************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 prdx2.phase.inp prdx2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST prdx2.phase.out_freqs : haplotype frequency estimates prdx2.phase.out_pairs : most likely haplotype pairs for each individual prdx2.phase.out_recom : estimates of recombination parameters prdx2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 10 Positions of loci: 1081 1090 2041 2511 3012 3097 3152 3458 4531 7182 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file prdx2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ATTGGCACCI 67.000000 2 ATTGGCACCD 21.000000 3 ATTGGCACTI 12.000000 4 ATTGGCACTD 1.000000 5 ATTGGTACCI 45.000000 6 ATGGGCGCCI 33.000000 7 GCGAACGACI 11.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (1,6) D003: (1,6) D004: (6,6) D005: (6,6) D006: (2,3) D007: (1,6) D008: (1,6) D009: (7,7) D010: (1,7) D011: (5,6) D012: (1,1) D013: (1,1) D014: (1,6) D015: (1,6) DY01: (6,6) DY02: (1,6) DY03: (1,6) DY04: (6,7) DY05: (1,7) DY06: (6,7) DY07: (6,7) DY08: (1,6) DY09: (1,6) DY10: (1,7) DY11: (1,6) DY12: (6,6) E101: (1,5) E102: (1,1) E103: (1,2) E104: (1,1) E105: (1,5) E106: (1,5) E107: (1,3) E108: (1,1) E109: (1,2) E110: (1,3) E111: (5,5) E112: (1,1) E113: (2,6) E114: (1,1) E115: (1,5) E116: (2,2) E117: (1,2) E118: (1,6) E119: (2,5) E120: (1,1) E121: (3,5) E122: (1,5) H101: (1,6) H102: (2,5) H103: (2,6) H104: (5,6) H105: (1,1) H106: (1,5) H107: (3,7) H108: (1,7) H109: (3,3) H110: (1,5) H111: (1,5) H112: (1,2) H113: (2,2) H114: (2,6) H115: (1,5) H116: (1,2) H117: (1,7) H118: (3,5) H119: (2,5) H120: (2,2) H121: (1,5) H122: (1,5) X101: (5,5) X102: (1,1) X103: (1,1) X104: (5,5) X105: (2,5) X106: (3,6) X107: (4,5) X108: (5,5) X109: (5,5) X110: (2,5) X111: (5,5) X112: (5,5) X113: (3,5) X114: (3,5) X115: (1,5) X116: (1,2) X117: (5,6) X118: (5,5) X119: (1,5) X120: (5,5) X121: (6,6) X122: (1,5) X123: (1,3) X124: (1,1) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A T T G G C A C C I A T T G G C A C C I 0 D002 A T T G G C A C C I A T G G G C G C C I 0 D003 A T T G G C A C C I A T G G G C G C C I 0 D004 A T G G G C G C C I A T G G G C G C C I 0 D005 A T G G G C G C C I A T G G G C G C C I 0 D006 A T T G G C A C C D A T T G G C A C T I 0 D007 A T T G G C A C C I A T G G G C G C C I 0 D008 A T T G G C A C C I A T G G G C G C C I 0 D009 G C G A A C G A C I G C G A A C G A C I 0 D010 A T T G G C A C C I G C G A A C G A C I 0 D011 A T T G G T A C C I A T G G G C G C C I 0 D012 A T T G G C A C C I A T T G G C A C C I 0 D013 A T T G G C A C [C] I A T T G G C A C C I 0 D014 A T T G G C A C C I A T G G G C G C C I 0 D015 A T T G G C A C C I A T G G G C G C C I 0 DY01 A T G G G C G C C I A T G G G C G C C I 0 DY02 A T T G G C A C C I A T G G G C G C C I 0 DY03 A T T G G C A C C I A T G G G C G C C I 0 DY04 A T G G G C G C C I G C G A A C G A C I 0 DY05 A T T G G C A C C I G C G A A C G A C I 0 DY06 A T G G G C G C C I G C G A A C G A C I 0 DY07 A T G G G C G C C I G C G A A C G A C I 0 DY08 A T T G G C A C C I A T G G G C G C C I 0 DY09 A T T G G C A C C I A T G G G C G C C I 0 DY10 A T T G G C A C C I G C G A A C G A C I 0 DY11 A T T G G C A C C I A T G G G C G C C I 0 DY12 A T G G G C G C C I A T G G G C G C C I 0 E101 A T T G G C A C C I A T T G G T A