************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 serg1.phase.inp serg1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST serg1.phase.out_freqs : haplotype frequency estimates serg1.phase.out_pairs : most likely haplotype pairs for each individual serg1.phase.out_recom : estimates of recombination parameters serg1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 24 Positions of loci: 386 604 2739 3251 3502 4068 5854 5859 6199 6576 6803 8757 8764 9372 11178 11717 11792 14814 14838 15486 16016 17116 18365 18835 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file serg1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACGDCCGCAACTAGCGTGGGGCTA 8.000000 2 GTGDCCCAAGCGAATCGAGAGTTG 1.000000 3 GTGDCCCAAGTGGATCGAGGACTG 1.000000 4 GTGDCCCAAGTGGATCGAGAGTTG 11.000000 5 GTGDCCCAAGTGGATCGATAGCTG 2.000000 6 GTGDCCCAAGTGGATCGATAGCCG 14.000000 7 GTGDCCGCAACTAGCGTGGGGCTA 9.000000 8 GTGDTCCAGGTGGATCGAGGACTG 3.000000 9 GTGICCCAAGTGGATCGATAGCCG 3.000000 10 GTGITTCAGGTGGATCGAGGACTG 32.000000 11 GTGITTCAGGTGGATCGATAGCCG 1.000000 12 GTADCCCAAGTGGATCGATAGCCG 9.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,8) DY02: (4,6) DY03: (4,6) DY04: (4,11) DY05: (4,5) DY06: (8,10) DY07: (1,10) DY08: (4,10) DY09: (10,10) DY10: (10,10) DY11: (4,10) DY12: (4,10) DY13: (4,4) DY14: (10,10) DY15: (10,10) DY16: (1,1) DY17: (4,10) DY18: (2,3) DY19: (6,12) DY20: (10,10) DY21: (5,8) DY22: (4,10) DY23: (1,1) DY24: (10,10) E101: (10,10) E102: (6,12) E103: (1,10) E104: (10,10) E105: (6,9) E106: (9,12) E107: (7,10) E108: (7,9) E109: (6,10) E110: (6,12) E111: (6,12) E112: (10,10) E113: (6,12) E114: (10,10) E115: (7,10) E116: (12,12) E117: (6,7) E118: (6,12) E119: (6,7) E120: (6,7) E121: (7,7) E122: (6,10) 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 D C C G C A A C T A G C G T G G G G C T A G T G D T C C A G G T G G A T C G A G G A C T G 0 DY02 G T G D C C C A A G T G G A T C G A G A G T T G G T G D C C C A A G T G G A T C G A T A G C C G 0 DY03 G T G D C C C A A G T G G A T C G A G A G T T G G T G D C C C A A G T G G A T C G A T A G C C G 0 DY04 G T G D C C C A A G T G G A T C G A (G) A G (T) (T) G G T G I T T C A G G T G G A T C G A (T) A G (C) (C) G 0 DY05 G T G D C C C A A G T G G A T C G A G A G T T G G T G D C C C A A G T G G A T C G A T A G C T G 0 DY06 G T G D T C C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY07 A C G D C C G C A A C T A G C G T G G G G C T A G T G I T T C A G G T G G A T C G A G G A C T G 0 DY08 G T G D C C C A A G T G G A T C G A G A G T T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY09 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY10 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY11 G T G D C C C A A G T G G A T C G A G A G T T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY12 G T G D C C C A A G T G G A T C G A G A G T T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY13 G T G D C C C A A G T G G A T C G A G A G T T G G T G D C C C A A G T G G A T C G A G A G T T G 0 DY14 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY15 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY16 A C G D C C G C A A C T A G C G T G G G G C T A A C G D C C G C A A C T A G C G T G G G G C T A 0 DY17 G T G D C C C A A G T G G A T C G A G A G T T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY18 G T G D C C C A A G (C) G (A) A T C G A G A G T T G G T G D C C C A A G (T) G (G) A T C G A G G A C T G 0 DY19 G T G D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 DY20 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY21 G T G D C C C A A G T G G A T C G A T A G C T G G T G D T C C A G G T G G A T C G A G G A C T G 0 DY22 G T G D C C C A A G T G G A T C G A G A G T T G G T G I T T C A G G T G G A T C G A G G A C T G 0 DY23 A C G D C C G C A A C T A G C G T G G G G C T A A C G D C C G C A A C T A G C G T G G G G C T A 0 DY24 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 E101 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 E102 G T G D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E103 A C G D C C G C A A C T A G C G T G G G G C T A G T G I T T C A G G T G G A T C G A G G A C T G 0 E104 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 E105 G T G D C C C A A G T G G A T C G A T A G C C G G T G I C C C A A G T G G A T C G A T A G C C G 0 E106 G T G I C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E107 G T G D C C G C A A C T A G C G T G G G G C T A G T G I T T C A G G T G G A T C G A G G A C T G 0 E108 G T G D C C G C A A C T A G C G T G G G G C T A G T G I C C C A A G T G G A T C G A T A G C C G 0 E109 G T G D C C C A A G T G G A T C G A T A G C C G G T G I T T C A G G T G G A T C G A G G A C T G 0 E110 G T G D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E111 G T G D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E112 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 E113 G T G D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E114 G T G I T T C A G G T G G A T C G A G G A C T G G T G I T T C A G G T G G A T C G A G G A C T G 0 E115 G T G D C C G C A A C T A G C G T G G G G C T A G T G I T T C A G G T G G A T C G A G G A C T G 0 E116 G T A D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E117 G T G D C C C A A G T G G A T C G A T A G C C G G T G D C C G C A A C T A G C G T