************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 glvr1.phase.inp glvr1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST glvr1.phase.out_freqs : haplotype frequency estimates glvr1.phase.out_pairs : most likely haplotype pairs for each individual glvr1.phase.out_recom : estimates of recombination parameters glvr1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 34 Positions of loci: 191 1004 1566 1737 1780 2115 2141 2331 2810 3187 4333 5171 5952 8317 8495 12704 12806 12865 13467 13551 14437 16047 16060 17420 17725 18587 18682 19815 20079 20196 20709 20754 21315 21637 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file glvr1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ATCGGDCCGGAGAGAIICAATTGGTGTATCTTGC 1.000000 2 ATCGGDCCGGAGAGAIICAATTGGTGTGTCTTAC 2.000000 3 ATCGGDCCGGAGAGAIICAATAGGTGTATCTTAC 1.000000 4 ATCGGDCCGGAGAGADDCAAGTGGGACGTCCTAA 1.000000 5 ATCGGDCCGGAGACGIICGATAGGTGTATTTCAC 1.000000 6 ATCGGDCCGGCGACAIICAATTGGTGTATCTTAC 1.000000 7 ATCGGDCCGGCGACAIICAATAGGTGTATCTTAC 2.000000 8 ATCGGDCCGAAAAGAIICGATAGGTGTATTTCAC 3.000000 9 ATCGGDCCGAAGAGAIICAATTGGTGTATTTTAC 1.000000 10 ATCGGDCCGAAGAGAIICAATAGGTGTATTTTAC 1.000000 11 ATCGGDCCGAAGAGAIICGATTGGTGTATTTCAC 1.000000 12 ATCGGDCCGAAGAGAIICGATAGGTGTATCTCAC 4.000000 13 ATCGGDCCGAAGAGAIICGATAGGTGTATTTTAC 1.000000 14 ATCGGDCCGAAGAGAIICGATAGGTGTATTTCAC 16.000000 15 ATCGGDCCGAAGAGAIICGGTTGGTGTATTTCAC 1.000000 16 ATCGGDCCGAAGAGAIICGGTAGGTGTATTTCAC 4.000000 17 ATCGTDCTGGAGACGIICAATAAGTGTATCTTGC 3.000000 18 ATCATICCGGAGACGIICAATTAGTGTACCTTGC 8.000000 19 ATCATICCGGAGACGIICAATAAGTGTACCTTGC 6.000000 20 ATCATICCGGAGACGIICGATAAGTGTATTTCAC 1.000000 21 GCGGGDTCGGCAAGAIDCAAGTGGGACGTCCTAA 3.000000 22 GCGGGDTCGGCAAGAIDTAAGTGCGACGTCCTAA 7.000000 23 GCGGGDTCGGCAAGADDCAAGTGGGACGTCCTAA 12.000000 24 GCGGGDTCGGCAGGAIDCAAGTGGGACGTCCTAA 6.000000 25 GCGGGDTCAGCAAGAIDCAAGTGGGACGTCCTAA 2.000000 26 GCGGGDTCAGCAAGAIDCAAGTGGTACGTCCTAA 1.000000 27 GCGGGDTCAGCAAGADDCAAGTGGGACGTCCTAA 3.000000 28 GCGGTDTCGGCAAGADDCAAGTGGGACGTCCTAA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (2,23) DY02: (18,21) DY03: (23,24) DY04: (19,19) DY05: (23,24) DY06: (17,23) DY07: (4,7) DY08: (9,24) DY09: (1,6) DY10: (23,23) DY11: (23,24) DY12: (23,27) DY13: (13,21) DY14: (3,28) DY15: (2,25) DY16: (18,26) DY17: (18,23) DY18: (24,25) DY19: (18,27) DY20: (18,21) DY21: (7,17) DY22: (10,17) DY23: (18,27) DY24: (18,24) E101: (14,14) E102: (8,14) E103: (22,22) E104: (18,23) E105: (16,20) E106: (14,19) E107: (22,23) E108: (5,19) E109: (12,12) E110: (14,14) E111: (14,16) E112: (14,16) E113: (12,12) E114: (14,23) E115: (14,22) E116: (11,22) E117: (8,14) E118: (14,22) E119: (14,14) E120: (15,22) E121: (8,19) E122: (16,19) E123: (14,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A T C G G D C C G G A G A G A I I C A A T T G G T [G] T G T C T T A C G C G G G D T C G G C A [A] G A [D] D C A A G T G G G A C G T C C T A A 0 DY02 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C [G] G C A A G A I D C A A G T G G G A C G T C C T A A 0 DY03 G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A G C G G G D T C G G C A G G A I D C A A G T G G G A C G T C C T A A 0 DY04 A T C A T I C C G G A G A C G I I C A A T A A G T G T A C C T T G C A T C A T I C C G G A G A C G I I C A A T A A G T G T A C C T T G C 0 DY05 G C G G G D T C G G C A A G A [D] D C A A G T G G G A C G T C C T A A G C G G G D T C G G C A G G A I D C A A G T G G G A C G T C C T A A 0 DY06 A T C G T D C T G G A G A C G I I C A A T A A G T G T A T C T T G C G C G G G D T C G G C A A G A [D] D C A A G T G G G A C G T C C T A A 0 DY07 A T C G G D C C G G (A) G A (G) A [D] D C A A G T G G G A C G T C C T A A A T C G G D C C G G (C) G A (C) A I I C A A T A G G T G T A T C T T A C 0 DY08 A T C G G D C C G A A G A G A I I C