************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 b3gt6.phase.inp b3gt6.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST b3gt6.phase.out_freqs : haplotype frequency estimates b3gt6.phase.out_pairs : most likely haplotype pairs for each individual b3gt6.phase.out_recom : estimates of recombination parameters b3gt6.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 9 Positions of loci: 3196 3293 3815 3915 4179 7741 7830 8415 10054 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file b3gt6.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACCIGDGAA 8.000000 2 ACCDGIGAA 2.000000 3 ACCDGIGGA 7.000000 4 ACCDGIAAA 28.000000 5 AACDGIAAG 18.000000 6 TCCDGIGGA 3.000000 7 TCCDAIGGA 13.000000 8 TCTDGIGGA 13.000000 9 TACIAIGGA 1.000000 10 TACDAIGGA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,1) DY02: (1,4) DY03: (3,7) DY04: (3,3) DY05: (3,8) DY06: (1,7) DY07: (1,4) DY08: (4,7) DY09: (5,7) DY10: (9,10) DY11: (7,8) DY12: (3,4) DY13: (1,4) DY14: (4,4) DY15: (2,6) DY16: (1,7) DY17: (4,4) DY18: (2,7) DY19: (4,5) DY20: (3,8) DY21: (7,7) DY22: (4,4) DY23: (1,3) DY24: (6,7) E101: (4,8) E102: (4,5) E103: (5,6) E104: (4,8) E105: (5,8) E106: (4,5) E107: (4,5) E108: (4,5) E109: (5,8) E110: (4,4) E111: (4,8) E112: (4,4) E113: (5,7) E114: (4,5) E115: (5,5) E116: (7,7) E117: (5,8) E118: (4,4) E119: (5,8) E120: (4,8) E121: (5,5) E122: (5,8) E123: (4,8) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A C C I G D G A A A C C I G D G A A 0 DY02 A C C I G D G A A A C C D G I A A A 0 DY03 A C C D G I G G A T C C D A I G G A 0 DY04 [A] C C D G I G G A A C C D G I G G A 0 DY05 A C C D G I G G A T C T D G I G G A 0 DY06 A C C I G D G A A T C C D A I G G A 0 DY07 A C C I G D G A A A C C D G I A A A 0 DY08 A C C D G I A A A T C C D A I G G A 0 DY09 A A C D G I A A G T C C D A I G G A 0 DY10 T A C I A I G G A T A C D A I G G A 0 DY11 [T] C C D [A] I G G A [T] C [T] D G I G G A 0 DY12 A C C D G I G G A A C C D G I A A A 0 DY13 A C C I G D G A A A C C D G I A A A 0 DY14 A C C D G I A A A A C C D G I A A A 0 DY15 (A) C C D G I G A A (T) C [C] D [G] I G G A 0 DY16 A C C I G D G A A T C C D A I G G A 0 DY17 A C C D G I A A A A C C D G I A A A 0 DY18 A C C D G I G (A) A T C C D A I G (G) A 0 DY19 A C C D G I A A A A A C D G I A A G 0 DY20 A C C D G I G G A T C T D G I G G A 0 DY21 T C C D A I G G A T C C D A I G G A 0 DY22 A C C D G I A A A A C C D G I A A A 0 DY23 A C C I G D G A A A C C D G I G G A 0 DY24 T C C D G I G G A T C C D A I G G A 0 E101 A C C D G I A A A T C T D G I G G A 0 E102 A C C D G I A A A A A C D G I A A G 0 E103 A A C D G I A A G [T] C [C] D [G] I G G A 0 E104 A C C D G I A A A T C T D G I G G A 0 E105 A A C D G I A A G T C T D G I G G A 0 E106 A C C D G I A A A A A C D G I A A G 0 E107 A C C D G I A A A A A C D G I A A G 0 E108 A C C D G I A A A A A C D G I A A G 0 E109 A A C D G I A A G T C T D G I G G A 0 E110 A C C D G I A A A A C C D G I A A A 0 E111 A C C D G I A A A T C T D G I G G A 0 E112 A C C D G I A A A A C C D G I A A A 0 E113 A A C D G I A A G T C C D A I G G A 0 E114 A C C D G I A A A A A C D G I A A G 0 E115 A A C D G I A A G A A C D G I A A G 0 E116 T C C D A I G G A T C C D A I G G A 0 E117 A A C D G I A A