************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 adr2a.phase.inp adr2a.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST adr2a.phase.out_freqs : haplotype frequency estimates adr2a.phase.out_pairs : most likely haplotype pairs for each individual adr2a.phase.out_recom : estimates of recombination parameters adr2a.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 12 Positions of loci: 221 605 1676 2153 3547 4582 5596 6412 6623 6645 10129 11312 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file adr2a.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GTCACGGCGCAA 6.000000 2 GTCACGCCGCAA 44.000000 3 GTCACGCCGCCA 4.000000 4 GTCAGGCCGCCA 7.000000 5 GTCAGGCCGCCG 1.000000 6 GTCAGGCCACCA 3.000000 7 GTCAGACAGCCG 9.000000 8 GTCAGACAGACA 3.000000 9 GTCAGACAGACG 5.000000 10 GTTAGGCCACCA 5.000000 11 GTTAGGCCACCG 2.000000 12 ACTCGGCCACCA 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,1) DY02: (2,11) DY03: (2,7) DY04: (4,4) DY05: (1,1) DY06: (7,11) DY07: (7,8) DY08: (2,10) DY09: (2,4) DY10: (6,8) DY11: (2,3) DY12: (2,8) DY13: (5,9) DY14: (4,9) DY15: (2,4) DY16: (1,4) DY17: (2,12) DY18: (2,6) DY19: (10,12) DY20: (7,9) DY21: (1,10) DY22: (2,6) DY23: (3,7) DY24: (10,12) E101: (2,7) E102: (2,2) E103: (2,7) E104: (2,7) E105: (2,2) E106: (2,3) E107: (2,2) E108: (2,12) E109: (2,2) E110: (2,2) E111: (2,2) E112: (2,2) E113: (2,7) E114: (2,9) E115: (2,2) E116: (2,12) E117: (2,2) E118: (2,2) E119: (2,9) E120: (2,10) E121: (2,4) E122: (2,3) E123: (2,2) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G T C A C G G C G C A A G T C A C G G C G C A A 0 DY02 G T C A C G C C G C A A G T T A G G C C A C C G 0 DY03 G T C A C G C C G C A A G T C A G A C A G C C G 0 DY04 G T C A G G C C G C C A G T C A G G C C G C C A 0 DY05 G T C A C G G C G C A A G T C A C G G C G C A A 0 DY06 G T C A G A C A G C C G G T T A G G C C A C C G 0 DY07 G T C A G A C A G (C) C G G T C A G A C A G (A) C A 0 DY08 G T C A C G C C G C A A G T T A G G C C A C C A 0 DY09 G T C A C G C C G C A A G T C A G G C C G C C A 0 DY10 G T C A G G C C A C C A G T C A G A C A G A C A 0 DY11 G T C A C G C C G C A A G T C A C G C C G C C A 0 DY12 G T C A C G C C G C A A G T C A G A C A G [A] C A 0 DY13 G T C A G G C C G C C G G T C A G A C A G A C G 0 DY14 G T C A G G C C G C C (A) G T C A G A C A G A C (G) 0 DY15 G T C A C G C C G C A A G T C A G G C C G C C A 0 DY16 G T C A C G G C G C A A G T C A G G C C G C C A 0 DY17 G T C A C G C C G C A A A C T C G G C C A C C A 0 DY18 G T C A C G C C G C A A G T C A G G C C A C C A 0 DY19 G T T A G G C C A C C A A C T C G G C C A C C A 0 DY20 G T C A G A C A G C C G G T C A G A C A G [A] C G 0 DY21 G T C A C G G C G C A A G T [T] A G G C C A C C A 0 DY22 G T C A C G C C G C A A G T C A G G C C A C C A 0 DY23 G T C A C G C C G C C A G T C A G A C A G C C G 0 DY24 G T T A G G C C A C C A A C T C G G C C A C C A 0 E101 G T C A C G C C G C A A G T C A G A C A G C C G 0 E102 G T C A C G C C G C A A G T C A C G C C G C A A 0 E103 G T C A C G C C G C A A G T C A G A C A G C C G 0 E104 G T C A C G C C G C A A G T C A G A C A G C C G 0 E105 G T C A C G C C G C A A G T C A C G C C G C A A 0 E106 G T C A C G C C G C A A G T C A C G C C G C C A 0 E107 G T C A C G C C G C A A G T C A C G C C G C A A 0 E108 G T C A C G C C G C A A A C T C G G C C A C C A 0 E109 G T C A C G C C G C A A G T C A C G C C G C A A 0 E110 G T C A C G C C G C A A G T C A C G C C G C A A 0 E111 G T C A C G C C G C A A G T C A C G C C G C A A 0 E112 G T C A C G C C G C A A G T C A C G C C G C A A 0 E113 G T C A C G C C G C A A G T C A G A C A G C C G 0 E114 G T C A C G C C G C A A G T C A G A C A G A C G 0 E115 G T C A C G C C G C A A G T C A C G C C G C A A 0 E116 G T C A C G C C G C A A A C T C G