************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 foxa3.phase.inp foxa3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST foxa3.phase.out_freqs : haplotype frequency estimates foxa3.phase.out_pairs : most likely haplotype pairs for each individual foxa3.phase.out_recom : estimates of recombination parameters foxa3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 25 Positions of loci: 81 103 885 1434 1615 1674 2112 2354 2631 3166 3386 4710 4790 5516 5634 5696 7627 7923 8448 9056 9327 10190 10628 12785 13029 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file foxa3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TTCCCATGGTACGGGAGAGACCCGC 2.000000 2 TTCCCATGGTACGGGAAGAATCCGG 6.000000 3 TTCCCATGGTACGGAAGAGACCCGG 3.000000 4 TTCCCATGGTACGGAAAGAATCCGG 1.000000 5 TTCCCATGGTCCGGGAGAGACCCAG 2.000000 6 TTCCCATGGTCCGGGAGAGACCCGC 2.000000 7 TTCCCATGGTCCGGGAGAGGCTCGG 7.000000 8 TTCCCGTGGTCCGGGAGAGACCCAG 1.000000 9 TTCCCGTGGTCCGGGAGAGACCCGG 1.000000 10 TTCCTATGGTACGGGAGAGACCCGG 17.000000 11 TTCCTATGGTACGGGAAGAACCCGG 1.000000 12 TTCTCATGGTACAGGAGAGACCCGG 3.000000 13 TTCTCATGGTACAGGAAGAACCCGG 1.000000 14 TTCTCATGGTACAGGAAGAATCCGG 18.000000 15 TTCTCATGGTACAGGGGAGACCAGG 1.000000 16 TTCTCATGGTACAGGGGAGACTCAG 3.000000 17 TTCTCATGGTACAAGGGAGACTCAG 5.000000 18 TTCTCATGGTCCGGGAGAGACCCAG 1.000000 19 TCCCCGCCGGACAGGAAGAATCCGG 1.000000 20 TCCCCGCCGGACAAGGGAGACTCAG 2.000000 21 TCACCGCCGTACGGGAGAGGCTCGG 1.000000 22 TCACCGCCGGACGGAAGAGACCCGG 5.000000 23 CTCCCGTGTTATGGGAGAGACCAGG 3.000000 24 CTCCCGTGTTATGGGAAGAATCCGC 3.000000 25 CTCCCGTGTTATGGGAAGAATTCAG 1.000000 26 CTCCCGTGTTATGGAAGAGACCAGG 1.000000 27 CTCCCGTGTGATGGAAGAGACCAGG 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,8) DY02: (3,3) DY03: (9,27) DY04: (6,24) DY05: (2,2) DY06: (3,17) DY07: (7,14) DY08: (5,15) DY09: (10,16) DY10: (2,7) DY11: (7,24) DY12: (4,14) DY13: (14,20) DY14: (18,20) DY15: (6,17) DY16: (2,25) DY17: (16,17) DY18: (5,16) DY19: (12,17) DY20: (2,7) DY21: (2,19) DY22: (1,24) DY23: (7,14) DY24: (10,17) E101: (21,27) E102: (11,14) E103: (10,10) E104: (12,23) E105: (10,14) E106: (7,10) E107: (22,26) E108: (22,23) E109: (10,14) E110: (10,10) E111: (10,14) E112: (10,14) E113: (14,22) E114: (10,14) E115: (10,13) E116: (7,14) E117: (10,14) E118: (12,23) E119: (10,10) E120: (14,22) E121: (10,14) E122: (14,14) E123: (14,22) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 T T C C C (A) T G G T A C G G G A G A G A C C C G C T T C C C (G) T G G T C C G G G A G A G A C C C A G 0 DY02 T T C C C A T G G T A C G G A A G A G A C C C G G T T C C C A T G G T A C G G A A G A G A C C C G G 0 DY03 T T C C C G T G G T C C G G G A G A G A C C C G G C T C C C G T G T G A T G G A A G A G A C C A G G 0 DY04 T T C C C A T G G T C C G G G A G A G A C C C G C C T C C C G T G T T A T G G G A A G A A T C C G C 0 DY05 T T C C C A T G G T A C G G G A A G A A T C C G G T T C C C A T G G T A C G G G A A G A A T C C G G 0 DY06 T T C C C A T G G T A C G G A A G A G A C C C G G T T C T C A T G G T A C A [A] G G G A G A C T C A G 0 DY07 T T C C C A T G G T C C G G G A G A G G C T C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 DY08 T T C [C] C A T G G T C C G G G A G A G A C C C A G T T C T C A T G G T A C A G G G G A G A C C A G G 0 DY09 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G G G A G A C T C A G 0 DY10 T T C C C A T G G T A C G G G A A G A A T C C G G T T C C C A T G G T C C G G G A G A G G C T C G G 0 DY11 T T C C C A T G G T C C G G G A G A G G C T C