************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 g109b.phase.inp g109b.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST g109b.phase.out_freqs : haplotype frequency estimates g109b.phase.out_pairs : most likely haplotype pairs for each individual g109b.phase.out_recom : estimates of recombination parameters g109b.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 23 Positions of loci: 1019 1776 2028 2130 2299 2374 2540 2733 2968 2997 2998 3225 3241 3312 3322 3391 3590 3657 3725 3740 4146 4235 4295 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file g109b.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GTCAATAAACTAGTATACATACC 1.000000 2 GTCAATAGACTAGTATACATACC 1.000000 3 GTCCCCGGGCTGCCGTGTATCCC 6.000000 4 GTCCCCGGGCTGCCGTGTACACC 2.000000 5 GTCCCCGGGCTGCCGTGTACCCC 16.000000 6 GTCCCCGGGCTGCCGGGTACCCC 1.000000 7 GTTAATGGACTAGTATGCATACT 2.000000 8 GTTAATGGACTAGTATGCGTACC 6.000000 9 GTTAATGGACTAGTATGCGTACT 4.000000 10 GCCCCCGGGCTGCCAGGCATACC 1.000000 11 GCCCCCGGGCTGCCAGGCACATC 17.000000 12 GCCCCCGGGGCGCCATGCACACC 1.000000 13 GCCCCCGGGGCGCCAGGCACATC 5.000000 14 TTCAATAAACTAGTATACATACC 25.000000 15 TTCAATAAACTAGTATGCGTACT 1.000000 16 TTCAATAGACTAGTATACATACC 3.000000 17 TTCAATGGACTAGTATGCGTACT 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (9,14) DY02: (5,8) DY03: (3,5) DY04: (11,14) DY05: (5,12) DY06: (14,14) DY07: (5,9) DY08: (8,8) DY09: (7,15) DY10: (5,9) DY11: (6,14) DY12: (5,5) DY13: (5,11) DY14: (5,14) DY15: (5,17) DY16: (5,7) DY17: (8,14) DY18: (3,11) DY19: (14,14) DY20: (5,11) DY21: (3,11) DY22: (5,8) DY23: (8,17) DY24: (9,14) E101: (1,11) E102: (14,14) E103: (14,16) E104: (4,5) E105: (10,11) E106: (11,11) E107: (5,11) E108: (11,14) E109: (11,14) E110: (11,16) E111: (13,14) E112: (5,13) E113: (3,11) E114: (13,14) E115: (11,16) E116: (14,14) E117: (13,14) E118: (3,11) E119: (11,14) E120: (14,14) E121: (2,13) E122: (3,4) E123: (14,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G T T A A T G G A C T A G T A T G C G T A C T T T C A A T A A A C T A G T A T A C A T A C C 0 DY02 G T C C C C G G G C T G C C G T G T A C C C C G T T A A T G G A C T A G T A T G C G T A C C 0 DY03 G T C C C C G G G C T G C C G T G T A T C C C G T C C C C G G G C T G C C G T G T A C C C C 0 DY04 G C C C C C G G G C T G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 DY05 G T C C C C G G G C T G C C G T G T A C C C C G C C C C C G G G G C G C C A T G C A C A C C 0 DY06 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A A A C T A G T A T A C A T A C C 0 DY07 G T C C C C G G G C T G C C G T G T A C C C C G T T A A T G G A C T A G T A T G C G T A C T 0 DY08 G T T A A T G G A C T A G T A T G C G T A C C G T T A A T G G A C T A G T A T G C G T A C C 0 DY09 G T T A A T G G A C T A G T A T G C (A) T A C T T T C A A T A A A C T A G T A T G C (G) T A C T 0 DY10 G T C C C C G G G C T G C C G T G T A C [C] C C G T T A A T G G A C T A G T A T G C G T A C T 0 DY11 G T C C C C G G G C T G C C G G G T A C C C C T T C A A T A A A C T A G T A T A C A T A C C 0 DY12 G T C C C C G G G C T G C C G T G T A C C C C G T C C C C G G G C T G C C G T G T A C C C C 0 DY13 G T C C C C G G G C T G C C G T G T A C C C C G C C C C C G G G C T G C C A G G C A C A T C 0 DY14 G T C C C C G G G C T G C C G T G T A C C C C T T C A A T A A A C T A G T A T A C A T A C C 0 DY15 G T C C C C G G G C T G C C G T G T A C C C C T T C A A T G G A C T A G T A T G C G T A C T 0 DY16 G T C C C C G G G C T G C C G T G T A C [C] C C G T T A A T G G A C T A G T A T G C A T A C T 0 DY17 G T T A A T G G A C T A G T A T G C G T A C C T T C A A T A A A C T A G T A T A C A T A C C 0 DY18 G T C C C C G G G C T G C C G T G T A T C C C G C C C C C G G G C T G C C A G G C A C A T C 0 DY19 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A A A C T A G T A T A C A T A C C 0 DY20 G T C C C C G G G C T G C C G T G T A C C C C G C C C C C G G G C T G C C A G G C A C A T C 0 DY21 G T C C C C G G