************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mgpxx.phase.inp mgpxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mgpxx.phase.out_freqs : haplotype frequency estimates mgpxx.phase.out_pairs : most likely haplotype pairs for each individual mgpxx.phase.out_recom : estimates of recombination parameters mgpxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 15 Positions of loci: 364 1710 2908 3039 4521 6264 6318 6746 7306 8883 8885 8967 8969 9211 9809 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mgpxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CATAGGCGTAAITCA 31.000000 2 CATGGGCGTAAITTA 6.000000 3 CATGGGCGAAAITTG 3.000000 4 CATGGGCGATGDATG 4.000000 5 CATGGGCAATGDATG 2.000000 6 CATGGACGATGDATG 1.000000 7 CATGGACAATGDATG 3.000000 8 CATGGATAATGDATG 25.000000 9 CACGGATAATGDATG 13.000000 10 TGTGAACAATGDATG 6.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,1) DY02: (1,10) DY03: (4,10) DY04: (7,8) DY05: (4,8) DY06: (1,1) DY07: (2,8) DY08: (1,2) DY09: (2,4) DY10: (1,4) DY11: (1,3) DY12: (1,5) DY13: (3,10) DY14: (3,7) DY15: (8,10) DY16: (1,2) DY17: (1,8) DY18: (1,2) DY19: (1,1) DY20: (6,7) DY21: (10,10) DY22: (8,8) DY23: (1,1) DY24: (1,8) E101: (1,9) E102: (8,9) E103: (8,8) E104: (1,8) E105: (8,8) E106: (1,9) E107: (1,9) E108: (8,8) E109: (9,9) E110: (8,9) E111: (8,9) E112: (1,2) E113: (1,8) E114: (1,9) E115: (8,8) E116: (1,8) E117: (1,8) E118: (1,8) E119: (1,9) E120: (1,8) E121: (1,9) E122: (9,9) E123: (1,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C A T A G G C G T A A I T C A C A T A G G C G T A A I T C A 0 DY02 C A T A G G C G T A A I T C A T G T G A A C A A T G D A T G 0 DY03 C A T G G G C G A T G D A T G T G T G A A C A A T G D A T G 0 DY04 C A T G G A C A A T G D A T G C A T G G A T A A T G D A T G 0 DY05 C A T G G G C G A T G D A T G C A T G G A T A A T G D A T G 0 DY06 C A T A G G C G T A A I T C A C A T A G G C G T A A I T C A 0 DY07 C A T G G G C G T A A I T T A C A T G G A T A A T G D A T G 0 DY08 C A T A G G C G T A A I T C A C A T G G G C G T A A I T T A 0 DY09 C A T G G G C G T A A I T T A C A T G G G C G A T G D A T G 0 DY10 C A T A G G C G T A A I T C A C A T G G G C G A T G D A T G 0 DY11 C A T A G G C G T A A I T C A C A T G G G C G A A A I T T G 0 DY12 C A T A G G C G T A A I T C A C A T G G G C A A T G D A T G 0 DY13 C A T G G G C G A A A I T T G T G T G A A C A A T G D A T G 0 DY14 C A T G G G C G A A A I T T G C A T G G A C A A T G D A T G 0 DY15 C A T G G A T A A T G D A T G T G T G A A C A A T G D A T G 0 DY16 C A T A G G C G T A A I T C A C A T G G G C G T A A I T T A 0 DY17 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 DY18 C A T A G G C G T A A I T C A C A T G G G C G T A A I T T A 0 DY19 C A T A G G C G T A A I T C A C A T A G G C G T A A I T C A 0 DY20 C A T G G A C G A T G D A T G C A T G G A C A A T G D A T G 0 DY21 T G T G A A C A A T G D A T G T G T G A A C A A T G D A T G 0 DY22 C A T G G A T A A T G D A T G C A T G G A T A A T G D A T G 0 DY23 C A T A G G C G T A A I T C A C A T A G G C G T A A I T C A 0 DY24 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E101 C A T A G G C G T A A I T C A C A C G G A T A A T G D A T G 0 E102 C A T G G A T A A T G D A T G C A C G G A T A A T G D A T G 0 E103 C A T G G A T A A T G D A T G C A T G G A T A A T G D A T G 0 E104 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E105 C A T G G A T A A T G D A T G C A T G G A T A A T G D A T G 0 E106 C A T A G G C G T A A I T C A C A C G G A T A A T G D A T G 0 E107 C A T A G G C G T A A I T C A C A C G G A T A A T G D A T G 0 E108 C A T G G A T A A T G D A T G C A T G G A T A A T G D A T G 0 E109 C A C G G A T A A T G D A T G C A C G G A T A A T G D A T G 0 E110 C A T G G A T A A T G D A T G C A C G G A T A A T G D A T G 0 E111 C A T G G A T A A T G D A T G C A C G G A T A A T G D A T G 0 E112 C A T A G G C G T A A I T C A C A T G G G C G T A A I T T A 0 E113 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E114 C A T A G G C G T A A I T C A C A C G G A T A A T G D A T G 0 E115 C A T G G A T A A T G D A T G C A T G G A T A A T