A A T T G G T G T A T T T T A C G C G G G D T C G G C A [G] G A I D C A A G T G G G A C G T C C T A A 0 DY09 A T C G G D C C G G A G A G A I I C A A T T G G T G T A T C T T (G) C A T C G G D C C G G C G A C A I I C A A T T G G T G T A T C T T (A) C 0 DY10 G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A 0 DY11 G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A G C G G G D T C G G C A G G A I D C A A G T G G G A C G T C C T A A 0 DY12 G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A G C G G G D T C A G C A A G A D D C A A G T G G G A C G T C C T A A 0 DY13 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T T A C G C G G G D T C G G C A A G A I D C A A G T G G G A C G T C C T A A 0 DY14 (A) (T) (C) G (G) D (C) C G G (A) (G) A G A I I C A A T A G G T G T A T C T T A C (G) (C) (G) G (T) D (T) C G G (C) (A) A G A D D C A A G T G G G A C G T C C T A A 0 DY15 A T C G G D C C G G A G A G A I I C A A T T G G T [G] T G T C T T A C G C G G G D T C A G C A A G A I D C A A G T G G G A C G T C C T A A 0 DY16 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C A G C A A G A I D C A A G T G G T A C G T C C T A A 0 DY17 A T C A T I C C G G A G A C G I I C A A T [T] A G T G T A C C T T G C G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A 0 DY18 G C G G G D T C G G C A G G A I D C A A G T G G G A C G T C C T A A G C G G G D T C A G C A A G A I D C A A G T G G G A C G T C C T A A 0 DY19 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C A G C A A G A D D C A A G T G G G A C G T C C T A A 0 DY20 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C G G C A A G A I D C A A G T G G G A C G T C C T A A 0 DY21 A T C G G D C C G G C G A [C] A I I C A A T A G G T G T A T C T T A C A T C G T D C T G G A G A C G I I C A A T A A G T G T A T C T T G C 0 DY22 A T C G G D C C G A A G A G A I I C A A T A G G T G T A T T T T A C A T C G T D C T G G A G A C G I I C A A T A A G T G T A T C T T G C 0 DY23 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C A G C A A G A D D C A A G T G G G A C G T C C T A A 0 DY24 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C G G C A G G A I D C A A G T G G G A C G T C C T A A 0 E101 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G A T [A] G G T G T A T T T C A C 0 E102 A T C G G D C C G A A A A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C 0 E103 G C G G G D T C G G C A A G A I D T A A G T G C G A C G T C C T A A G C G G G D T C G G C A A G A I D T A A G T G C G A C G T C C T A A 0 E104 A T C A T I C C G G A G A C G I I C A A T T A G T G T A C C T T G C G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A 0 E105 A T C G G D C C G A A G A G A I I C G (G) T A (G) G T G T A T T T C A C A T C A T I C C G G A G A C G I I C G (A) T A (A) G T G T A T T T C A C 0 E106 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C A T I C C G G A G A C G I I C A A T A A G T G T A C C T T G C 0 E107 G C G G G D T C G G C A A G A I D T A A G T G C G A C G T C C T A A G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A 0 E108 A T C (G) (G) [D] C C G G A G A C G I I C G A T A G G T G T A T [T] T C A C A T C (A) (T) [I] C C G G A G A C G I I C A A T A A G T G T A C C T T G C 0 E109 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T C T C A C A T C G G D C C G A A G A G A I I C G A T A G G T G T A T C T C A C 0 E110 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G A T [A] G G T G T A T T T C A C 0 E111 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G G T A G G T G T A T T T C A C 0 E112 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G G T A G G T G T A T T T C A C 0 E113 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T C T C A C A T C G G D C C G A A G A G A I I C G A T A G G T G T A T C T C A C 0 E114 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C