************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 hmgb1.phase.inp hmgb1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST hmgb1.phase.out_freqs : haplotype frequency estimates hmgb1.phase.out_pairs : most likely haplotype pairs for each individual hmgb1.phase.out_recom : estimates of recombination parameters hmgb1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 23 Positions of loci: 359 675 1011 1472 2173 4052 4510 4742 5118 5274 5313 5590 7512 7531 7551 7556 7627 8644 8728 8745 9243 9263 9503 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file hmgb1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AAATGCATCCGAIIADIDGTATC 22.000000 2 AAATACATCCGAIIADIDGTATC 6.000000 3 ACGTGCGCCCGGIIAIIIGGACT 2.000000 4 ACGCGCGCCCGGIIAIIIGGACT 1.000000 5 ACGCGCGCCCGGIDAIDIGGACT 8.000000 6 GAATGCATCCGAIIADIDGTATC 2.000000 7 GAATGCATCCGAIIADIDGTGTC 7.000000 8 GAATGCATCTGAIIADIDGTATC 8.000000 9 GAATGCATTCGAIIADIDGTATC 9.000000 10 GAATGCATTCGAIIGDIDGTATC 4.000000 11 GAATGGATCCCADIADIIATATC 21.000000 12 GCGCGCGCCCGGIDAIDIGGACT 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (3,6) DY02: (9,10) DY03: (1,8) DY04: (5,9) DY05: (1,4) DY06: (1,12) DY07: (1,12) DY08: (5,5) DY09: (1,12) DY10: (3,11) DY11: (1,8) DY12: (8,12) DY13: (8,9) DY14: (5,5) DY15: (1,6) DY16: (1,8) DY17: (1,10) DY18: (9,10) DY19: (8,9) DY20: (5,9) DY21: (5,8) DY22: (5,9) DY23: (9,11) DY24: (8,10) E101: (11,11) E102: (1,2) E103: (11,11) E104: (1,2) E105: (11,11) E106: (11,11) E107: (2,11) E108: (1,11) E109: (1,7) E110: (1,11) E111: (1,11) E112: (1,11) E113: (1,7) E114: (1,2) E115: (2,2) E116: (1,7) E117: (1,11) E118: (11,11) E119: (7,11) E120: (1,7) E121: (11,11) E122: (7,9) E123: (1,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A C G T G C G C C C G G I I A I I I G G A C T G A A T G C A T C C G A I I A D I D G T A T C 0 DY02 G A A T G C A T T C G A I I A D I D G T A T C G A A T G C A T T C G A I I G D I D G T A T C 0 DY03 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C T G A I I A D I D G T A T C 0 DY04 A C G C G C G C C C G G I D A I D I G G A C T G A A T G C A T T C G A I I [A] D I D G T A T C 0 DY05 A A A T G C A T C C G A I I A D I D G T A T C A C G C G C G C C C G G I I A I I I G G A C T 0 DY06 (A) A A T G C A T C C G A I I A D I D G T A T C (G) C G C G C G C C C G G I D A I D I G G A C T 0 DY07 (A) A A T G C A T C C G A I I A D I D G T A T C (G) C G C G C G C C C G G I D A I D I G G A C T 0 DY08 [A] C G C G C G C C C G G I D A I D I G G A C T A C G C G C G C C C G G I D A I D I G G A C T 0 DY09 (A) A A T G C A T C C G A I I A D I D G T A T C (G) C G C G C G C C C G G I D A I D I G G A C T 0 DY10 A C G T G C G C C C G G I I A I I I G G A C T G A A T G G A T C C C A D I A D I I A T A T C 0 DY11 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C T G A I I A D I D G T A T C 0 DY12 G A A T G C A T C T G A I I A D I D G T A T C G C G C G C G C C C G G I D A I D I G G A C T 0 DY13 G A A T G C A T C T G A I I A D I D G T A T C G A A T G C A T T C G A I I A D I D G T A T C 0 DY14 A C G C G C G C C C G G I D A I D I G G A C T A C G C G C G C C C G G I D A I D I G G A C T 0 DY15 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C C G A I I A D I D G T A T C 0 DY16 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C T G A I I A D I D G T A T C 0 DY17 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T T C G A I I G D I D G T A T C 0 DY18 G A A T G C A T T C G A I I A D I D G T A T C G A A T G C A T T C G A I I G D I D G T A T C 0 DY19 G A A T G C A T C T G A I I A D I D G T A T C G A A T G C A T T C G A I I A D I D G T A T C 0 DY20 A C G C G C G C C C G G I D A I D I G G A C T G A A T G C A T T C G A I I [A] D I D G T A T C 0 DY21 A C G C G C G C C C G G