************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 g109a.phase.inp g109a.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST g109a.phase.out_freqs : haplotype frequency estimates g109a.phase.out_pairs : most likely haplotype pairs for each individual g109a.phase.out_recom : estimates of recombination parameters g109a.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 19 Positions of loci: 101 231 393 1126 1237 2701 2721 2990 2991 3005 3062 3143 3220 3595 3842 4000 4975 5051 5366 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file g109a.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TAGCCCGGCGTAACATGAA 7.000000 2 TAGCCCGGCGTAACATGGA 1.000000 3 TAGCCCGGCGTAATATGAA 4.000000 4 TGGCCCGGCGTAACATGAA 2.000000 5 TGGCTCGGCGTAACCCGAA 28.000000 6 TGACTCGGCGTAACCCGAA 1.000000 7 CGGCCCGGCGTAATATGGA 1.000000 8 CGGCTCGGCGTAACCCGGA 1.000000 9 CGGACCGCTTCGGCATCAG 1.000000 10 CGGACCGCTTCGGCATCGG 23.000000 11 CGACTCGGCGTAACATGGA 2.000000 12 CGACTCAGCGTAACATGGA 13.000000 13 CGACTTAGCGTAACATGGA 9.000000 14 CGAATCAGCGTAACATGGA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (3,5) DY02: (1,10) DY03: (10,10) DY04: (5,11) DY05: (10,12) DY06: (5,5) DY07: (3,10) DY08: (1,1) DY09: (4,4) DY10: (3,10) DY11: (5,9) DY12: (10,10) DY13: (10,12) DY14: (8,10) DY15: (2,10) DY16: (7,10) DY17: (1,5) DY18: (10,12) DY19: (5,5) DY20: (10,11) DY21: (10,12) DY22: (1,10) DY23: (1,1) DY24: (3,5) E101: (5,13) E102: (5,5) E103: (5,5) E104: (10,10) E105: (13,13) E106: (12,13) E107: (10,13) E108: (5,13) E109: (5,13) E110: (5,12) E111: (6,12) E112: (10,12) E113: (10,13) E114: (5,12) E115: (5,12) E116: (5,5) E117: (5,12) E118: (13,14) E119: (5,12) E120: (5,5) E121: (5,12) E122: (10,10) E123: (5,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 T A G C C C G G C G T A A T A T G A A T G G C T C G G C G T A A C C C G A A 0 DY02 T A G C C C G G C G T A A C A T G A A C G G A C C G C T T C G G C A T C G G 0 DY03 C G G A C C G C T T C G G C A T C G G C G G A C C G C T T C G G C A T C G G 0 DY04 T G G C T C G G C G T A A C C C G A A C G A C T C G G C G T A A C A T G G A 0 DY05 C G G A C C G C T T C G G C A T C G G C G A C T C A G C G T A A C A T G G A 0 DY06 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 0 DY07 T A G C C C G G C G T A A T A T G A A C G G A C C G C T T C G G C A T C G G 0 DY08 T A G C C C G G C G T A A C A T G [A] A T A G C C C G G C G T A A C A T G A A 0 DY09 T G G C C C G G C G T A A C A T G A A T G G C C C G G C G T A A C A T G A A 0 DY10 T A G C C C G G C G T A A T A T G A A C G G A C C G C T T C G G C A T C G G 0 DY11 T G G C T C G G C G T A A C C C G A A C G G A C C G C T T C G G C A T C A G 0 DY12 C G G A C C G C T T C G G C A T C G G C G G A C C G C T T C G G C A T C G G 0 DY13 C G G A C C G C T T C G G C A T C G G C G A C T [C] A G C G T A A C A T G G A 0 DY14 C G G C T C G G C G T A A C C C G G A C G G A C C G C T T C G G C A T C G G 0 DY15 T A G C C C G G C G T A A C A T G G A C G G A C C G C T T C G G C A T C G G 0 DY16 C G G C C C G G C G T A A (T) A T G G A C G G A C C G C T T C G G (C) A T C G G 0 DY17 T A G C C C G G C G T A A C A T G A A T G G C T C G G C G T A A C C C G A A 0 DY18 C G G A C C G C T T C G G C A T C G G C G A C T C A G C G T A A C A T G G A 0 DY19 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 0 DY20 C G G A C C G C T T C G G C A T C G G C G A C T C G G C G T A A C A T G G A 0 DY21 C G G A C C G C T T C G G C A T C G G C G A C T [C] A G C G T A A C A T G G A 0 DY22 T A G C C C G G C G T A A C A T G A A C G G A C C G C T T C G G C A T C G G 0 DY23 T [A] G C C C G G C G T A A C A T G A A T A G C C C G G C G T A A C A T G A A 0 DY24 T A G C C C G G C G T A A T A T G A A T G G C T C G G C G T A A C C C G A A 0 E101 T G G C T C G G C G T A A C C C G A A C G A C T T A G C G T A A C A T G G A 0 E102 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 0 E103 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 0 E104 C G G A C C G C T T C G G C A T C G G C G G A C C G C T T C G G C A T C G G 0 E105 C G A C T T A G C G T A A C A T G G A C G A C T T A G C G T A A C A T G G A 0 E106 C G A C T C A G C G T A A C A T G G A C G A C T T A G C G T A A C A T G G A 0 E107 C G G A C C G C T T C G G C A T C G G C G A C T T A G C G T A A C A T G G A 0 E108 T G G C T C G G C G T A A C C C G A A C G A C T T A G C G T A A C A T G G A 0 E109 T G G C T C G G C G T A A C C C G A A C G A C T T A G C G T A A C A T G G A 0 E110 T G G C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E111 T G A C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E112 C G G A C C G C T T C G G C A T C G G C G A C T C A G C G T A A C A T G G A 0 E113 C G G A C C G C T T C G G C A T C G G C G A C T T A G C G T A A C A T G G A 0 E114 T G G C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E115 T G G C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E116 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 0 E117 T G G C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E118 C G A (C) T T A G C G T A A C A T G G