C C I 0 E102 A T T G G C A C [C] I A T T G G C A C C I 0 E103 A T T G G C A C C I A T T G G C A C C D 0 E104 A T T G G C A C [C] I A T T G G C A C C I 0 E105 A T T G G C A C C I A T T G G T A C C I 0 E106 A T T G G C A C C I A T T G G T A C C I 0 E107 A T T G G C A C C I A T T G G C A C T I 0 E108 A T T G G C A C C I A T T G G C A C C I 0 E109 A T T G G C A C C I A T T G G C A C C D 0 E110 A T T G G C A C C I A T T G G C A C T I 0 E111 A T T G G T A C C I A T T G G T A C C I 0 E112 A T T G G C A C C I A T T G G C A C C I 0 E113 A T T G G C A C C D A T G G G C G C C I 0 E114 A T T G G C A C [C] I A T T G G C A C C I 0 E115 A T T G G C A C C I A T T G G T A C C I 0 E116 A T T G G C A C C D A T T G G C A C C D 0 E117 A T T G G C A C C I A T T G G C A C C D 0 E118 A T T G G C A C C I A T G G G C G C C I 0 E119 A T T G G C A C C D A T T G G T A C C I 0 E120 A T T G G C A C C I A T T G G C A C C I 0 E121 A T T G G C A C T I A T T G G T A C C I 0 E122 A T T G G C A C C I A T T G G T A C C I 0 H101 A T T G G C A C C I A T G G G C G C C I 0 H102 A T T G G C A C C D A T T G G T A C C I 0 H103 A T T G G C A C C D A T G G G C G C C I 0 H104 A T T G G T A C C I A T G G G C G C C I 0 H105 A T T G G C A C [C] I A T T G G C A C C I 0 H106 A T T G G C A C C I A T T G G T A C C I 0 H107 A T T G G C A C T I G C G A A C G A C I 0 H108 A T T G G C A C C I G C G A A C G A C I 0 H109 A T T G G C A C T I A T T G G C A C T I 0 H110 A T T G G C A C C I A T T G G T A C C I 0 H111 A T T G G C A C C I A T T G G T A C C I 0 H112 A T T G G C A C C I A T T G G C A C C D 0 H113 A T T G G C A C C D A T T G G C A C C D 0 H114 A T T G G C A C C D A T G G G C G C C I 0 H115 A T T G G C A C C I A T T G G T A C C I 0 H116 A T T G G C A C C I A T T G G C A C C D 0 H117 A T T G G C A C C I G C G A A C G A C I 0 H118 A T T G G C A C T I A T T G G T A C C I 0 H119 A T T G G C A C C D A T T G G T A C C I 0 H120 A T T G G C A C C D A T T G G C A C C D 0 H121 A T T G G C A C C I A T T G G T A C C I 0 H122 A T T G G C A C C I A T T G G T A C C I 0 X101 A T T G G T A C C I A T T G G T A C C I 0 X102 A T T G G C A C [C] [I] A T T G G C A C C I 0 X103 A T T G G C A C C I A T T G G C A C C I 0 X104 A T T G G T A C C I A T T G G T A C C I 0 X105 A T T G G C A C C D A T T G G T A C C I 0 X106 A T T G G C A C T I A T G G G C G C C I 0 X107 A T T G G C A C (T) (D) A T T G G T A C (C) (I) 0 X108 A T T G G T A C C I A T T G G T A C C I 0 X109 A T T G G T A C C I A T T G G T A C C I 0 X110 A T T G G C A C C D A T T G G T A C C I 0 X111 A T T G G T A C C I A T T G G T A C C I 0 X112 A T T G G T A C C I A T T G G T A C C I 0 X113 A T T G G C A C T I A T T G G T A C C I 0 X114 A T T G G C A C T I A T T G G T A C C I 0 X115 A T T G G C A C C I A T T G G T A C C I 0 X116 A T T G G C A C C I A T T G G C A C C D 0 X117 A T T G G T A C C I A T G G G C G C C I 0 X118 A T T G G T A C C I A T T G G T A C C I 0 X119 A T T G G C A C C I A T T G G T A C C I 0 X120 A T T G G T A C C I A T T G G T A C C I 0 X121 A T G G G C G C C I A T G G G C G C C I 0 X122 A T T G G C A C C I A T T G G T A C C I 0 X123 A T T G G C A C C I A T T G G C A C T I 0 X124 A T T G G C A C [C] I A T T G G C A C C I 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 D001 = = = = = = = = = = = = = = = = = = = = 0 D002 ? ? T = = = A = = = ? ? G = = = G = = = 0 D003 = = T = = = A = ? = = = G = = = G = ? = 0 D004 = = = = = = = = = = = = = = = = = = = = 0 D005 = = = = = = = = = = = = = = = = = = = = 0 D006 = = = = = = = = C D = = = = = = = = T I 0 D007 = = T = = = A = = = = = G = = = G = = = 0 D008 = = T = = = A = = = = = G = = = G = = = 0 D009 = = = = = = = = ? = = = = = = = = = ? = 0 D010 A T T G G = A C = ? G C G A A = G A = ? 