G G C T C C C G T G T T A T G G G A A G A A T C C G C 0 DY12 T T C C C A T G G T A C G G (A) A [A] G [A] A [T] C C G G T T C T C A T G G T A C A G (G) A A G A A T C C G G 0 DY13 T (T) C (T) C (A) [T] (G) G (T) A C A G G A A G A A T C C G G T (C) C (C) C (G) [C] (C) G (G) A C A A G G G A G A C T C A G 0 DY14 T T C (T) C A T G G T (C) C (G) (G) G (A) G A G A C (C) C A G T C C (C) C G C C G G (A) C (A) (A) G (G) G A G A C (T) C A G 0 DY15 T T C C C A T G G T C C G G G A G A G A C C C G C T T C T C A T G G T A C A A G G G A G A C T C A G 0 DY16 T T C C C A T G G T A C G G G A A G A A T C C G G C T C C C G T G T T A T G G G A A G A A T T C A G 0 DY17 T T C T C A T G G T A C A G G G G A G A C T C A G T T C T C A T G G T A C A A G G G A G A C T C A G 0 DY18 T T C C C A T G G T C C G G G A G A G A C C C A G T T C T C A T G G T A C A G G G G A G A C T C A G 0 DY19 T T C T C A T G G T A C A G G A G A G A C C C G G T T C T C A T G G T A C A A G G G A G A C T C A G 0 DY20 T T C C C A T G G T A C G G G A A G A A T C C G G T T C C C A T G G T C C G G G A G A G G C T C G G 0 DY21 T T C C C A T G G T A C (G) G G A A G A A T C C G G T C [C] C C G C C G G A C (A) G G A A G A A T C C G G 0 DY22 T T C C C A T G G T A C G G G A G A G A C C C G C C T C C C G T G T T A T G G G A A G A A T C C G C 0 DY23 T T C C C A T G G T C C G G G A G A G G C T C G G T T C [T] C A T G G T A C [A] G G A A G A A T C C G G 0 DY24 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A A G G G A G A C T C A G 0 E101 T C A C C G C C G T A C G G G A G A G G C T C G G C T C C C G T G T G A T G G A A G A G A C C A G G 0 E102 T T C C T A T G G T A C G G G A A G A A (C) C C G G T T C T C A T G G T A C A G G A A G A A (T) C C G G 0 E103 T T C C T A T G G T A C G G G A G A G A C C C G G T T C C T A T G G T A C G G G A G A G A C C C G G 0 E104 T T C T C A T G G T A C A G G A G A G A C C C G G C T C C C G T G T T A T G G G A G A G A C C A G G 0 E105 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E106 T T C C C A T G G T C C G G G A G A G G C T C G G T T C C T A T G G T A C G G G A G A G A C C C G G 0 E107 T C A C C G C C G G A C G G A A G A G A C C C G G C T C C C G T G T T A T G G A A G A G A C C A G G 0 E108 T C A C C G C C G G A C G G A A G A G A C C C G G C T C C C G T G T T A T G G G A G A G A C C A G G 0 E109 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E110 T T C C T A T G G T A C G G G A G A G A C C C G G T T C C T A T G G T A C G G G A G A G A C C C G G 0 E111 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E112 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E113 T T C T C A T G G T A C A G G A A G A A T C C G G T C A C C G C C G G A C G G A A G A G A C C C G G 0 E114 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E115 T T C (C) (T) A T G G T A C (G) G G A G A G A C C C G G T T C (T) (C) A T G G T A C (A) G G A A G A A C C C G G 0 E116 T T C C C A T G G T C C G G G A G A G G C T C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E117 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E118 T T C T C A T G G T A C A G G A G A G A C C C G G C T C C C G T G T T A T G G G A G A G A C C A G G 0 E119 T T C C T A T G G T A C G G G A G A G A C C C G G T T C C T A T G G T A C G G G A G A G A C C C G G 0 E120 T T C T C A T G G T A C A G G A A G A A T C C G G T C A C C G C C G G A C G G A A G A G A C C C G G 0 E121 T T C C T A T G G T A C G G G A G A G A C C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E122 T T C T C A T G G T A C A G G