************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ptgds.phase.inp ptgds.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ptgds.phase.out_freqs : haplotype frequency estimates ptgds.phase.out_pairs : most likely haplotype pairs for each individual ptgds.phase.out_recom : estimates of recombination parameters ptgds.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 20 Positions of loci: 119 142 474 739 1680 2077 2330 2404 3465 3466 5576 5599 6170 6183 6500 6512 6547 6785 7158 7727 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ptgds.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCCCGGDCTCAGAGAGCAAC 2.000000 2 CCCCGGDCTCAGAGGGCAAC 14.000000 3 CCCCGGDCTCAGAAAGCAAC 4.000000 4 CCTTGGICTCAGCGGTCAAC 3.000000 5 CCTTGAICTCAGAAGGGTAA 7.000000 6 CCTTAAICTCAGAGGGCAAC 4.000000 7 CCTTAAICTCAGAGGGCACC 1.000000 8 TCTTGGICTCAGCGGTCAAC 1.000000 9 TTTTGGICTCAGCGGTCACC 26.000000 10 TTTTGGICTCAACGGTCACC 11.000000 11 TTTTGGICTCTGCGGTCACC 7.000000 12 TTTTGGICCTAGCGGTCACC 7.000000 13 TTTTGGIGTCAGCGGTCACC 7.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,13) DY02: (5,13) DY03: (3,12) DY04: (9,9) DY05: (3,3) DY06: (4,9) DY07: (5,12) DY08: (5,11) DY09: (6,11) DY10: (4,12) DY11: (9,12) DY12: (9,9) DY13: (5,12) DY14: (7,9) DY15: (3,12) DY16: (13,13) DY17: (6,12) DY18: (1,4) DY19: (9,13) DY20: (9,13) DY21: (6,11) DY22: (6,9) DY23: (8,9) DY24: (9,13) E101: (9,10) E102: (2,2) E103: (9,10) E104: (2,11) E105: (5,10) E106: (2,10) E107: (9,10) E108: (2,9) E109: (9,11) E110: (2,2) E111: (5,10) E112: (2,10) E113: (2,5) E114: (9,10) E115: (2,10) E116: (9,9) E117: (9,9) E118: (2,11) E119: (10,11) E120: (9,9) E121: (2,9) E122: (2,10) E123: (2,9) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C C C C G G D C T C A G A G A G C A A C T T T T G G I G T C A G C G G T C A C C 0 DY02 C C T T G A I C T C A G A A G G G T A A T T T T G G I G T C A G C G G T C A C C 0 DY03 C C C C G G D C T C A G A A A G C A A C T T T T G G I C C T A G C G G T C A C C 0 DY04 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A G C G G T C A C C 0 DY05 C C C C G G D C T C A G A A A G C A A C C C C C G G D C T C A G A A A G C A A C 0 DY06 C C T T G G I C T C A G C G G T C A A C T T T T G G I C T C A G C G G T C A C C 0 DY07 C C T T G A I C T C A G A A G G G T A A T T T T G G I C C T A G C G G T C A C C 0 DY08 C C T T G A I C T C A G A A G G G T A A T T T T G G I C T C T G C G G T C A C C 0 DY09 C C T T A A I C T C A G A G G G C A A C T T T T G G I C T C T G C G G T C A C C 0 DY10 C C T T G G I C T C A G C G G T C A A C T T T T G G I C C T A G C G G T C A C C 0 DY11 T T T T G G I C T C A G C G G T C A C C T T T T G G I C C T A G C G G T C A C C 0 DY12 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A G C G G T C A C C 0 DY13 C C T T G A I C T C A G A A G G G T A A T T T T G G I C C T A G C G G T C A C C 0 DY14 C C T T A A I C T C A G A G G G C A C C T T T T G G I C T C A G C G G T C A C C 0 DY15 C C C C G G D C T C A G A A A G C A A C T T T T G G I C C T A G C G G T C A C C 0 DY16 T T T T G G I G T C A G C G G T C A C C T T T T G G I G T C A G C G G T C A C C 0 DY17 C C T T A A I C T C A G A G G G C A A C T T T T G G I C C T A G C G G T C A C C 0 DY18 C C C C G G D C T C A G A G A G C A A C C C T T G G I C T C A G C G G T C A A C 0 DY19 T T T T G G I C T C A G C G G T C A C C T T T T G G I G T C A G C G G T C A C C 0 DY20 T T T T G G I C T C A G C G G T C A C C T T T T G G I G T C A G C G G T C A C C 0 DY21 C C T T A A I C T C A G A G G G C A A C T T T T G G I C T C T G C G G T C A C C 0 DY22 C C T T A A I C T C A G A G G G C A A C T T T T G G I C T C A G C G G T C A C C 0 DY23 T C T T G G I C T C A G C G G T C A A C T T T T G G I C T C A G C G G T C A C C 0 DY24 T T T T G G I C T C A G C G G T C A C C T T T T G G I G T C A G C G G T C A C C 0 E101 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A A C G G T C A C C 0 E102 C C C C G G D C T C A G A G G G C A A C C C C C G G D C T C A G A G G G C A A C 0 E103 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A A C G G T C A C C 0 E104 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C T G C G G T C A C C 0 E105 C C T T G A I C T C A G A A G G G T A A T T T T G G I C T C A A C G G T C A C C 0 E106 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A A C G G T C A C C 0 E107 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A A C G G T C A C C 0 E108 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A G C G G T C A C C 0 E109 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C T G C G G T C A C C 0 E110 C C C C G G D C T C A G A G G G C A A C C C C C G G D C T C A G A G G G C A A C 0 E111 C C T T G A I C T C A G A A G G G T A A T T T T G G I C T C A A C G G T C A C C 0 E112 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A A C G G T C A C C 0 E113 C C C C G G D C T C A G A G G G C A A C C C T T G A I C T C A G A A G G G T A A 0 E114 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A A C G G T C A C C 0 E115 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A A C G G T C A C C 0 E116 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A G C G G T C A C C 0 E117 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A G C G G T C A C C 0 E118 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C T G C G G T C A C C 0 E119 T T T T G G I C T C A A C G G T C A C C T T T T G G I C T C T G C G G T C A C C 0 E120 T T T T G G I C T C A G C G G T C A C C T T T T G G I C T C A G C G G T C A C C 0 E121 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A G C G G T C A C C 0 E122 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A A C G G T C A C C 0 E123 C C C C G G D C T C A G A G G G C A A C T T T T G G I C T C A G C G G T C A C 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 DY01 C C C C = = D C = = = = A = A G = = A ? T T T T = = I G = = = = C = G T = = C ? 