************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 klf4x.phase.inp klf4x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST klf4x.phase.out_freqs : haplotype frequency estimates klf4x.phase.out_pairs : most likely haplotype pairs for each individual klf4x.phase.out_recom : estimates of recombination parameters klf4x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 8 Positions of loci: 872 3578 4244 4836 5527 5917 6365 7055 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file klf4x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCGADGIA 5.000000 2 CCGADGDA 1.000000 3 CCGAIGDA 7.000000 4 CTGTDGIA 5.000000 5 TCGADGIA 57.000000 6 TCGADGIT 7.000000 7 TCGADAIA 5.000000 8 TCAADGIA 7.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,5) DY02: (1,5) DY03: (1,5) DY04: (3,5) DY05: (3,6) DY06: (1,6) DY07: (5,6) DY08: (5,5) DY09: (4,6) DY10: (3,5) DY11: (4,4) DY12: (5,7) DY13: (2,5) DY14: (4,5) DY15: (3,5) DY16: (5,6) DY17: (5,6) DY18: (5,7) DY19: (5,7) DY20: (1,7) DY21: (5,7) DY22: (3,5) DY23: (3,4) DY24: (3,5) E101: (5,5) E102: (5,8) E103: (5,5) E104: (5,5) E105: (5,5) E106: (5,5) E107: (5,5) E108: (5,5) E109: (5,8) E110: (5,5) E111: (5,5) E112: (5,6) E113: (5,8) E114: (5,5) E115: (5,5) E116: (5,8) E117: (5,8) E118: (5,8) E119: (5,5) E120: (5,5) E121: (5,5) E122: (5,8) 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 C C G A D G I A T C G A D G I A 0 DY02 C C G A D G I A T C G A D G I A 0 DY03 C C G A D G I A T C G A D G I A 0 DY04 C C G A I G D A T C G A D G I A 0 DY05 C C G A I G D A T C G A D G I T 0 DY06 (C) C G A D G I A (T) C G A D G I T 0 DY07 T C G A D G I A T C G A D G I T 0 DY08 T C G A D G I A T C G A D G I A 0 DY09 C T G T D G I A T C G A D G I T 0 DY10 C C G A I G D A T C G A D G I A 0 DY11 C T G T D G I A C T G T D G I A 0 DY12 T C G A D G I A T C G A D A I A 0 DY13 (C) C G A D G D A (T) C G A D G I A 0 DY14 C T G T D G I A T C G A D G I A 0 DY15 C C G A I G D A T C G A D G I A 0 DY16 T C G A D G I A T C G A D G I T 0 DY17 T C G A D G I A T C G A D G I T 0 DY18 T C G A D G I A T C G A D A I A 0 DY19 T C G A D G I A T C G A D A I A 0 DY20 (C) C G A D G I A (T) C G A D A I A 0 DY21 T C G A D G I A T C G A D A I A 0 DY22 C C G A I G D A T C G A D G I A 0 DY23 C C G A I G D A C T G T D G I A 0 DY24 C C G A I G D A T C G A D G I A 0 E101 T C G A D G I A T C G A D G I A 0 E102 T C G A D G I A T C A A D G I A 0 E103 T C G A D G I A T C G A D G I A 0 E104 T C G A D G I A T C G A D G I A 0 E105 T C G A D G I A T C G A D G I A 0 E106 T C G A D G I A T C G A D G I A 0 E107 T C G A D G I A T C G A D G I A 0 E108 T C G A D G I A T C G A D G I A 0 E109 T C G A D G I A T C A A D G I A 0 E110 T C G A D G I A T C G A D G I A 0 E111 T C G A D G I A T C G A D G I A 0 E112 T C G A D G I A T C G A D G I T 0 E113 T C G A D G I A T C A A D G I A 0 E114 T C G A D G I A T C G A D G I A 0 E115 T C G A D G I A T C G A D G I A 0 E116 T C G A D G I A T C A A D G I A 0 E117 T C G A D G I A T C A A D G I A 0 E118 T C G A D G I A T C A A D G I A 0 E119 T C G A D G I A T C G A D G I A 0 E120 T C G A D G I A T C G A D G I A 0 E121 T C G A D G I A T C G A D G I A 0 E122 T C G A D G I A T C A A D G I A 0 E123 T C G A D G I A T C G A D G I 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 C = = = = = = = T = = = = = = = 0 DY02 C = = = ? = = = T = = = ? = = = 0 DY03 C = = = ? = = = T = = = ? = = = 0 DY04 C = = = I = D = T = = = D = I = 0 DY05 C = = = I = D A T = = = D = I T 0 DY06 (C) = = = = = = A (T) = = = = = = T 0 DY07 = = = = = = = A = = = = = = = T 0 DY08 = = = = ? = = = = = = = ? = = = 0 DY09 C T = T = = = A T C = A = = = T 0 DY10 C = = = I = D = T = = = D = I = 0 DY11 = = = = ? = = = = = = = ? = = = 0 DY12 = = = = = G = = = = = = = A = = 0 DY13 (C) = = = = = D = (T) = = = = = I = 0 DY14 C T = T = = = = T C = A = = = = 0 DY15 C = = = I = D = T = = = D = I = 0 DY16 = = = = = = = A = = = = = = = T 0 DY17 = = = = = = = A = = = = = = = T 0 DY18 = = = = = G = = = = = = = A = = 0 DY19 = = = = ? G = = = = = = ? A = = 0 DY20 (C) = = = = G = = (T) = = = = A = = 0 DY21 = = = = = G = = = = = = = A = = 0 DY22 C = = = I = D = T = = = D = I = 0 DY23 = C = A I = D = = T = T D = I = 0 DY24 C = = = I = D = T = = = D = I = 0 E101 = = = = = = = = = = = = = = = = 0 E102 = = G = = = = = = = A = = = = = 0 E103 = = = = = = = = = = = = = = = = 0 E104 = = = = = = = = = = = = = = = = 0 E105 = = = = = = = = = = = = = = = = 0 E106 = = = = = = = = = = = = = = = = 0 E107 = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = = = = = = = = = 0 E109 = = G = = = = = = = A = = = = = 0 E110 = = = = = = = = = = = = = = = = 0 E111 = = = = = = = = = = = = = = = = 0 E112 = = = = = = = A = = = = = = = T 0 E113 = = G = = = = = = = A = = = = = 0 E114 = = = = = = = = = = = = = = = = 0 E115 = ? = = ? = = = = ? = = ? = = = 0 E116 = = G = = = = = = = A = = = = = 0 E117 = = G = = = = = = = A = = = = = 0 E118 = = G = = ? ? = = = A = = ? ? = 0 E119 = ? = = ? = = = = ? = = ? = = = 0 E120 = = = = = = = = = = = = = = = = 0 E121 = = = = = = = = = = = = = = = = 0 E122 = = G = ? = = = = = A = ? = = = 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 0.97 0.89 = = = = = = 1.00 = = = = = = = 1.00 = = = = ? = = = 1.00 1.00 = 1.00 = = = 0.96 1.00 = = = 1.00 = 1.00 = = = = = ? = = = = = = = = 1.00 = = 0.67 = = = = = 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 = = = 1.00 = 1.00 = = = = = = = = 1.00 = = = = = = = 1.00 = = = = = 1.00 = = = = = = ? 1.00 = = 0.89 = = = = 1.00 = = = = = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 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