I D A I D I G G A C T G A A T G C A T C T G A I I A D I D G T A T C 0 DY22 A C G C G C G C C C G G I D A I D I G G A C T G A A T G C A T T C G A I I [A] D I D G T A T C 0 DY23 G A A T G C A T T C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 DY24 G A A T G C A T C T G A I I A D I D G T A T C G A A T G C A T T C G A I I G D I D G T A T C 0 E101 G A A T G G A T C C C A D I A D I I A T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E102 A A A T G C A T C C G A I I A D I D G T A T C A A A T A C A T C C G A I I A D I D G T A T C 0 E103 G A A T G G A T C C C A D I A D I I A T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E104 A A A T G C A T C C G A I I A D I D G T A T C A A A T A C A T C C G A I I A D I D G T A T C 0 E105 G A A T G G A T C C C A D I A D I I A T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E106 G A A T G G A T C C C A D I A D I I A T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E107 A A A T A C A T C C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E108 A A A T G C A T C C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E109 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C C G A I I A D I D G T G T C 0 E110 A A A T G C A T C C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E111 A A A T G C A T C C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E112 A A A T G C A T C C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E113 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C C G A I I A D I D G T G T C 0 E114 A A A T G C A T C C G A I I A D I D G T A T C A A A T A C A T C C G A I I A D I D G T A T C 0 E115 A A A T A C A T C C G A I I A D I D G T A T C A A A T A C A T C C G A I I A D I D G T A T C 0 E116 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C C G A I I A D I D G T G T C 0 E117 A A A T G C A T C C G A I I A D I D G T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E118 G A A T G G A T C C C A D I A D I I A T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E119 G A A T G C A T C C G A I I A D I D G T G T C G A A T G G A T C C C A D I A D I I A T A T C 0 E120 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C C G A I I A D I D G T G T C 0 E121 G A A T G G A T C C C A D I A D I I A T A T C G A A T G G A T C C C A D I A D I I A T A T C 0 E122 G A A T G C A T C C G A I I A D I D G T G T C G A A T G C A T T C G A I I A D I D G T A T C 0 E123 A A A T G C A T C C G A I I A D I D G T A T C G A A T G C A T C C G A I I A D I D G T G T C 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 G = ? = G C = = = G = = = I ? I = G = C T G A A = ? = A T = = = A = = = D ? D = T = T C 0 DY02 = = = = = = ? = = = = = = = A = = = = = = = = = = = = = = ? = = = = = = = G = = = = = = = = 0 DY03 A = = = = = = = = C = = = = = = = = = = = = ? G = = = = = = = = T = = = = = = = = = = = = ? 0 DY04 A C G C ? = ? C C = = G = D ? ? ? I = G = C T G A A T ? = ? T T = = A = I ? ? ? D = T = T C 0 DY05 = A A T = = A T = = = A = = = D = D = T = T C = C G C = = G C = = = G = = = I = I = G = C T 0 DY06 (A) A A T = = A T = = = A = I ? ? I D = T = T ? (G) C G C = = G C = = = G = D ? ? D I = G = C ? 0 DY07 (A) A A ? = = A T = = = A = I ? ? I D = T = T C (G) C G ? = = G C = = = G = D ? ? D I = G = C T 0 DY08 ? ? = = = = = ? = = = = = = = = = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = 0 DY09 (A) A ? T = = A T = = = A = I ? ? ? D = T = T C (G) C ? C = = G C = = = G = D ? ? ? I = G = C T 0 DY10 A C G = = C G C = = G G I ? ? I = = G G = C T G A A = = G A T = = C A D ? ? D = = A T = T C 0 DY11 A = = = = = = = = C = = = = = = = = = = = = = G = = = = = = = = T = = = = = = = = = = = = = 0 DY12 = A A T = = A T = T = A = I ? ? I D = T = T ? = C G C = = G C = C = G = D ? ? D I = G = C ? 