G C C A C C A 0 E117 G T C A C G C C G C A A G T C A C G C C G C A A 0 E118 G T C A C G C C G C A A G T C A C G C C G C A A 0 E119 G T C A C G C C G C A A G T C A G A C A G A C G 0 E120 G T C A C G C C G C A A G T T A G G C C A C C A 0 E121 G T C A C G C C G C A A G T C A [G] G C C G C C A 0 E122 G T C A C G C C G C A A G T C A C G C C G C C A 0 E123 G T C A C G C C G C A A G T C A C G C C G C A 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 = = C = C = = = G = A A = = T = G = = = A = C G 0 DY03 = = = = C G = ? = = A A = = = = G A = ? = = C G 0 DY04 = = = = = = ? = = = = = = = = = = = ? = = = = = 0 DY05 = = = = = = = ? ? ? = = = = = = = = = ? ? ? = = 0 DY06 = = C = = A = A G = = = = = T = = G = C A = = = 0 DY07 = = = = = = = = = (C) = G = = = = = = = = = (A) = A 0 DY08 = = C = C = = ? G ? A = = = T = G = = ? A ? C = 0 DY09 = = = = C ? = = = = A = = = = = G ? = = = = C = 0 DY10 = = = = = G = C A C = = = = = = = A = A G A = = 0 DY11 = = = = = = = ? = = A = = = = = = = = ? = = C = 0 DY12 = = ? = C G = ? ? ? A = = = ? = G A = ? ? ? C = 0 DY13 ? ? = = = G = C = C = = ? ? = = = A = A = A = = 0 DY14 = = = = = G = C = C = (A) = = = = = A = A = A = (G) 0 DY15 = = = = C = = = = = A = = = = = G = = = = = C = 0 DY16 = = ? ? C = G = = = A ? = = ? ? G = C = = = C ? 0 DY17 G T C A C = = ? ? ? A = A C T C G = = ? ? ? C = 0 DY18 = = = = C = = = G = A = = = = = G = = = A = C = 0 DY19 G T = A = = = ? ? ? = = A C = C = = = ? ? ? = = 0 DY20 = = = = = = = ? ? ? = = = = = = = = = ? ? ? = = 0 DY21 = = ? = C = G = G = ? = = = ? = G = C = A = ? = 0 DY22 = = = = C = = = G = A = = = = = G = = = A = C = 0 DY23 = = = = C G = C = = = A = = = = G A = A = = = G 0 DY24 G T = A = = = = = = ? = A C = C = = = = = = ? = 0 E101 = = = = C G = C = = A A = = = = G A = A = = C G 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = C G = C = = A ? = = = = G A = A = = C ? 0 E104 = = ? = C G = C = = A A = = ? = G A = A = = C G 0 E105 = ? = = = = = = = = = = = ? = = = = = = = = = = 0 E106 = = = = = = = = = = A = = = = = = = = = = = C = 0 E107 = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 G T C A C = = = G = A = A C T C G = = = A = C = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 ? ? = = = = = = = = = = ? ? = = = = = = = = = = 0 E111 = ? = = = = = ? ? ? = ? = ? = = = = = ? ? ? = ? 0 E112 = ? = = = = = ? ? ? = = = ? = = = = = ? ? ? = = 0 E113 ? ? = = C G = C = = A A ? ? = = G A = A = = C G 0 E114 = = ? = C G = C = C A A = = ? = G A = A = A C G 0 E115 = ? ? = = = = = = = = = = ? ? = = = = = = = = = 0 E116 G T C A C = = ? ? ? A = A C T C G = = ? ? ? C = 0 E117 = = = = = = = = = = ? = = = = = = = = = = = ? = 0 E118 ? = = = = = = = = = = = ? = = = = = = = = = = = 0 E119 = = = = C G = ? = C A A = = = = G A = ? = A C G 0 E120 = = C = C = = ? ? ? A = = = T = G = = ? ? ? C = 0 E121 = = = = ? = = = = = A = = = = = ? = = = = = C = 0 E122 = = = = = = = = = = A ? = = = = = = = = = = C ? 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 0.97 = = = = 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 = = = = = 0.99 ? = = = = 1.00 = = = = = = 1.00 = 1.00 0.99 1.00 = = = = = = = = = ? = = 1.00 = = = ? = 1.00 1.00 = ? ? ? 0.99 = ? ? = = = 1.00 = 1.00 = 0.98 = = = = = = = 1.00 = 1.00 = 0.99 = 0.86 = = = = 0.99 = = = = = 1.00 = = = ? ? 1.00 = 0.97 = = = 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 = 0.98 = 1.00 = ? = = = = = 1.00 = = = 0.99 = 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 = 0.99 1.00 0.99 = ? ? = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = ? ? ? 1.00 = = = = = = = = = = = ? = ? = = = = = = = = = = = = = = = 1.00 1.00 = ? = 0.99 1.00 0.99 = = 0.99 = 1.00 = = ? ? ? 1.00 = = = = = ? = = = = = 1.00 = = = = = = = = = = = 1.00 ? = = = = = = = = = = = = END PHASEPROBS