G C T G C C G T G T A T C C C G C C C C C G G G C T G C C A G G C A C A T C 0 DY22 G T C C C C G G G C T G C C G T G T A C C C C G T T A A T G G A C T A G T A T G C G T A C C 0 DY23 G T T A A T G G A C T A G T A T G C G T A C C T T C A A T G G A C T A G T A T G C G T A C T 0 DY24 G T T A A T G G A C T A G T A T G C G T A C T T T C A A T A A A C T A G T A T A C A T A C C 0 E101 G T C A A T A A A C T A G T A T A C A T A C C G C C C C C G G G C T G C C A G G C A C A T C 0 E102 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A A A C T A G T A T A C A T A C C 0 E103 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A G A C T A G T A T A C A T A C C 0 E104 G T C C C C G G G C T G C C G T G T A C A C C G T C C C C G G G C T G C C G T G T A C C C C 0 E105 G C C C C C G G G C T G C C A G G C A T A C C G C C C C C G G G C T G C C A G G C A C A T C 0 E106 G C C C C C G G G C T G C C A G G C A C A T C G C C C C C G G G C T G C C A G G C A C A T C 0 E107 G T C C C C G G G C T G C C G T G T A C C C C G C C C C C G G G C T G C C A G G C A C A T C 0 E108 G C C C C C G G G C T G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 E109 G C C C C C G G G C T G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 E110 G C C C C C G G G C T G C C A G G C A C A T C T T C A A T A G A C T A G T A T A C A T A C C 0 E111 G C C C C C G G G G C G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 E112 G T C C C C G G G C T G C C G T G T A C C C C G C C C C C G G G G C G C C A G G C A C A T C 0 E113 G T C C C C G G G C T G C C G T G T A T C C C G C C C C C G G G C T G C C A G G C A C A T C 0 E114 G C C C C C G G G G C G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 E115 G C C C C C G G G C T G C C A G G C A C A T C T T C A A T A G A C T A G T A T A C A T A C C 0 E116 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A A A C T A G T A T A C A T A C C 0 E117 G C C C C C G G G G C G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 E118 G T C C C C G G G C T G C C G T G T A T C C C G C C C C C G G G C T G C C A G G C A C A T C 0 E119 G C C C C C G G G C T G C C A G G C A C A T C T T C A A T A A A C T A G T A T A C A T A C C 0 E120 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A A A C T A G T A T A C A T A C C 0 E121 G T C A A T A G A C T A G T A T A C A T A C C G C C C C C G G G G C G C C A G G C A C A T C 0 E122 G T C C C C G G G C T G C C G T G T A (T) C C C G T C C C C G G G C T G C C G T G T A (C) A C C 0 E123 T T C A A T A A A C T A G T A T A C A T A C C T T C A A T A A A C T A G T A T A C A T 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 ? = T = = = G G = = = ? ? = = = G = G = = = T ? = C = = = A A = = = ? ? = = = A = A = = = C 0 DY02 = = C C C C = = G = = G ? C G = = T A C C = = = = T A A T = = A = = A ? T A = = C G T A = = 0 DY03 = = = = = = = ? = = = ? ? = = = = = = T = = = = = = = = = = ? = = = ? ? = = = = = = C = = = 0 DY04 G C = C C C G G G = = G C C = G G = = C = T = T T = A A T A A A = = A G T = T A = = T = C = 0 DY05 ? T = = = = = = = C T = = = G = = T = = C = = ? C = = = = = = = G C = = = A = = C = = A = = 0 DY06 = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = 0 DY07 = = C C C C = = G = = G C C G = = T A C C = C = = T A A T = = A = = A G T A = = C G T A = T 0 DY08 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 DY09 G = T = = = G G = = = ? ? = = = = = (A) = = = = T = C = = = A A = = = ? ? = = = = = (G) = = = = 0 DY10 = = C C C C = = G = = G C C G = = T A C ? = C = = T A A T = = A = = A G T A = = C G T ? = T 0 DY11 G = = C C C G G G = = ? ? C G G G T = C C = = T = = A A T A A A = = ? ? T A T A C = T A = = 0 DY12 = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 DY13 = T = = = = = = = = = = = = G T = ? = = C C = = C = = = = = = = = = = = = A G = ? = = A T = 0 DY14 ? = = C C C G G G = = G C C G = G T = C C = = ? = = A A T A A A = = A G T A = A C = T A = = 0 DY15 ? = = C C C = = G = = G C C G = = T A C C = C ? = = A A T = = A = = A G T A = = C G T A = T 0 DY16 = = C C C C = = G = = G C C G = = T = C ? = C = = T A A T = = A = = A G T A = = C = T ? = T 0 DY17 ? = T = = = G G = = = = = = = = G = G = = = = ? = C = = = A A = = = = = = = = A = A = = = = 0 DY18 = T = = = = = = = = = = = = G T = T = T C C = = C = = = = = = = = = = = = A G = C = C A T = 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 = T = = = = = = = = = = = = G T = T = = C C = = C = = = = = = = = = = = = A G = C = = A T = 0 DY21 = T = = ? = = = = = = = = = G T = ? = T ? C = = C = = ? = = = = = = = = = A G = ? = C ? T = 0 DY22 = = C C C C = = G = = G C C G = = T A C C = = = = T A A T = = A = = A G T A = = C G T A = = 0 DY23 G = T = = = = = = = = = = = = = = = = = = = C T = C = = = = = = = = = = = = = = = = = = = T 0 DY24 G = T = = = G G = = = = = = = = G = G = = = T T = C = = = A A = = = = = = = = A = A = = = C 0 E101 = T = A A T A A A = = ? ? T = T A = = T = C = = C = C C C G G G = = ? ? C = G G = = C = T = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = ? = = A = = = = = = = = = = = = = = = = = = = ? = = G = = = = = = = = = = = = = = = 0 E104 = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = C = = 0 E105 ? = = = = = = = = = = = ? = = = = = = T = C = ? = = = = = = = = = = = ? = = = = = = C = T = 0 E106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = T = = = = = = = = = = = = G T = T = = C C = = C = = = = = = = = = = = = A G = C = = A T = 0 E108 G C = C C C G G G = = G C C = G G = = C = T = T T = A A T A A A = = A G T = T A = = T = C = 0 E109 G C = C C C G G G = = ? ? C = G G = = C ? ? ? T T = A A T A A A = = ? ? T = T A = = T ? ? ? 0 E110 G C = C C C G = G = = G ? C = G G = = C = T = T T = A A T A = A = = A ? T = T A = = T = C = 0 E111 G C = C C C G G G G C G ? C = G G = = C = T = T T = A A T A A A C T A ? T = T A = = T = C = 0 E112 = T = = = = = = = C T = ? = G T = T = = C C = = C = = = = = = = G C = ? = A G = C = = A T = 0 E113 ? T = = = = = = = = = = = = G T = T = T C C = ? C = = = = = = = = = = = = A G = C = C A T = 0 E114 G C = C C C G G G G C G C C = G G = = C = T = T T = A A T A A A C T A G T = T A = = T = C = 0 E115 G C = C C C G = G = = G C C = G G = = C = T = T T = A A T A = A = = A G T = T A = = T = C = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 G C = C C C G G G G C G C C = G G = = C = T = T T = A A T A A A C T A G T = T A = = T = C = 0 E118 = T = = = = = = = = = = = = G T = T = T C C = = C = = = = = = = = = = = = A G = C = C A T = 0 E119 G C = C C C G G G = = G C C = G G = = C = T = T T = A A T A A A = = A G T = T A = = T = C = 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E121 = T = A A T A = A C T A G T = T A = = T = C = = C = C C C G = G G C G C C = G G = = C = T = 0 E122 = = = = = = = = = = = = = = = = = = = (T) C = = = = = = = = = = = = = = = = = = = = = (C) A = = 0 E123 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = 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 = = = ? ? = = = = = 0.56 = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 ? = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = ? ? 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = ? = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 1.00 = ? = = 1.00 1.00 = ? = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = ? = = 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = = 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 = ? = 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 = = 0.97 = 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 = = ? = = = = = = = = = = = ? = = = = = = 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 ? ? ? 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 = 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 = 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 = 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 = = = = = = = = = = = = = = = = = = = = 0.88 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS