************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 nfe2x.phase.inp nfe2x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST nfe2x.phase.out_freqs : haplotype frequency estimates nfe2x.phase.out_pairs : most likely haplotype pairs for each individual nfe2x.phase.out_recom : estimates of recombination parameters nfe2x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 3 Positions of loci: 4055 4312 6589 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file nfe2x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGG 77.000000 2 ATA 17.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,1) DY02: (1,1) DY03: (1,1) DY04: (1,1) DY05: (1,1) DY06: (1,1) DY07: (1,1) DY08: (1,1) DY09: (1,1) DY10: (1,1) DY11: (1,1) DY12: (1,1) DY13: (1,1) DY14: (1,1) DY15: (1,1) DY16: (1,1) DY17: (1,1) DY18: (1,1) DY19: (1,1) DY20: (1,1) DY21: (1,1) DY22: (1,1) DY23: (1,1) DY24: (1,1) E101: (1,2) E102: (1,2) E103: (1,1) E104: (1,2) E105: (2,2) E106: (1,2) E107: (1,2) E108: (2,2) E109: (1,1) E110: (1,2) E111: (1,1) E112: (1,2) E113: (1,1) E114: (1,1) E115: (1,1) E116: (1,1) E117: (1,2) E118: (1,1) E119: (1,2) E120: (1,2) E121: (1,2) E122: (1,2) E123: (1,2) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G G G G G G 0 DY02 G G G G G G 0 DY03 G G G G G G 0 DY04 G G G G G G 0 DY05 G G G G G G 0 DY06 G G G G G G 0 DY07 G G G G G G 0 DY08 G G G G G G 0 DY09 G G G G G G 0 DY10 G G G G G G 0 DY11 G G G G G G 0 DY12 G G G G G G 0 DY13 G G G G G G 0 DY14 G G G G G G 0 DY15 G G G G G G 0 DY16 G G G G G G 0 DY17 G G G G G G 0 DY18 G G G G G G 0 DY19 G G G G G G 0 DY20 G G G G G G 0 DY21 G G G G G G 0 DY22 G G G G G G 0 DY23 G G G G G G 0 DY24 G G G G G G 0 E101 G G G A T A 0 E102 G G G A T A 0 E103 G G G G G G 0 E104 G G G A T A 0 E105 A T A A T A 0 E106 G G G A T A 0 E107 G G G A T A 0 E108 A T A A T A 0 E109 G G G G G G 0 E110 G G G A T A 0 E111 G G G G G G 0 E112 G G G A T A 0 E113 G G G G G G 0 E114 G G G G G G 0 E115 G G G G G G 0 E116 G G G G G G 0 E117 G G G A T A 0 E118 G G G G G G 0 E119 G G G A T A 0 E120 G G G A T A 0 E121 G G G A T A 0 E122 G G G A T A 0 E123 G G G A T 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 = = = = = = 0 DY02 = = = = = = 0 DY03 = = ? = = ? 0 DY04 = = = = = = 0 DY05 = = = = = = 0 DY06 = = = = = = 0 DY07 = = = = = = 0 DY08 = = = = = = 0 DY09 = = = = = = 0 DY10 = = = = = = 0 DY11 = = = = = = 0 DY12 = = = = = = 0 DY13 = = = = = = 0 DY14 = = = = = = 0 DY15 = = = = = = 0 DY16 = = = = = = 0 DY17 = = = = = = 0 DY18 = = = = = = 0 DY19 = = = = = = 0 DY20 = = = = = = 0 DY21 = = = = = = 0 DY22 = = = = = = 0 DY23 = = = = = = 0 DY24 = = = = = = 0 E101 G G G A T A 0 E102 G G ? A T ? 0 E103 = = = = = = 0 E104 G G G A T A 0 E105 = = = = = = 0 E106 G G G A T A 0 E107 G G G A T A 0 E108 = = = = = = 0 E109 = = = = = = 0 E110 G G G A T A 0 E111 = = = = = = 0 E112 G G G A T A 0 E113 = = = = = = 0 E114 = = = = = = 0 E115 = = = = = = 0 E116 = = = = = = 0 E117 G G G A T A 0 E118 = = = = = = 0 E119 G G G A T A 0 E120 G G G A T A 0 E121 G G G A T A 0 E122 G G G A T A 0 E123 G G ? A T ? 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 ? END PHASEPROBS