0 D011 = = T = = T A = ? = = = G = = C G = ? = 0 D012 = = = = = = = = = = = = = = = = = = = = 0 D013 = = = = = = = = ? = = = = = = = = = ? = 0 D014 = = T = = = A = = = = = G = = = G = = = 0 D015 = = T = = = A = ? = = = G = = = G = ? = 0 DY01 = = = = = = = = ? = = = = = = = = = ? = 0 DY02 = = T = = = A = = = = = G = = = G = = = 0 DY03 = = T = = = A = = = = = G = = = G = = = 0 DY04 A T = G G = = C ? = G C = A A = = A ? = 0 DY05 A T T G G = A C = ? G C G A A = G A = ? 0 DY06 A T = G G = = C ? = G C = A A = = A ? = 0 DY07 A T = G G = = C ? = G C = A A = = A ? = 0 DY08 = = T = = = A = ? = = = G = = = G = ? = 0 DY09 = = T = = = A = ? = = = G = = = G = ? = 0 DY10 A T T G G = A C ? = G C G A A = G A ? = 0 DY11 = = T = = = A = ? = = = G = = = G = ? = 0 DY12 = = = = = = = = ? = = = = = = = = = ? = 0 E101 = = = = = C = = = = = = = = = T = = = = 0 E102 = = = = = = = = ? = = = = = = = = = ? = 0 E103 = = = = = = = = = I = = = = = = = = = D 0 E104 = = = = = = = = ? = = = = = = = = = ? = 0 E105 = = = = = C = = = = = = = = = T = = = = 0 E106 = = = = = C = = ? = = = = = = T = = ? = 0 E107 = = = = = = = = C = = = = = = = = = T = 0 E108 = = = = = = = = = = = = = = = = = = = = 0 E109 = = = = = = = = = I = = = = = = = = = D 0 E110 = = = = = = = = C = = = = = = = = = T = 0 E111 = = = = = = = = ? = = = = = = = = = ? = 0 E112 = = = = = = = = = = = = = = = = = = = = 0 E113 = = T = = = A = = D = = G = = = G = = I 0 E114 = = = = = = = = ? = = = = = = = = = ? = 0 E115 = = = = = C = = = = = = = = = T = = = = 0 E116 = = = = = = = = ? = = = = = = = = = ? = 0 E117 = = = = = = = = = I = = = = = = = = = D 0 E118 = = T = = = A = = = = = G = = = G = = = 0 E119 = = = = = C = = ? D = = = = = T = = ? I 0 E120 = = = = = = = = = = = = = = = = = = = = 0 E121 = = = = = C = = T = = = = = = T = = C = 0 E122 = = = = = C = = ? = = = = = = T = = ? = 0 H101 = = T = = = A = = = = = G = = = G = = = 0 H102 = = = = = C = = = D = = = = = T = = = I 0 H103 = = T = = = A = = D = = G = = = G = = I 0 H104 = = T = = T A = = = = = G = = C G = = = 0 H105 = = = = = = = = ? = = = = = = = = = ? = 0 H106 = = = = = C = = ? = = = = = = T = = ? = 0 H107 A T T G G = A C T = G C G A A = G A C = 0 H108 A T T G G = A C ? = G C G A A = G A ? = 0 H109 = = = = = = = = = = = = = = = = = = = = 0 H110 = = = = = C = = = = = = = = = T = = = = 0 H111 = = = = = C = = = = = = = = = T = = = = 0 H112 = = = = = = = = = I = = = = = = = = = D 0 H113 = = = = = = = = = = = = = = = = = = = = 0 H114 = = T = = = A = = D = = G = = = G = = I 0 H115 = = = = = C = = = = = = = = = T = = = = 0 H116 = = = = = = = = ? I = = = = = = = = ? D 0 H117 A T T G G = A C ? = G C G A A = G A ? = 0 H118 = = = = = C = = T = = = = = = T = = C = 0 H119 = = = = = C = = = D = = = = = T = = = I 0 H120 = = = = = = = = = = = = = = = = = = = = 0 H121 = = = = = C = = ? = = = = = = T = = ? = 0 H122 = = = = = C = = ? = = = = = = T = = ? = 0 X101 = = = = = = = = = = = = = = = = = = = = 0 X102 = = = = = = = = ? ? = = = = = = = = ? ? 0 X103 = = = = = = = = = = = = = = = = = = = = 0 X104 = = = = = = = = = = = = = = = = = = = = 0 X105 = = = = = C = = ? D = = = = = T = = ? I 0 X106 = = T = = = A = T = = = G = = = G = C = 0 X107 = = = = = C = = (T) (D) = = = = = T = = (C) (I) 0 X108 = = = = = = = = ? = = = = = = = = = ? = 0 X109 = = = = = = = = = = = = = = = = = = = = 0 X110 = = = = = C = = ? D = = = = = T = = ? I 0 X111 = = = ? = = = = = = = = = ? = = = = = = 0 X112 = = = = = = = = ? = = = = = = = = = ? = 0 X113 = = = = = C = = T = = = = = = T = = C = 0 X114 = = = = = C = = T = = = = = = T = = C = 0 X115 = = = = = C = = ? = = = = = = T = = ? = 0 X116 = = = = = = = = ? I = = = = = = = = ? D 0 X117 = = T = = T A = = = = = G = = C G = = = 0 X118 = = ? ? = = = = ? ? = = ? ? = = = = ? ? 0 X119 = = = = = C = = = = = = = = = T = = = = 0 X120 = = = = = = = = ? = = = = = = = = = ? = 0 X121 = = = = = = = = = = = = = = = = = = = = 0 X122 = = = = = C = = ? = = = = = = T = = ? = 0 X123 = = = = = = = = C = = = = = = = = = T = 0 X124 = = = = = = = = ? = = = = = = = = = ? = 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 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.91 1.00 = = 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = = = = = = = = = = = ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = ? = = 1.00 = = 1.00 1.00 = ? = = = = = = = = = = = = = = = = = = = ? = = = 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = ? = = = = = = = = = ? = = = 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = ? 1.00 1.00 = 1.00 1.00 = = 1.00 ? = 1.00 1.00 = 1.00 1.00 = = 1.00 ? = = = 1.00 = = = 1.00 = ? = = = 1.00 = = = 1.00 = ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? = = = 1.00 = = = 1.00 = ? = = = = = = = = = ? = = = = = = 1.00 = = = = = = = = = = = = ? = = = = = = = = = = 1.00 = = = = = = = = ? = = = = = = 1.00 = = = = = = = = = 1.00 = = ? = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = ? = = = = = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = = = = = = = = ? = = = = = = 1.00 = = = = = = = = = = = = ? = = = = = = = = = = 1.00 = = 1.00 = = = 1.00 = = = = = = = = 0.94 = = ? 1.00 = = = = = = = = = = = = = = = 0.92 = = 1.00 = = = = = = 1.00 = = ? = = = 1.00 = = = 1.00 = = = = = = = = 0.95 = = = 1.00 = = 1.00 = = = 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = = = = = ? = = = = = = 1.00 = = ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = = = = = 1.00 = = = = = = = = = = = = ? 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? = = = = = = 0.92 = = 1.00 = = = = = = 0.95 = = = 1.00 = = = = = = = = = = = = = = = 1.00 = = ? = = = = = = 1.00 = = ? = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 0.94 = = ? 1.00 = = 1.00 = = = 1.00 = 1.00 = = = = = = 1.00 = = 0.65 0.72 = = = = = = = = ? = = = = = = = = = = = = = = = = 0.94 = = ? 1.00 = = = ? = = = = = = = = = = = = = = ? = = = = = = 0.92 = = 1.00 = = = = = = 0.92 = = 1.00 = = = = = = 1.00 = = ? = = = = = = = = = ? 1.00 = = 1.00 = = 1.00 1.00 = = = = = ? ? = = = = ? ? = = = = = 1.00 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 1.00 = = ? = = = = = = = = = 1.00 = = = = = = = = = ? = END PHASEPROBS