************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 il1f9.phase.inp il1f9.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il1f9.phase.out_freqs : haplotype frequency estimates il1f9.phase.out_pairs : most likely haplotype pairs for each individual il1f9.phase.out_recom : estimates of recombination parameters il1f9.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 22 Positions of loci: 1037 2628 2657 3748 3786 6015 6599 8654 9074 9913 10310 10659 11321 11497 11768 13299 17720 17953 18129 18587 19101 19464 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il1f9.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AGCDGTTGAGGACTGTGGGAGG 3.000000 2 AGCDGTTGAGGACTGTGGCAGG 1.000000 3 AGCDGTTTAAGCCTGAAGGAAG 9.000000 4 AGCDGTTTAAGCCTGTAGGAAG 1.000000 5 AGCDGCTGAGCAGCATGGGCGG 2.000000 6 AGCDGCTGAGCAGCATGGGCGA 2.000000 7 AGCDGCGGAGCAGCATGAGCGG 10.000000 8 AGCDGCGGGGCAGCATAGGAGG 13.000000 9 AGCDACTGAGGAGTGTGGGAGG 3.000000 10 AGCDACTGAGCAGCATGGGCGA 5.000000 11 AGCIGCTGAGCAGCATGGGCGG 16.000000 12 ATCDGCTGGGCAGCATAGGAGG 9.000000 13 GGCDGTTGAGGACTGTGGGAGG 1.000000 14 GGCDGTTGAGGACTGTGGCAGG 13.000000 15 GGCDGTTGAGGACTGTGGCCGG 1.000000 16 GGTDGTTGAGGACTGTGGGAGG 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (3,16) DY02: (12,14) DY03: (10,14) DY04: (1,10) DY05: (7,14) DY06: (1,7) DY07: (3,14) DY08: (1,9) DY09: (6,14) DY10: (16,16) DY11: (10,12) DY12: (3,14) DY13: (4,12) DY14: (12,14) DY15: (3,12) DY16: (6,10) DY17: (12,12) DY18: (9,12) DY19: (3,7) DY20: (5,9) DY21: (3,16) DY22: (3,3) DY23: (10,12) DY24: (3,16) E101: (8,8) E102: (7,11) E103: (8,8) E104: (7,13) E105: (11,11) E106: (11,11) E107: (7,11) E108: (11,14) E109: (11,11) E110: (2,8) E111: (7,15) E112: (7,11) E113: (8,11) E114: (8,14) E115: (8,11) E116: (8,8) E117: (8,14) E118: (14,14) E119: (11,14) E120: (5,11) E121: (7,11) E122: (7,11) E123: (8,8) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A G C D G T T T A A G C C T G A A G G A A G G G T D G T T G A G G A C T G T G G G A G G 0 DY02 A T C D G C T G G G C A G C A T A G G A G G G G C D G T T G A G G A C T G T G G C A G G 0 DY03 A G C D A C T G A G C A G C A T G G G C G A G G C D G T T G A G G A C T G T G G C A G G 0 DY04 A G C D G T T G A G G A C T G T G G G A G G A G C D A C T G A G C A G C A T G G G C G A 0 DY05 A G C D G C G G A G C A G C A T G A G C G G G G C D G T T G A G G A C T G T G G C A G G 0 DY06 A G C D G T T G A G G A C T G T G G G A G G A G C D G C G G A G C A G C A T G A G C G G 0 DY07 A G C D G T T T A A G C C T G A A G G A A G [G] G C D G T T G A G G A C T G T G G C A G G 0 DY08 A G C D G T T G A G G A C T G T G G G A G G A G C D [A] C T G A G G A G T G T G G G A G G 0 DY09 A G C D G C T G A G C A G C A T G G G C G A G G C D G T T G A G G A C T G T G G C A G G 0 DY10 G G T D G T T G A G G A C T G T G G G A G G G G T D G T T G A G G A C T G T G G G A G G 0 DY11 A G C D A C T G A G C A G C A T G G G C G A A T C D G C T G G G C A G C A T A G G A G G 0 DY12 A G C D G T T T A A G C C T G A A G G A A G G G C D G T T G A G G A C T G T G G C A G G 0 DY13 A G C D G T T T A A G C C T G T A G G A A G A T C D G C T G G G C A G C A T A G G A G G 0 DY14 A T C D G C T G G G C A G C A T A G G A G G G G C D G T T G A G G A C T G T G G C A G G 0 DY15 A G C D G T T T A A G C C T G A A G G A A G A T C D G C T G G G C A G C A T A G G A G G 0 DY16 A G C D G C T G A G C A G C A T G G G C G A A G C D A C T G A G C A G C A T G G G C G A 0 DY17 A T C D G C T G G G C A G C A T A G G A G G A T C D G C T G G G C A G C A T A G G A G G 0 DY18 A G C D [A] C T G A G G A G T G T G G G A G G A T C D G C T G G G C A G C A T A G G A G G 0 DY19 A G C D G T T T A A G C C T G A A G G A A G A G C D G C G G A G C A G C A T G A G C G G 0 DY20 A G C D (G) C T G A G C A G C A T G G G C G G A G C D (A) C T G A G G A G T G T G G G A G G 0 DY21 A G C D G T T T A A G C C T G A A G G A A G G G T D G T T G A G G A C T G T G G G A G G 0 DY22 A G C D G T T T A A G C C T G A A G G A A G A G C D G T T T A A G C C T G A A G G A A G 0 DY23 A G C D [A] C T G A G C A G C A T G G G C G A A T C D G C T G G G C A G C A T A G G A G G 0 DY24 A G C D G T T T A A G C C T G A A G G A A G G G T D G T T G A G G A C T G T G G G A G G 0 E101 A G C D G C G G G G C A G C A T A G G A G G A G C D G C G G G G C A G C A T A G G A G G 0 E102 A G C D G C G G A G C A G C A T G A G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E103 A G C D G C G G G G C A G C A T A G G A G G A G C D G C G G G G C A G C A T A G G A G G 0 E104 (A) G C D G C G G A G C A G C A T G A G C G G (G) G C D G T T G A G G A C T G T G G G A G G 0 E105 A G C I G C T G A G C A G C A T G G G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E106 A G C I G C T G A G C A G C A T G G G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E107 A G C D G C G G A G C A G C A T G A G C G G A G C [I] G C T G A G C A G C A T G G G C G G 0 E108 A G C I G C T G A G C A G C A T G G G C G G [G] G C D G T T G A G G A C T G T G G C A G G 0 E109 A G C I G C T G A G C A G C A T G G G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E110 A G C D G T T G A G G A C T G T G G C A G G A G C D G C G G G G C A G C A T A G G A G G 0 E111 A G C D G C G G A G C A G C A T G A G C G G G G C D G T T G A G G A C T G T G G C C G G 0 E112 A G C D G C G G A G C A G C A T G A G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E113 A G C D G C G G G G C A G C A T A G G A G G A G C I G C T G A G C A G C A T G G G C G G 0 E114 A G C D G C G G G G C A G C A T A G G A G G [G] G C D G T T G A G G A C T G T G G C A G G 0 E115 A G C D G C G G G G C A G C A T A G G A G G A G C I G C T G A G C A G C A T G G G C G G 0 E116 A G C D G C G G G G C A G C A T A G G A G G A G C D G C G G G G C A G C A T A G G A G G 0 E117 A G C D G C G G G G C A G C A T A G G A G G [G] G C D G T T G A G G A C T G T G G C A G G 0 E118 G G C D G T T G A G G A C T G T G G C A G G [G] G C D G T T G A G G A C T G T G G C A G G 0 E119 A G C I G C T G A G C A G C A T G G G C G G G G C D G T T G A G G A C T G T G G C A G G 0 E120 A G C D G C T G A G C A G C A T G G G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E121 A G C D G C G G A G C A G C A T G A G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E122 A G C D G C G G A G C A G C A T G A G C G G A G C I G C T G A G C A G C A T G G G C G G 0 E123 A G C D G C G G G G C A G C A T A G G A G G A G C D G C G G G G C A G C A T A G G A 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 ? = C = = = = T = A = C = = = A A = = = A = ? = T = = = = G = G = A = = = T G = = = G = 0 DY02 A T = = = C = = G = C = G C A = ? ? G = ? ? G G = = = T = = A = G = C T G = ? ? C = ? ? 0 DY03 A = = = A C = = = = C = G C A = = = G C = A G = = = G T = = = = G = C T G = = = C A = G 0 DY04 = = = = G T = = = = G = C T G = = = = A = G = = = = A C = = = = C = G C A = = = = C = A 0 DY05 A = = = = C G = = = C = ? C A = = A G C = = G = = = = T T = = = G = ? T G = = G C A = = 0 DY06 = = = = = T T ? ? = G = C T G = = G = A = = = = = = = C G ? ? = C = G C A = = A = C = = 0 DY07 ? = = = = = = T = A = C = = = A A = G = A = ? = = = = = = G = G = A = = = T G = C = G = 0 DY08 = = = ? ? T = = ? = = = C = = = = = = = = = = = = ? ? C = = ? = = = G = = = = = = = = = 0 DY09 A = = = = C = = = = C = G C A = = = G C = A G = = = = T = = = = G = C T G = = = C A = G 0 DY10 = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = 0 DY11 = G = = A = = = A = = = = = = = G = = C = A = T = = G = = = G = = = = = = = A = = A = G 0 DY12 A = = = = = = T = A = C = = = A A = G = A = G = = = = = = G = G = A = = = T G = C = G = 0 DY13 = G = = = T = T A A G C C T G = = = = = A = = T = = = C = G G G C A G C A = = = = = G = 0 DY14 A T = = = C = = G = C = G C A = ? ? ? = ? = G G = = = T = = A = G = C T G = ? ? ? = ? = 0 DY15 = G = = = T = T A A G C C T G A = = = = A = = T = = = C = G G G C A G C A T = = = = G = 0 DY16 = = = = G = = = ? = = = = = = = = = = = = = = = = = A = = = ? = = = = = = = = = = = = = 0 DY17 = = = = ? = = = = ? ? = = = = = = = = = = = = = = = ? = = = = ? ? = = = = = = = = = = = 0 DY18 = G = ? ? = = = A = G = = T G = G = = = = = = T = ? ? = = = G = C = = C A = A = = = = = 0 DY19 = = = = = T T T = A G C C T G A A G = A A = = = = = = C G G = G C A G C A T G A = C G = 0 DY20 = = = = (G) = = = ? = C = = C A = = = = C = = = = = = (A) = = = ? = G = = T G = = = = A = = 0 DY21 A = C = = = = T = A = C ? ? = A A = = = A = G = T = = = = G = G = A ? ? = T G = = = G = 0 DY22 = = = ? ? = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = 0 DY23 = G = ? ? = = = A = = = ? ? ? = G = = C = A = T = ? ? = = = G = = = ? ? ? = A = = A = G 0 DY24 ? = C = = = = T ? A = C = = = A A = = = A = ? = T = = = = G ? G = A = = = T G = = = G = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = D = = G = = = = = = = = = = A = = = = = = = I = = T = = = = = = = = = = G = = = = 0 E103 ? = = = = = = = = = = = = = = = ? ? ? = = = ? = = = = = = = = = = = = = = = ? ? ? = = = 0 E104 (A) = = = = C G = = = C = ? C A = = A = C = = (G) = = = = T T = = = G = ? T G = = G = A = = 0 E105 ? = = = = = = = = = = = = = = = = = = ? = = ? = = = = = = = = = = = = = = = = = = ? = = 0 E106 = = = = = = = = ? = = ? = = = = = = = = = = = = = = = = = = ? = = ? = = = = = = = = = = 0 E107 = = = ? ? = G = = = = ? = = = = = A = = = = = = = ? ? = T = = = = ? = = = = = G = = = = 0 E108 ? = = I = C = = ? = C ? G C A = = = G C = = ? = = D = T = = ? = G ? C T G = = = C A = = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 = = = = = T T = A = G = C T G = G = C = = = = = = = = C G = G = C = G C A = A = G = = = 0 E111 A = = = = C G = ? = C = G C A = = A G = = = G = = = = T T = ? = G = C T G = = G C = = = 0 E112 ? = = D = = G = = = = = = = = = = A = = = = ? = = I = = T = = = = = = = = = = G = = = = 0 E113 = = = D = = G = G = = = = = = = A = = A = = = = = I = = T = A = = = = = = = G = = C = = 0 E114 ? = = = = C G = G = C = G C A = A = G = = = ? = = = = T T = A = G = C T G = G = C = = = 0 E115 = = = D = = G = G = = = = = = = A = = A = = = = = I = = T = A = = = = = = = G = = C = = 0 E116 = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = 0 E117 ? = = = = C G = G = C = ? ? A = A = G = = = ? = = = = T T = A = G = ? ? G = G = C = = = 0 E118 ? = = = = = = = = = = = ? ? = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = 0 E119 A = = I = C = = ? = C = G C A = = = G C = = G = = D = T = = ? = G = C T G = = = C A = = 0 E120 = = = D = = = = = = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = = = = = = 0 E121 = = = D = = G = = = = = = = = = = A = = = = = = = I = = T = = = = = = = = = = G = = = = 0 E122 = = = D = = G = = = = = = = = = = A = = = = = = = I = = T = = = = = = = = = = G = = = = 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 = = = = 0.98 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 = = = = = 0.82 = = = ? = 1.00 = = 1.00 1.00 = = = = 1.00 = = 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 = = = = ? = = = = = = = = = = = = = = = ? ? ? = = = 0.85 = = = = 1.00 1.00 = = = 1.00 = ? 1.00 1.00 = = 1.00 = 1.00 = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = ? = = ? = = = = = = = = = = = = = ? ? = 1.00 = = = = ? = = = = = 1.00 = = = = ? = = 1.00 = 1.00 = = ? = 1.00 ? 1.00 1.00 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 = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS