0 H106 = G = = = T G = T = A = = = C A = C 0 H107 = = = = = C = = = = = = = = T = = = 0 H108 = G = = = T G = T = A = = = C A = C 0 H109 = = = = = = = = = = = = = = = = = = 0 H110 C A G D A = A G C T G A I G = G A T 0 H111 = G = = = T G = T = A = = = C A = C 0 H112 = = = = = = = = = = = = = = = = = = 0 H113 = G = = = T G = T = A = = = C A = C 0 H114 = G = = = T G = T = A = = = C A = C 0 H115 C A G D A = A G C T G A I G = G A T 0 H116 ? = = = = = = = = ? = = = = = = = = 0 H117 = G = ? = T G = T = A = ? = C A = C 0 H118 = G = = = T G = T = A = = = C A = C 0 H119 = G = = = T G = T = A = = = C A = C 0 H120 = G = = = T G = T = A = = = C A = C 0 H121 = = = = = = = = = = = = = = = = = = 0 H122 = = = ? = = = = = = = = ? = = = = = 0 X125 = G = = = T G = T = A = = = C A = C 0 X126 C = G D A T = G = T = A I G C = A = 0 X127 = = = = = = = = = = = = = = = = = = 0 X128 ? = = = = = = = = ? = = = = = = = = 0 X129 = = = = = = = = ? = = = = = = = = ? 0 X130 ? = = = = = = = = ? = = = = = = = = 0 X131 = G = = = T G = T = A = = = C A = C 0 X132 = G = ? = T G = T = A = ? = C A = C 0 X133 C A G D A = A G C T G A I G = G A T 0 X134 C = G D A T = G = T = A I G C = A = 0 X135 = = = = = = = = = = = = = = = = = = 0 X136 = G = ? = T G = T = A = ? = C A = C 0 X137 = = = = = = = = = = = = = = = = = = 0 X138 = = = = = = = = = = = = = = = = = = 0 X139 = = = = = = = = = = = = = = = = = = 0 X140 = = = = = = = = = = = = = = = = = = 0 X141 = = ? ? = = = = = = = ? ? = = = = = 0 X142 = = = = = = = = = = = = = = = = = = 0 X143 = = = ? = = = = = = = = ? = = = = = 0 X144 = = = = = = = = = = = = = = = = = = 0 X145 = = = = = = = = = = = = = = = = = = 0 X146 = = = = = = = = ? = = = = = = = = ? 0 X147 = G = = = T G = T = A = = = C A = C 0 X148 = = = = = = = = = = = = = = = = = = 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 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 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 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? = = = = = = = = = 1.00 = ? = 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = ? = = = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = ? = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 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