G C G G G D T C G G C A A G A D D C A A G T G G G A C G T C C T A A 0 E115 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C G C G G G D T C G G C A A G A I D T A A G T G C G A C G T C C T A A 0 E116 A T C G G D C C G A A G A G A I I C G A T T G G T G T A T T T C A C G C G G G D T C G G C A A G A I D T A A G T G C G A C G T C C T A A 0 E117 A T C G G D C C G A A A A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G A T [A] G G T G T A T T T C A C 0 E118 A T C G G D C C G A A G A G A I I C G A T [A] G G T G T A T T T C A C G C G G G D T C G G C A A G A I D T A A G T G C G A C G T C C T A A 0 E119 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C 0 E120 A T C G G D C C G A A G A G A I I C G (G) T T G G T G T A T T T C A C G C G G G D T C G G C A A G A I D T A (A) G T G C G A C G T C C T A A 0 E121 A T C G G D C C G A A A A G A I I C G A T A G G T G T A T T T C A C A T C A T I C C G G A G A C G I I C A A T A A G T G T A C C T T G C 0 E122 A T C G G D C C G A A G A G A I I C G G T A G G T G T A T T T C A C A T C A T I C C G G A G A C G I I C A A T A A G T G T A C C T T G C 0 E123 A T C G G D C C G A A G A G A I I C G A T A G G T G T A T T T C A C A T C G G D C C G A A G A G A I I C G A T A G G T G T A T [T] T C A 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 T C ? ? = C = = = A G ? = = ? ? ? = = T = = = T ? T ? ? = T = = C G C G ? ? = T = = = C A ? = = ? ? ? = = G = = = G ? C ? ? = C = = A 0 DY02 A T ? ? ? ? ? ? ? = A ? = ? G = I = = = T = A ? T G T ? ? = T = G C G C ? ? ? ? ? ? ? = C ? = ? A = D = = = G = G ? G A C ? ? = C = A A 0 DY03 = ? ? ? ? = = = = = = = A = = D ? = = = = = = = = = = ? ? ? = = = = = ? ? ? ? = = = = = = = G = = I ? = = = = = = = = = = ? ? ? = = = = 0 DY04 = = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = 0 DY05 = = ? ? ? = = = = = = = A = = ? ? = = = = = = ? = ? = ? = = ? ? = = = = ? ? ? = = = = = = = G = = ? ? = = = = = = ? = ? = ? = = ? ? = = 0 DY06 A T ? ? ? = C T = = A G = C G ? ? = = = T A A ? T ? T ? ? ? T = G C G C ? ? ? = T C = = C A = G A ? ? = = = G T G ? G ? C ? ? ? C = A A 0 DY07 = = = ? ? = = = = = (A) = = (G) = ? ? = = = G T = ? G ? ? ? ? ? C = = A = = = ? ? = = = = = (C) = = (C) = ? ? = = = T A = ? T ? ? ? ? ? T = = C 0 DY08 A T C ? ? = C = = A A G ? = = = I = = = T = = = T ? T A = T T = = C G C G ? ? = T = = G C A ? = = = D = = = G = = = G ? C G = C C = = A 0 DY09 = = = ? ? ? ? ? = = A = = G = = = = = = = = = = = ? = = = = = = (G) = = = = ? ? ? ? ? = = C = = C = = = = = = = = = = = ? = = = = = = (A) = 0 DY10 ? ? = ? ? = = = = = ? = = = = = = = = = ? = = = = = = = = = = = = = ? ? = ? ? = = = = = ? = = = = = = = = = ? = = = = = = = = = = = = = 0 DY11 = = = = = = = = ? = = = A = = D = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = G = = I = = = = = = = = = = = = = = = = = = 0 DY12 = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY13 A T C = = = C = = A A G = = = = I = G = T A = = T G T A = T T = = ? G C G = = = T = = G C A = = = = D = A = G T = = G A C G = C C = = ? 0 DY14 (A) (T) (C) = (G) = (C) = = = (A) (G) = = = I I = = = T A = = T ? T A = = T = = C (G) (C) (G) = (T) = (T) = = = (C) (A) = = = D D = = = G T = = G ? C G = = C = = A 0 DY15 A T C = = = C = G = A G = = = = I = = = T = = = T ? T = ? = T = = C G C G = = = T = A = C A = = = = D = = = G = = = G ? C = ? = C = = A 0 DY16 A T C ? ? I C = G = A G = C G = I = = = T = A = = G T A C = T = G C G C G ? ? D T = A = C A = G A = D = = = G = G = = A C G T = C = A A 0 DY17 A T C A T ? ? ? = = A G = C G I I = = = T ? ? ? T ? T A C = T = ? ? G C G G G ? ? ? = = C A = G A D D = = = G ? ? ? G ? C G T = C = ? ? 0 DY18 = = = = = = = = G = = = G = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = A = = = A = = = = = = = ? = = = = = = = = = = = ? ? 