G D A T G 0 E116 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E117 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E118 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E119 C A T A G G C G T A A I T C A C A C G G A T A A T G D A T G 0 E120 C A T A G G C G T A A I T C A C A T G G A T A A T G D A T G 0 E121 C A T A G G C G T A A I T C A C A C G G A T A A T G D A T G 0 E122 C A C G G A T A A T G D A T G C A C G G A T A A T G D A T G 0 E123 C A T A G G C G T A A I T C A C A T G G G C A A T G D A 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 ? ? G G = G T A A I T C A T G ? ? A A = A A T G D A T G 0 DY03 C A = = G G = G ? = = = = = = T G = = A A = A ? = = = = = = 0 DY04 = = = = = = C = = = = = = = = = = = = = = T = = = = = = = = 0 DY05 = = = = = G C G = = = = = = = = = = = = A T A = = = = = = = 0 DY06 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY07 = = = = = G C G T A A I T = A = = = = = A T A A T G D A = G 0 DY08 = = = A = = = = = = = = = ? = = = = G = = = = = = = = = ? = 0 DY09 = = = = = = = = T A A I T = A = = = = = = = = A T G D A = G 0 DY10 = = = A = = = = T A A I T C A = = = G = = = = A T G D A T G 0 DY11 = = = A = = = = T = = = = C A = = = G = = = = A = = = = T G 0 DY12 = = = A = = = G T ? ? I T ? ? = = = G = = = A A ? ? D A ? ? 0 DY13 C A = = G G = G = A A I T = = T G = = A A = A = T G D A = = 0 DY14 ? = = = = G = G = A A I T = = ? = = = = A = A = T G D A = = 0 DY15 ? A = = G = T = = = = = = = = ? G = = A = C = = = = = = = = 0 DY16 = = = A = = = = = = = = = C = = = = G = = = = = = = = = T = 0 DY17 = = = A = G C G T A A I T C A = = = G = A T A A T G D A T G 0 DY18 ? = = A = = = = = = = = = C = ? = = G = = = = = = = = = T = 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 = = = = = = = G = = = = = = = = = = = = = = A = = = = = = = 0 DY21 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY22 ? ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = 0 DY23 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY24 = = = A = G C G T A A I T C A = = = G = A T A A T G D A T G 0 E101 = = T A = G C G T ? ? ? ? C A = = C G = A T A A ? ? ? ? T G 0 E102 = = T = = = = = = = = = = = = = = C = = = = = = = = = = = = 0 E103 ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 E104 = = = A = G C G T A A I T C A = = = G = A T A A T G D A T G 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 ? = T A = G C G T A A I T C A ? = C G = A T A A T G D A T G 0 E107 ? = T A = G C G T A A I T C A ? = C G = A T A A T G D A T G 0 E108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E109 ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 E110 ? = T = = = = = = = = = = = = ? = C = = = = = = = = = = = = 0 E111 = = T = = = = = = = = = = = = = = C = = = = = = = = = = = = 0 E112 ? = = A = = = = = = = = = C = ? = = G = = = = = = = = = T = 0 E113 ? = = A = G C G T A A I T ? ? ? = = G = A T A A T G D A ? ? 0 E114 ? = T A = G C G T A A I T C A ? = C G = A T A A T G D A T G 0 E115 ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 E116 ? = = A = G C G T A A I T ? A ? = = G = A T A A T G D A ? G 0 E117 ? = = A = G C G T A A I T C A ? = = G = A T A A T G D A T G 0 E118 ? = = A = G C G T A A I T ? A ? = = G = A T A A T G D A ? G 0 E119 ? = T A = G C G T A A ? ? C A ? = C G = A T A A T G ? ? T G 0 E120 = = = A = G C G T A A I T C A = = = G = A T A A T G D A T G 0 E121 ? = T A = G C G T A A I T C A ? = C G = A T A A T G D A T G 0 E122 ? = = = = = = = = = = ? ? = = ? = = = = = = = = = = ? ? = = 0 E123 = = = A = = = G T A A ? ? C A = = = G = = = A A T G ? ? T G 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 = = = 1.00 1.00 ? ? 1.00 1.00 ? ? 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = ? = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = ? 1.00 = = 1.00 = 1.00 = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = = = = = = = ? = 0.99 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 ? ? ? = 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 ? = 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 ? = 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 END PHASEPROBS