A C G A (A) T C A G C G T A A C A T G G A 0 E119 T G G C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E120 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 0 E121 T G G C T C G G C G T A A C C C G A A C G A C T C A G C G T A A C A T G G A 0 E122 C G G A C C G C T T C G G C A T C G G C G G A C C G C T T C G G C A T C G G 0 E123 T G G C T C G G C G T A A C C C G A A T G G C T C G G C G T A A C C C G A A 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 = = C = = = = = = = = T A T ? = = = G = = T = = = = = = = = C C C ? = = 0 DY02 T A = C = = = G C G T A A = = = G A A C G = A = = = C T T C G G = = = C G G 0 DY03 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY04 T = G = = = = = = = = = = = C C ? ? = C = A = = = = = = = = = = = A T ? ? = 0 DY05 ? ? ? ? ? = G C T T C G G = = = ? ? G ? ? ? ? ? = A G C G T A A = = = ? ? A 0 DY06 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = 0 DY07 T A = C = = = G C G T A A T = = ? ? A C G = A = = = C T T C G G C = = ? ? G 0 DY08 = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = ? ? = 0 DY09 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY10 T A = C = = = G C G T A A T = = G A A C G = A = = = C T T C G G C = = C G G 0 DY11 T = = C T = = G C G T A A = C C G = A C = = A C = = C T T C G G = A T C = G 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY13 = = G A C ? ? ? ? T C G G = = = C = G = = A C T ? ? ? ? G T A A = = = G = A 0 DY14 = = = C T = = G C G T A A = C ? G = A = = = A C = = C T T C G G = A ? C = G 0 DY15 T A = C = = = G C G T A A = = = G = A C G = A = = = C T T C G G = = = C = G 0 DY16 = = = C = = = G C G T A A (T) = = G = A = = = A = = = C T T C G G (C) = = C = G 0 DY17 = A = = C = = = = = = = = = A T = = = = G = = T = = = = = = = = = C C = = = 0 DY18 = = G A C = G C T T C G G = = = ? ? G = = A C T = A G C G T A A = = = ? ? A 0 DY19 ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 DY20 = = G A C = = C T T C G G = = ? C = G = = A C T = = G C G T A A = = ? G = A 0 DY21 = = G A C ? ? C T T C G G = = ? C = G = = A C T ? ? G C G T A A = = ? G = A 0 DY22 T A = C = = = G C G T A A = = ? G A A C G = A = = = C T T C G G = = ? C G G 0 DY23 ? ? ? = = = = = = = = = = = = ? = = = ? ? ? = = = = = = = = = = = = ? = = = 0 DY24 = A = = C = = = = = = = = T A T = = = = G = = T = = = = = = = = C C C = = = 0 E101 T = G = = C G = = = = = = = C C = A = C = A = = T A = = = = = = = A T = G = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 ? ? ? = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = 0 E106 = = = = = C = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = 0 E107 = = G A C C G C T T C G G = = = C = G = = A C T T A G C G T A A = = = G = A 0 E108 T = ? = = C G = = = = = = = C ? = A = C = ? = = T A = = = = = = = A ? = G = 0 E109 T = ? = = C G = = = = = = = C C = A = C = ? = = T A = = = = = = = A T = G = 0 E110 T = G = = = G = = = = = = = C ? = A = C = A = = = A = = = = = = = A ? = G = 0 E111 T = = = = = G = = = = = = = C ? = A = C = = = = = A = = = = = = = A ? = G = 0 E112 = = G A C = G C T T C G G = = = C = G = = A C T = A G C G T A A = = = G = A 0 E113 = = G A C C G C T T C G G = = = C = G = = A C T T A G C G T A A = = = G = A 0 E114 T = G = = = G = = = = = = = C C = A = C = A = = = A = = = = = = = A T = G = 0 E115 ? = G = = = G = = = = = = = C C = A = ? = A = = = A = = = = = = = A T = G = 0 E116 = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 E117 T = G = = = G = = = ? = = = C C = A = C = A = = = A = = = ? = = = A T = G = 0 E118 = = = (C) = T = = = = = = = = = = = = = = = = (A) = C = = = = = = = = = = = = = 0 E119 T = G = = = G = = = = = = = C C = A = C = A = = = A = = = = = = = A T = G = 0 E120 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? 0 E121 T = G = = = G = = = = = = = C C = A = C = A = = = A = = = = = = = A T = G = 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 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 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 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 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 ? ? ? ? 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? 1.00 = 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 0.83 = = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = ? ? 1.00 ? = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = ? 1.00 = 1.00 = = 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 1.00 = = ? 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 = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = ? = = 1.00 1.00 = = = = = = = 1.00 ? = 1.00 = 1.00 = ? = = 1.00 1.00 = = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = = = 1.00 ? = 1.00 = 1.00 = = = = = 1.00 = = = = = = = 1.00 ? = 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = 1.00 1.00 = 1.00 = ? = 1.00 = = = 1.00 = = = = = = = 1.00 1.00 = 1.00 = = = ? = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 = = = ? = = = 1.00 1.00 = 1.00 = = = = 0.51 = 1.00 = = = = = = = = = = = = = 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