0 DY19 ? T C A T I C = G = A G = C G I I = = = T = A ? T G T A ? = ? ? G C ? C G G G D T = A = C A = G A D D = = = G = G ? G A C G ? = ? ? A A 0 DY20 A T C A T I C = = = A G = C G = I = = = T = A = T G T A C = T = G C G C G G G D T = = = C A = G A = D = = = G = G = G A C G T = C = A A 0 DY21 = ? ? = G = = C = = C = = ? A = = = = = = = G ? = = = = = = = = A = = ? ? = T = = T = = A = = ? G = = = = = = = A ? = = = = = = = = G = 0 DY22 = = = = G = = C = A = = ? G A = = = = = = = G ? = = = = = T = = A = = = = = T = = T = G = = ? C G = = = = = = = A ? = = = = = C = = G = 0 DY23 A T C A T I C = G = A G = C G I I = = = T = A ? T G T A ? = T = G C G C G G G D T = A = C A = G A D D = = = G = G ? G A C G ? = C = A A 0 DY24 A T C A T ? ? ? = = A G A C G = I = = = T = A ? T G T A C = ? ? G C G C G G G ? ? ? = = C A G G A = D = = = G = G ? G A C G T = ? ? A A 0 E101 = = = = = ? ? ? = = = = = = = = = = = = = ? ? = = ? = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = ? ? = = ? = = = = = = = = 0 E102 = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = ? 0 E103 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 A T C A T I C = = = A G = C G I I = = = T = A = T G T A C = ? = G C G C G G G D T = = = C A = G A D D = = = G = G = G A C G T = ? = A A 0 E105 = = = G G D = = = A = = = G A = = = = (G) = = (G) = = = = = = = = = = = = = = A T I = = = G = = = C G = = = = (A) = = (A) = = = = = = = = = = = 0 E106 = = = G G D = = = A = = = G A = = = G = = = G ? = = ? = T T = C A = = = = A T I = = = G = = = C G = = = A = = = A ? = = ? = C C = T G = 0 E107 = = ? = = = = = = = = = = = = I = T = = = = = C = = = ? = = = = = = = = ? = = = = = = = = = = = = D = C = = = = = G = = = ? = = = = = = 0 E108 = = = (G) (G) ? ? ? = = = = = = = = = = G = = = G = = = = = T ? = C A = = = = (A) (T) ? ? ? = = = = = = = = = = A = = = A = = = = = C ? = T G = 0 E109 = = = = = ? ? ? = = = = = = = = = = = = = ? ? = = ? = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = ? ? = = ? = = = = = = = = 0 E110 = = = = = ? ? ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = 0 E111 = = = = = = = = ? = = = = = = = = = = A = = = = = = = ? = = = = = = = = = = = = = = ? = = = = = = = = = = G = = = = = = = ? = = = = = = 0 E112 = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = ? ? 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? = = 0 E114 A T C = = = C = = A ? G = = = I I = G = T A = = T ? T ? ? T T C = ? G C G = = = T = = G ? A = = = D D = A = G T = = G ? C ? ? C C T = ? 0 E115 A T C = = ? ? ? = A A G = = = = I C G = T A = G T ? T ? ? T ? ? = C G C G = = ? ? ? = G C A = = = = D T A = G T = C G ? C ? ? C ? ? = A 0 E116 A T C = = ? ? ? = A A G ? = = = I C G = T = = G T ? T ? ? T T C = C G C G = = ? ? ? = G C A ? = = = D T A = G = = C G ? C ? ? C C T = A 0 E117 = = = = = ? ? ? = = = A = = = = = = = = ? ? ? = = ? = = = = = = = = = = = = = ? ? ? = = = G = = = = = = = = ? ? ? = = ? = = = = = = = = 0 E118 A T C = = ? ? ? ? A A G = = = ? ? ? G = ? ? ? G ? G T A ? T ? ? = C G C G = = ? ? ? ? G C A = = = ? ? ? A = ? ? ? C ? A C G ? C ? ? = A 0 E119 = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E120 A T C = = ? ? ? = A A G = = = = I ? G (G) T = = G ? ? ? A ? T T C = C G C G = = ? ? ? = G C A = = = = D ? A (A) G = = C ? ? ? G ? C C T = A 0 E121 = = = G G ? ? ? = A = A = ? A = = = G = = = G = = = = = T T = C A = = = = A T ? ? ? = G = G = ? G = = = A = = = A = = = = = C C = T G = 0 E122 = = = G G ? ? ? = A = = = G A = = = G G = = G ? = = = = T T = C A = = = = A T ? ? ? = G = = = C G = = = A A = = A ? = = = = C C = T G = 0 E123 = = = = = ? ? ? = = = = = ? = = = = = = = = = = = = = ? ? ? = = = = = = = = = ? ? ? = = = = = ? = = = = = = = = = = = = = ? ? ? = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? 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