G G G G C T A 0 E118 G T G D C C C A A G T G G A T C G A T A G C C G G T A D C C C A A G T G G A T C G A T A G C C G 0 E119 G T [G] D C C C A A G T G G A T C G A T A G C C G G T G D C C G C A A C T A G C G T G G G G C T A 0 E120 G T G D C C C A A G T G G A T C G A T A G C C G G T G D C C G C A A C T A G C G T G G G G C T A 0 E121 G T G D C C G C A A C T A G C G T G G G G C T A G T G D C C G C A A C T A G C G T G G G G C T A 0 E122 G T G D C C C A A G T G G A T C G A T A G C C G G T G I T T C A G G T G G A T C G A G G A C T G 0 E123 A C G D C C G C A A C T A G C G T G G G G C T A G T G D C C G C A A C T A G C G T G G G G C T 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 A C = = C = G C A A C T A G C G T G = = G = = A G T = = T = C A G G T G G A T C G A = = A = = G 0 DY02 ? ? = = = = = = = = = = = = = = = = G = = T T = ? ? = = = = = = = = = = = = = = = = T = = C C = 0 DY03 = = = = = = = = = = = = = = = = = = G = = T T = = = = = = = = = = = = = = = = = = = T = = C C = 0 DY04 = = = D C C = = A = = = = = = = = = (G) = = (T) (T) = = = = I T T = = G = = = = = = = = = (T) = = (C) (C) = 0 DY05 = = = = = = = = = = = = = = = ? ? = G = = T = = = = = = = = = = = = = = = = = ? ? = T = = C = = 0 DY06 = = = D = C = = = = = = = = = = = ? ? ? = = = = = = = I = T = = = = = = = = = = = ? ? ? = = = = 0 DY07 A C = D C C G C A A C T A G C G T G = = G = = A G T = I T T C A G G T G G A T C G A = = A = = G 0 DY08 = = = D C C = = A = = = = = = = = = = A G T = = = = = I T T = = G = = = = = = = = = = G A C = = 0 DY09 = = ? ? ? = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = 0 DY10 = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 0 DY11 = = = D C C = = A = = = = = = = = = = A G T = = = = = I T T = = G = = = = = = = = = = G A C = = 0 DY12 = = = D C C = = A = = = = = = = = = = A G T = = = = = I T T = = G = = = = = = = = = = G A C = = 0 DY13 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY14 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY15 ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = 0 DY16 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = 0 DY17 = = = D C C = = A = = = = = = = = = = A G T = = = = = I T T = = G = = = = = = = = = = G A C = = 0 DY18 = = = = = = = = = = (C) = (A) = = = = = = A G T = = = = = = = = = = = = (T) = (G) = = = = = = G A C = = 0 DY19 = = G = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = 0 DY20 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY21 = = = = C = = = A = = = = = = = = = T A G = = = = = = = T = = = G = = = = = = = = = G G A = = = 0 DY22 = = = D C C = = A = = = = = ? ? ? = = A G T = = = = = I T T = = G = = = = = ? ? ? = = G A C = = 0 DY23 = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = 0 DY24 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = G = = = ? ? ? ? = = = = = = = = = = = = = = = = A = = = ? ? ? ? = = = = = = = = = = = = = = 0 E103 A C = D C C G C A A C T A G C G T G = = G = = A G T = I T T C A G G T G G A T C G A = = A = = G 0 E104 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0 E105 = = = D = = = = = = = ? ? ? = = = = = = = = = = = = = I = = = = = = = ? ? ? = = = = = = = = = = 0 E106 = = G I = = = = = = = = = = = = = = = = = = = = = = A D = = = = = = = = = = = = = = = = = = = = 0 E107 = = = D C C G C A A C ? ? ? C G T G = = G = = A = = = I T T C A G G T ? ? ? T C G A = = A = = G 0 E108 = = = D = = G C = A C T A G C G T G G G = = T A = = = I = = C A = G T G G A T C G A T A = = C G 0 E109 = = = D C C = = A = = = = = = = = = T A G = C = = = = I T T = = G = = = = = = = = = G G A = T = 0 E110 = = G = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = 0 E111 = = G = = = = = = = = = = = = = = = = = = ? = = = = A = = = = = = = = = = = = = = = = = = ? = = 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = G = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 = = = D C C G C A A C T A G C G T G = = G = = A = = = I T T C A G G T G G A T C G A = = A = = G 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = C A = G T G G A T C G A T A = = C G = = = = = = G C = A C T A G C G T G G G = = T A 0 E118 = = G = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = 0 E119 = = ? = = = C A = G T G G A T C G A T A = = C G = = ? = = = G C = A C T A G C G T G G G = = T A 0 E120 = = = = = = C A = G T G G A T C G A T A = ? C G = = = = = = G C = A C T A G C G T G G G = ? T A 0 E121 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E122 = = = D C C = = A = = = = = = = = = T A G = C = = = = I T T = = G = = = = = = = = = G G A = T = 0 E123 A C = = = = = = = = = = = = = = = = = = = = = = G T = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = 0.61 = = 0.61 0.61 = = = = = = = = = = = = = = = = ? ? = 1.00 = = 1.00 = = = = = 1.00 = 1.00 = = = = = = = = = = = ? ? ? = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = = 0.50 = 0.50 = = = = = = 1.00 1.00 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = 1.00 1.00 1.00 = = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = ? ? ? = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = ? ? ? ? = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 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 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 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = ? 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