G T C T D G I G G A 0 E118 A C C D G I A A A A C C D G I A A A 0 E119 A A C D G I A A G T C T D G I G G A 0 E120 A C C D G I A A A T C T D G I G G A 0 E121 A A C D G I A A G A A C D G I A A G 0 E122 A A C D G I A A G T C T D G I G G A 0 E123 A C C D G I A A A T C T D G I G G 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 = = = I = D G = = = = = D = I A = = 0 DY03 A = = = G = = = = T = = = A = = = = 0 DY04 ? ? = = = = = = = ? ? = = = = = = = 0 DY05 A ? C = = = = = = T ? T = = = = = = 0 DY06 ? ? = I G D = A = ? ? = D A I = G = 0 DY07 ? ? = I = D G = = ? ? = D = I A = = 0 DY08 ? ? = = G = A A = ? ? = = A = G G = 0 DY09 A A = = G = A A G T C = = A = G G A 0 DY10 = = = I = = = = = = = = D = = = = = 0 DY11 ? ? ? ? ? = = = = ? ? ? ? ? = = = = 0 DY12 ? ? = = = = G G = ? ? = = = = A A = 0 DY13 = = ? ? ? D G = = = = ? ? ? I A = = 0 DY14 = = ? ? ? = = = = = = ? ? ? = = = = 0 DY15 (A) = ? ? ? = = A = (T) = ? ? ? = = G = 0 DY16 A = = I G D = A = T = = D A I = G = 0 DY17 = = = = = = = = = = = = = = = = = = 0 DY18 A = = = G = = (A) = T = = = A = = (G) = 0 DY19 = C = = = = = = A = A = = = = = = G 0 DY20 A = C = = = = = = T = T = = = = = = 0 DY21 = = = = = = = = = = = = = = = = = = 0 DY22 = = = = = = = = = = = = = = = = = = 0 DY23 = = = I = D = A = = = = D = I = G = 0 DY24 = = = = G = = = = = = = = A = = = = 0 E101 A = C = = = A A = T = T = = = G G = 0 E102 = C = = = = = = A = A = = = = = = G 0 E103 ? ? ? ? ? = A A G ? ? ? ? ? = G G A 0 E104 A = C = = = A A = T = T = = = G G = 0 E105 A A C = = = A ? G T C T = = = G ? A 0 E106 = C ? ? = = = = A = A ? ? = = = = G 0 E107 = C = = = = = = A = A = = = = = = G 0 E108 = C = = = = = = A = A = = = = = = G 0 E109 ? ? C = = = A A G ? ? T = = = G G A 0 E110 = = = = = = = = = = = = = = = = = = 0 E111 A ? C = = = A A = T ? T = = = G G = 0 E112 = = = = = = = = = = = = = = = = = = 0 E113 A A = = G = A A G T C = = A = G G A 0 E114 ? ? = = = = = = A ? ? = = = = = = G 0 E115 = = = = = = = = = = = = = = = = = = 0 E116 ? ? = = = = = = = ? ? = = = = = = = 0 E117 ? ? C = = = A A G ? ? T = = = G G A 0 E118 = ? = = = = = = = = ? = = = = = = = 0 E119 A A C = = = A A G T C T = = = G G A 0 E120 A = C = = = A A = T = T = = = G G = 0 E121 ? ? = = = = = = = ? ? = = = = = = = 0 E122 ? ? C ? = = A A G ? ? T ? = = G G A 0 E123 ? ? C = = = A A = ? ? T = = = 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 = 1.00 1.00 = = ? ? = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = = = 1.00 = = = = = ? ? ? ? ? = = = = ? ? = = = = 1.00 1.00 = = = ? ? ? 1.00 1.00 = = = = ? ? ? = = = = 0.87 = ? ? ? = = 0.99 = 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = = = 1.00 = = 0.86 = = 1.00 = = = = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 = = = = = = 1.00 ? ? ? ? ? = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 ? 1.00 = 1.00 ? ? = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = = = = = 1.00 ? ? 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = 1.00 ? 1.00 = = = 1.00 1.00 = = = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 ? ? = = = = = = 1.00 = = = = = = = = = ? ? = = = = = = = ? ? 1.00 = = = 1.00 1.00 1.00 = ? = = = = = = = 1.00 1.00 1.00 = = = 1.00 1.00 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