A A G A A T C C G G T T C T C A T G G T A C A G G A A G A A T C C G G 0 E123 T T C T C A T G G T A C A G G A A G A A T C C G G T C A C C G C C G G A C G G A A G A G A C C C 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 DY01 ? ? ? ? = (A) = ? = = A ? ? = = = ? = = = ? = = G C ? ? ? ? = (G) = ? = = C ? ? = = = ? = = = ? = = A G 0 DY02 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 DY03 ? ? = ? = = ? ? G T C ? ? ? ? ? ? = = = ? = C = = ? ? = ? = = ? ? T G A ? ? ? ? ? ? = = = ? = A = = 0 DY04 T = ? = = A ? = G = C C = = = = G ? ? = C = = = = C = ? = = G ? = T = A T = = = = A ? ? = T = = = = 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY06 = = ? C = = = = = ? ? = G ? A A = ? = = = C = G = = = ? T = = = = = ? ? = A ? G G = ? = = = T = A = 0 DY07 = = = C = = = = = = C = G = = = G A G G C T = = = = = = T = = = = = = A = A = = = A G A A T C = = = 0 DY08 ? ? = ? = = = ? = = C ? ? = = A ? = = = = = C A = ? ? = ? = = = ? = = A ? ? = = G ? = = = = = A G = 0 DY09 ? ? = C T = ? = = = = ? ? = = ? ? = = = = C = G = ? ? = T C = ? = = = = ? ? = = ? ? = = = = T = A = 0 DY10 = = = = = = ? = = = A = = = = ? A G A A T C = = = = = = = = = ? = = = C = = = = ? G A G G C T = = = 0 DY11 T = = = = A ? = G = C ? = = = = G ? G G C T = = G C = = = = G ? = T = A ? = = = = A ? A A T C = = C 0 DY12 = = = C = = ? = = = = ? G = (A) = ? = ? = ? = = = = = = = T = = ? = = = = ? A = (G) = ? = ? = ? = = = = 0 DY13 = (T) = (T) = (A) ? (G) = (T) = = = G = A A G A = T C = G = = (C) = (C) = (G) ? (C) = (G) = = = A = G G A G = C T = A = 0 DY14 = T = (T) = A ? G = T (C) = (G) (G) = (A) = = = = = (C) = ? = = C = (C) = G ? C = G (A) = (A) (A) = (G) = = = = = (T) = ? = 0 DY15 = = = C = = = = = = C = G G = A = = = = = C = G C = = = T = = = = = = A = A A = G = = = = = T = A G 0 DY16 T = = ? = A ? = G = = C = = = = = ? = = = C = G ? C = = ? = G ? = T = = T = = = = = ? = = = T = A ? 0 DY17 = = = = = = ? = = = = = = G = = = = = = = = = = = = = = = = = ? = = = = = = A = = = = = = = = = = = 0 DY18 ? ? = C = = ? = = = C = G = = A = = = = = C = = = ? ? = T = = ? = = = A = A = = G = = = = = T = = = 0 DY19 = = = = = = ? = = = = = = G = A = = ? = = C = G = = = = = = = ? = = = = = = A = G = = ? = = T = A = 0 DY20 = = = = = = = = = = A = = = = = A G ? A T C = = = = = = = = = = = = = C = = = = = G A ? G C T = = = 0 DY21 = T ? = = A T G = T = = (G) ? ? = ? = = = = = = ? = = C ? = = G C C = G = = (A) ? ? = ? = = = = = = ? = 0 DY22 T = = = = A ? = G = = C = = = = G ? G = C = = = = C = = = = G ? = T = = T = = = = A ? A = T = = = = 0 DY23 = = = ? = = = ? = = C ? ? = = = ? A G G C T = = = = = = ? = = = ? = = A ? ? = = = ? G A A T C = = = 0 DY24 = = = ? T = ? = = = = ? ? G = A ? = = = = C = G = = = = ? C = ? = = = = ? ? A = G ? = = = = T = A = 0 E101 T C A = = = ? C G T = C = = G = = = = G ? T C = = C T C = = = ? G T G = T = = A = = = = A ? C A = = 0 E102 = = ? C T = = = = = = = G = = = = = = = (C) = = = = = = ? T C = = = = = = = A = = = = = = = (T) = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0 E104 T = = T = A = = G = = C A = = = = = ? = ? = C = = C = = C = G = = T = = T G = = = = = ? = ? = A = = 0 E105 = = = C T = = = = = = = G = = = G A G = C = = ? = = = = T C = = = = = = = A = = = A G A = T = = ? = 0 E106 = = = ? C = = = = = C = = = = = = = = G = T = = = = = = ? T = = = = = A = = = = = = = = A = C = = = 0 E107 T C A ? = = C C ? G = ? ? = = = ? = = = ? = C = = C T C ? = = T G ? T = ? ? = = = ? = = = ? = A = = 0 E108 T C A = = = ? C G G = C = = A = = = = = ? = C = = C T C = = = ? G T T = T = = G = = = = = ? = A = = 0 E109 = = = C T = ? = = = = = ? ? ? = G A G = C = = = = = = = T C = ? = = = = = ? ? ? = A G A = T = = = = 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 = = = C T = = = = = = = G = = = G A G = C = = = = = = = T C = = = = = = = A = = = A G A = T = = = = 0 E112 = = = C T = = = = = = = G = = = G A ? = C = = = = = = = T C = = = = = = = A = = = A G ? = T = = = = 0 E113 = T C T = A T G = T = = A = G = A G A = T = = = = = C A C = G C C = G = = G = A = G A G = C = = = = 0 E114 = = = C T = ? = = = = = G = = = G A G = C = = = ? = = = T C = ? = = = = = A = = = A G A = T = = = ? 0 E115 = = ? (C) (T) = ? = = = = = (G) = = = G A G = = = = = = = = ? (T) (C) = ? = = = = = (A) = = = A G A = = = = = = 0 E116 = = = ? = = ? = = = C = G = = = G A G G C T = = = = = = ? = = ? = = = A = A = = = A G A A T C = = = 0 E117 = = = C T = ? = = = = = G ? ? = G A G = C = = = = = = = T C = ? = = = = = A ? ? = A G A = T = = = = 0 E118 T = ? T = A ? = G = = C A = = = = ? = = = = ? = = C = ? C = G ? = T = = T G = = = = ? = = = = ? = = 0 E119 = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = 0 E120 = T ? T = A T G = ? = = A ? ? ? A ? ? = T = = = = = C ? C = G C C = ? = = G ? ? ? G ? ? = C = = = = 0 E121 = = = C T = = = = = = = G ? ? = G A G = C = = = = = = = T C = = = = = = = A ? ? = A G A = T = = = = 0 E122 = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = = = = = = = = ? 0 E123 = T C T = A ? G = T = = A = G = A G A = T = = = = = C A C = G ? C = G = = G = A = G A G = C = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS ? ? ? ? = 0.69 = ? = = 0.98 ? ? = = = ? = = = ? = = 1.00 0.98 = = = = = = ? = = = = = = = = = = = = = = = = = = ? ? = ? = = ? ? 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 ? ? = = 0.98 ? = = = = = 1.00 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 ? = 1.00 = 1.00 ? = = = = 1.00 ? 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = ? = = = = ? 1.00 = 0.76 = ? = ? = ? = = = = = 0.60 = 0.52 = 0.60 ? 0.60 = 0.60 = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = 0.97 = 0.79 = 0.97 ? 0.97 = 1.00 0.75 = 0.73 0.73 = 0.73 = = = = = 0.73 = ? = = = = 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 = = = = = = = = = = = ? ? = 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 = = 0.89 ? ? = ? = = = = = = ? = 0.99 = = = = 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 0.99 0.99 = = = ? 0.99 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 ? 1.00 1.00 = = = = ? 0.95 1.00 = = = = = = = 0.95 = = = = = = = 0.67 = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 1.00 = = 1.00 = 1.00 = = 1.00 = = 1.00 1.00 = = = = = ? = ? = 1.00 = = = = = 0.99 0.99 = = = = = = = 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 0.98 = 1.00 = = 0.98 = = = = = ? = 1.00 = = = = = 0.98 0.98 = ? = = = = = ? ? ? = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 0.99 = = = = = = = 0.99 = = = 1.00 1.00 1.00 = 1.00 = = = = = = = 0.99 0.99 = = = = = = = 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 0.99 0.99 = 0.99 = = = = = = = 0.99 0.99 = ? = = = = = 0.99 = = = 1.00 1.00 1.00 = 1.00 = = = ? = = ? 0.59 0.58 = ? = = = = = 0.59 = = = 1.00 1.00 1.00 = = = = = = = = = ? = = ? = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = 0.99 0.99 = ? = = = = = 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 ? ? = 0.99 = = = = = = = 0.99 0.99 = = = = = = = 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 0.99 0.99 = 0.99 = = = = END PHASEPROBS