0 DY02 C C = = = A = C = = = = A A = G G T A A T T = = = G = G = = = = C G = T C A C C 0 DY03 C C C C = = D = T C = = A A A G = = A = T T T T = = I = C T = = C G G T = = C = 0 DY04 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY06 C C = = = = = = = = = = = = = = = = A = T T = = = = = = = = = = = = = = = = C = 0 DY07 C C = = = A = = T C = = A A = G G T A ? T T = = = G = = C T = = C G = T C A C ? 0 DY08 C C = = = A = = = = A = A A = G G T A A T T = = = G = = = = T = C G = T C A C C 0 DY09 C C = = A A = = = = A = A = = G = = A ? T T = = G G = = = = T = C = = T = = C ? 0 DY10 C C = = = = = = T C = = = = = = = = A = T T = = = = = = C T = = = = = = = = C = 0 DY11 = = = ? = = = = T C = = = = = = = = = = = = = ? = = = = C T = = = = = = = = = = 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY13 C C = = = A = = T C = = A A = G G T A A T T = = = G = = C T = = C G = T C A C C 0 DY14 C C = = A A = = = = = = A = = G = = = = T T = = G G = = = = = = C = = T = = = = 0 DY15 C C C C = = D = T C = = A A A G = = A = T T T T = = I = C T = = C G G T = = C = 0 DY16 = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 DY17 C C = = A A = = T C = = A = = G = = A ? T T = = G G = = C T = = C = = T = = C ? 0 DY18 = = C C = = D = = = = = A = A G = = = = = = T T = = I = = = = = C = G T = = = = 0 DY19 = = = = = = = C = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = 0 DY20 = = = = = = = C = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = 0 DY21 C C = = A A = = = = A = A = = G = = A = T T = = G G = = = = T = C = = T = = C = 0 DY22 C C = = A A = = = = = = A = = G = = A = T T = = G G = = = = = = C = = T = = C = 0 DY23 = C = = = = = = = = = = = = = = = = A = = T = = = = = = = = = = = = = = = = C = 0 DY24 = = = = = = = C = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = 0 E101 = = = = = = = = = = = G = = = = = = = ? = = = = = = = = = = = A = = = = = = = ? 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = A = = = = = = = = 0 E104 C C C C = = D = = = A = A = = G = = ? = T T T T = = I = = = T = C = = T = = ? = 0 E105 C C = = = A = = = = = G A A = G G T A A T T = = = G = = = = = A C G = T C A C C 0 E106 C C C C = = D = = = = G A = = G = = A = T T T T = = I = = = = A C = = T = = C = 0 E107 = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = A = = = = = = = = 0 E108 C C C C = = D = = = = = A = = G = = A = T T T T = = I = = = = = C = = T = = C = 0 E109 = = = = = = = = = = A = = = = = = = = ? = = = = = = = = = = T = = = = = = = = ? 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 C C = = = A = = = = = G A A = G G T ? A T T = = = G = = = = = A C G = T C A ? C 0 E112 C C C C = = D = = = = G A = = G = = A = T T T T = = I = = = = A C = = T = = C = 0 E113 = = C C = G D = = = = = = G = = C A = C = = T T = A I = = = = = = A = = G T = A 0 E114 = = = = = = = = ? ? = G = = = = = = ? = = = = = = = = = ? ? = A = = = = = = ? = 0 E115 C C C C = = D = = = = G A = = G = = A = T T T T = = I = = = = A C = = T = = C = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? 0 E118 C C C C = = D = = = A = A = = G = = A = T T T T = = I = = = T = C = = T = = C = 0 E119 = = = = = = = = = = A A = = = = = = = = = = = = = = = = = = T G = = = = = = = = 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E121 C C C C = = D = = = = = A = = G = = A = T T T T = = I = = = = = C = = T = = C = 0 E122 C C C C = = D = = = = G A = = G = = A = T T T T = = I = = = = A C = = T = = C = 0 E123 C C C C = = D = ? ? = = A = = G = = A = T T T T = = I = ? ? = = C = = T = = 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 0.99 = = = = 1.00 = 0.95 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 = = = = 0.99 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = 0.95 = 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 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = = = = ? = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = = 1.00 = = 1.00 = = 1.00 ? = = 1.00 1.00 = = 1.00 = = = = = 1.00 = 0.95 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 = = 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 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 = = = = 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 = = = = = 0.99 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 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 = = = = = = = = = = = 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 = = = = 0.99 1.00 = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = ? ? = = 1.00 = = 1.00 = = 1.00 = END PHASEPROBS