************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cebpa.phase.inp cebpa.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cebpa.phase.out_freqs : haplotype frequency estimates cebpa.phase.out_pairs : most likely haplotype pairs for each individual cebpa.phase.out_recom : estimates of recombination parameters cebpa.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 16 Positions of loci: 67 1878 2677 3501 3779 4181 4673 4752 4772 5114 5407 5629 5700 5840 5912 6058 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cebpa.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCGACCTCGACGCDTG 46.000000 2 CCGACCTCGACGCDCG 11.000000 3 CCGACCTTGACGCDCG 6.000000 4 CCGGCCTCGACGCDTG 2.000000 5 CCTGGTCCTGTAAICA 1.000000 6 CTGACCTCGACGCDCG 5.000000 7 TCGACCTCGACGCDTG 1.000000 8 TCTGGTCCTGTAAICA 22.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,1) DY02: (1,8) DY03: (1,8) DY04: (1,1) DY05: (1,8) DY06: (2,6) DY07: (4,8) DY08: (1,8) DY09: (1,1) DY10: (1,1) DY11: (6,8) DY12: (1,2) DY13: (1,7) DY14: (1,8) DY15: (1,1) DY16: (1,8) DY17: (6,8) DY18: (6,6) DY19: (8,8) DY20: (4,8) DY21: (5,8) DY22: (1,1) DY23: (1,8) DY24: (1,8) E101: (1,3) E102: (3,3) E103: (1,1) E104: (1,8) E105: (1,8) E106: (8,8) E107: (1,2) E108: (1,2) E109: (3,8) E110: (1,8) E111: (1,2) E112: (1,1) E113: (1,1) E114: (1,2) E115: (1,1) E116: (2,3) E117: (1,8) E118: (2,3) E119: (1,2) E120: (1,2) E121: (1,1) E122: (1,2) E123: (1,1) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 DY02 C C G A C C T C G A C G C D [T] G T C T G G T C C T G T A A I C A 0 DY03 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 DY04 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 DY05 C C G A C C T C G A C G C D [T] G T C T G G T C C T G T A A I C A 0 DY06 C C G A C C T C G A C G C D C G C T G A C C T C G A C G C D C G 0 DY07 C C G G C C T C G A C G C D [T] G T C T G G T C C T G T A A I C A 0 DY08 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 DY09 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 DY10 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 DY11 C T G A C C T C G A C G C D C G T C T G G T C C T G T A A I C A 0 DY12 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 DY13 C C G A C C T C G A C G C D T G T C G A C C T C G A C G C D T G 0 DY14 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 DY15 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 DY16 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 DY17 C T G A C C T C G A C G C D C G T C T G G T C C T G T A A I C A 0 DY18 C T G A C C T C G A C G C D C G C T G A C C T C G A C G C D C G 0 DY19 T C T G G T C C T G T A A I C A T C T G G T C C T G T A A I C A 0 DY20 C C G G C C T C G A C G C D [T] G T C T G G T C C T G T A A I C A 0 DY21 C C T G G T C C T G T A A I C A T C T G G T C C T G T A A I C A 0 DY22 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 DY23 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 DY24 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 E101 C C G A C C T C G A C G C D T G C C G A C C T T G A C G C D C G 0 E102 C C G A C C T T G A C G C D C G C C G A C C T T G A C G C D C G 0 E103 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 E104 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 E105 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 E106 T C T G G T C C T G T A A I C A T C T G G T C C T G T A A I C A 0 E107 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E108 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E109 C C G A C C T T G A C G C D C G T C T G G T C C T G T A A I C A 0 E110 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 E111 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E112 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 E113 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 E114 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E115 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 E116 C C G A C C T C G A C G C D C G C C G A C C T T G A C G C D C G 0 E117 C C G A C C T C G A C G C D T G T C T G G T C C T G T A A I C A 0 E118 C C G A C C T C G A C G C D C G C C G A C C T T G A C G C D C G 0 E119 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E120 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E121 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T G 0 E122 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D C G 0 E123 C C G A C C T C G A C G C D T G C C G A C C T C G A C G C D T 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 = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 DY02 C = ? A C C T ? ? A C G C D ? ? T = ? G G T C ? ? G T A A I ? ? 