0 DY13 = = = = = = = = C T = = = = = = = = = = = = = = = = = = = = = T C = = = = = = = = = = = = = 0 DY14 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY15 A = = = = = = = = = = = = = = = = = = = = = ? G = = = = = = = = = = = = = = = = = = = = = ? 0 DY16 ? ? = = = = = = = C = = = = = = = = = = = = = ? ? = = = = = = = T = = = = = = = = = = = = = 0 DY17 A = = = = = = = C = = = = = A = = = = = = = = G = = = = = = = T = = = = = G = = = = = = = = 0 DY18 = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = 0 DY19 = = = = = = = = C T = = = = = = = = = = = = ? = = = = = = = = T C = = = = = = = = = = = = ? 0 DY20 A C G C = = G C C = = G = D ? ? D I = G = C ? G A A T = = A T T = = A = I ? ? I D = T = T ? 0 DY21 A C G C = = G C = C = G = D ? ? D ? ? ? = C ? G A A T = = A T = T = A = I ? ? I ? ? ? = T ? 0 DY22 A C G C = = G C C = = G = D ? ? D I = G = C T G A A T = = A T T = = A = I ? ? I D = T = T C 0 DY23 = = = = = C = = T = G = I ? = = = D G = = = ? = = = = = G = = C = C = D ? = = = I A = = = ? 0 DY24 ? = = = = = = = C T = = = = A = = = = = = = = ? = = = = = = = T C = = = = G = = = = = = = = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 ? = = = G = = = = = = = = = = = = = = = = = = ? = = = A = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = = = = G = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = 0 E105 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 E106 = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = 0 E107 A = = = A C = = = = G = I ? = = = D G = = = ? G = = = G G = = = = C = D ? = = = I A = = = ? 0 E108 ? ? ? ? = C = = = = G = I ? = = = D G = = = = ? ? ? ? = G = = = = C = D ? = = = I A = = = = 0 E109 A = = = = = = = = = = = = = = = = = = = A = = G = = = = = = = = = = = = = = = = = = = G = = 0 E110 A = = = = C = = = = G = I ? = = = D G = = = = G = = = = G = = = = C = D ? = = = I A = = = = 0 E111 A = = = = C = = = = G = I ? = = = D G = = = = G = = = = G = = = = C = D ? = = = I A = = = = 0 E112 A = = = = C = = = = G = I ? = = = D G = = = ? G = = = = G = = = = C = D ? = = = I A = = = ? 0 E113 A = = = = = = = = = = = = = = = = = = = A = = G = = = = = = = = = = = = = = = = = = = G = = 0 E114 = = = = G = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 ? = = = = = = = = = = = = = = = = ? = = A = = ? = = = = = = = = = = = = = = = = ? = = G = = 0 E117 A = = = = C = = = = G = I ? = = = D G = = = = G = = = = G = = = = C = D ? = = = I A = = = = 0 E118 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0 E119 = = ? ? = C = = = = G = I ? = = = D G = G = = = = ? ? = G = = = = C = D ? = = = I A = A = = 0 E120 A = = = = = = = = = = = = = = = = = = = A = = G = = = = = = = = = = = = = = = = = = = G = = 0 E121 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E122 = = = = = = = = C = = = = = = = = = = = G = = = = = = = = = = T = = = = = = = = = = = A = = 0 E123 A = = = = = = = = = = = = = = = ? = = = A = = G = = = = = = = = = = = = = = = ? = = = 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 = = = = = = = = 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 0.61 1.00 1.00 1.00 = = 1.00 1.00 = = = 1.00 = 1.00 ? ? 1.00 1.00 = 1.00 = 1.00 ? 0.61 1.00 1.00 ? = = 1.00 1.00 = = = 1.00 = 1.00 ? ? 1.00 1.00 = 1.00 = 1.00 1.00 ? ? = = = = = ? = = = = = = = = = = = = = = = 0.62 1.00 ? 1.00 = = 1.00 1.00 = = = 1.00 = 1.00 ? ? ? 1.00 = 1.00 = 1.00 1.00 1.00 1.00 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 = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = 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 ? 0.98 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 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 = 1.00 ? = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? = 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