0 DY03 C = ? ? C C T = G A C G C D ? ? T = ? ? G T C = T G T A A I ? ? 0 DY04 = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 DY05 C = ? A C C T ? ? A C G C D ? ? T = ? G G T C ? ? G T A A I ? ? 0 DY06 = C = = = ? = = = = = = = = = = = T = = = ? = = = = = = = = = = 0 DY07 C = ? = C C T = G A C G C D ? ? T = ? = G T C = T G T A A I ? ? 0 DY08 ? = ? A C C T = G A C ? ? D ? ? ? = ? G G T C = T G T ? ? I ? ? 0 DY09 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY10 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY11 C T G A C C T = G A C G C D ? ? T C T G G T C = T G T A A I ? ? 0 DY12 = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = C = 0 DY13 C = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = 0 DY14 C = ? A C ? T = G A C G C D ? ? T = ? G G ? C = T G T A A I ? ? 0 DY15 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY16 ? = ? A C C T = G A C G C D ? ? ? = ? G G T C = T G T A A I ? ? 0 DY17 C T G A C C T = G A C G C D ? ? T C T G G T C = T G T A A I ? ? 0 DY18 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY19 = = ? = = = = = = = = ? ? = = = = = ? = = = = = = = = ? ? = = = 0 DY20 C = G = C C T = G A C G C D ? ? T = T = G T C = T G T A A I ? ? 0 DY21 C = ? = = = = = = = = = = = = = T = ? = = = = = = = = = = = = = 0 DY22 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY23 C = G A C C T = G A C G C D ? ? T = T G G T C = T G T A A I ? ? 0 DY24 C = ? A C C T = G A C G C D ? ? T = ? G G T C = T G T A A I ? ? 0 E101 = = ? = = = = C = = = = = = T = = = ? = = = = T = = = = = = C = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 C = G A C C T = G A C G C D ? ? T = T G G T C = T G T A A I ? ? 0 E105 C = G A C C T = G A C G C D ? ? T = T G G T C = T G T A A I ? ? 0 E106 = = = = = = = = = = = ? ? = = = = = = = = = = = = = = ? ? = = = 0 E107 = = ? = = = = = = = = = = = T = = = ? = = = = = = = = = = = C = 0 E108 = = ? = = = = = = = = = = = T = = = ? = = = = = = = = = = = C = 0 E109 C = G ? C C T T G A C ? ? D ? ? T = T ? G T C C T G T ? ? I ? ? 0 E110 C = G A C C T = G A C G C D ? ? T = T G G T C = T G T A A I ? ? 0 E111 = = = ? = = = = = = = = = = T = = = = ? = = = = = = = = = = C = 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 = = = = = ? = = = = = = = = T = = = = = = ? = = = = = = = = C = 0 E115 = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 E116 = ? ? = = = = C = = = = = ? = = = ? ? = = = = T = = = = = ? = = 0 E117 C = G A C C T = G ? ? G C D ? ? T = T G G T C = T ? ? A A I ? ? 0 E118 = = = = = = = C = = = ? ? = = = = = = = = = = T = = = ? ? = = = 0 E119 = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = C = 0 E120 = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = C = 0 E121 = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 E122 = = = = = = = = = = = = = ? T = = = = = = = = = = = = = = ? C = 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 1.00 1.00 ? ? ? = ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? ? 1.00 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 0.92 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = 1.00 = ? 1.00 1.00 ? 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? = = = = = = = = = = = = = = = = ? = ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 0.94 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? = = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 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 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 = = = = = = = = = = = = = = = = = END PHASEPROBS