************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 atox1.phase.inp atox1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST atox1.phase.out_freqs : haplotype frequency estimates atox1.phase.out_pairs : most likely haplotype pairs for each individual atox1.phase.out_recom : estimates of recombination parameters atox1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 18 Positions of loci: 939 1710 2236 3553 3714 3773 4523 7782 9020 11707 12982 15669 16393 16578 16732 18557 18558 19159 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file atox1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCCGCGGAACACATTTGG 3.000000 2 CCCGCGGAACGTGGCCAG 9.000000 3 CCCGCGGAACGTGGCTGG 1.000000 4 CCCGCGGACCACATTTGG 35.000000 5 CCCGCAGAAGACATTTGG 1.000000 6 CCCGCAGGAGACATTTGG 1.000000 7 CCAATGGGACACATTTGC 1.000000 8 CTCGCGGAAGACATTTGG 3.000000 9 CTCGCAGAAGACATTTGG 87.000000 10 CTCGCAGGAGACATTTGG 1.000000 11 CTCGCAAAAGACATTTGG 10.000000 12 CTAGCAAAAGACATTTGG 4.000000 13 TCCGCGGAACACATTTGG 1.000000 14 TCCGCGGAACATAGTTGG 5.000000 15 TCCGCGGAACATGGTCAG 1.000000 16 TCCGTGGAACACATTTGG 2.000000 17 TCCATGGAACACATTTGG 1.000000 18 TCCATGGAACACATTTGC 4.000000 19 TCAATGGAACACATTTGC 10.000000 20 TCAATGGGACACATTTGC 9.000000 21 TCAATGGGCCACATTTGC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,4) D002: (2,9) D003: (2,9) D004: (11,11) D005: (14,19) D006: (9,11) D007: (3,19) D008: (16,16) D009: (18,19) D010: (9,9) D011: (2,9) D012: (9,11) D013: (9,11) D014: (4,18) D015: (2,8) DY01: (2,8) DY02: (2,17) DY03: (15,19) DY04: (1,14) DY05: (9,10) DY06: (11,11) DY07: (11,18) DY08: (1,14) DY09: (2,13) DY10: (11,14) DY11: (8,19) DY12: (11,18) E101: (4,9) E102: (9,9) E103: (9,9) E104: (4,9) E105: (9,9) E106: (4,9) E107: (4,20) E108: (9,9) E109: (4,20) E110: (9,20) E111: (9,20) E112: (4,4) E113: (4,9) E114: (9,9) E115: (4,9) E116: (9,9) E117: (6,9) E118: (9,9) E119: (9,9) E120: (9,20) E121: (4,20) E122: (9,9) H101: (4,9) H102: (2,9) H103: (12,19) H104: (1,12) H105: (9,9) H106: (7,9) H107: (4,9) H108: (4,20) H109: (4,12) H110: (4,9) H111: (19,20) H112: (4,9) H113: (4,9) H114: (4,9) H115: (4,4) H116: (4,9) H117: (4,9) H118: (4,19) H119: (14,19) H120: (4,9) H121: (19,20) H122: (5,21) X101: (4,9) X102: (4,9) X103: (9,9) X104: (4,9) X105: (9,9) X106: (9,9) X107: (9,9) X108: (4,9) X109: (9,12) X110: (4,4) X111: (9,9) X112: (9,9) X113: (9,9) X114: (9,9) X115: (9,9) X116: (9,9) X117: (4,9) X118: (9,9) X119: (9,9) X120: (9,9) X121: (9,9) X122: (4,9) X123: (4,9) X124: (9,9) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C C C G C G G A A C G T G G C C A G C C C G C G G A [C] C A C A T T T G G 0 D002 C C C G C G G A A C G T G G C C A G C T C G C A G A A G A C A T T T G G 0 D003 C C C G C G G A A C G T G G C C A G C T C G C A G A A G A C A T T T G G 0 D004 C T C G C A A A A G A C A T T T G G C T C G C A A A A G A C A T T T G G 0 D005 T C C G C G G A A C A T A G T T G G T C A A T G G A A C A C A T T T G C 0 D006 C T C G C A G A A G A C A T T T G G C T C G C A A A A G A C A T T T G G 0 D007 C C C G C G G A A C G T G G C T G G T C A A T G G A A C A C A T T T G C 0 D008 T C C G T G G A A C A C A T T T G G T C C G T G G A A C A C A T T T G G 0 D009 T C C A T G G A A C A C A T T T G C T C A A T G G A A C A C A T T T G C 0 D010 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 D011 C C C G C G G A A C G T G G C C A G C T C G C A G A A G A C A T T T G G 0 D012 C T C G C A G A A G A C A T T T G G C T C G C A A A A G A C A T T T G G 0 D013 C T C G C A G A A G A C A T T T G G C T C G C A A A A G A C A T T T G G 0 D014 C C C G C G G A C C A C A T T T G G T C C A T G G A A C A C A T T T G C 0 D015 C C C G C G G A A C G T G G C C A G C T C G C G G A A G A C A T T T G G 0 DY01 C C C G C G G A A C G T G G C C A G C T C G C G G A A G A C A T T T G G 0 DY02 C C C G C G G A A C G T G G C C A G T C C A T G G A A C A C A T T T G G 0 DY03 T C C G C G G A A C A T G G T C A G T C A A T G G A A C A C A T T T G C 0 DY04 C C C G C G G A A C A C A T T T G G T C C G C G G A A C A T A G T T G G 0 DY05 C T C G C A G A A G A C A T T T G G C T C G C A G G A G A C A T T T G G 0 DY06 C T C G C A A A A G A C A T T T G G C T C G C A A A A G A C A T T T G G 0 DY07 C T C G C A A A A G A C A T T T G G T C C A T G G A A C A C A T T T G C 0 DY08 C C C G C G G A A C A C A T T T G G T C C G C G G A A C A T A G T T G G 0 DY09 (C) C C G C G G A A C G T G G C C A G (T) C C G C G G A A C A C A T T T G G 0 DY10 C T C G C A A A A G A C A T T T G G T C C G C G G A A C A T A G T T G G 0 DY11 C T C G C G G A A G A C A T T T G G T C A A T G G A A C A C A T T T G C 0 DY12 C T C G C A A A A G A C A T T T G G T C C A T G G A A C A C A T T T G [C] 0 E101 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E102 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E103 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E104 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E105 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E106 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E107 C C C G C G G A C C A C A T T T G G T C A A T G G G A C A C A T T T G C 0 E108 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E109 C C C G C G G A C C A C A T T T G G T C A A T G G G A C A C A T T T G C 0 E110 C T C G C A G A A G A C A T T T G G T C A A T G G G A C A C A T T T G C 0 E111 C T C G C A G A A G A C A T T T G G [T] C A A T G G G A C A C A T T T G C 0 E112 C C C G C G G A C C A C A T T T G G C C C G C G G A [C] C A C A T T T G G 0 E113 C C C G C G G A [C] C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E114 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E115 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E116 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E117 C (C) C G C A G G A G A C A T T T G G C (T) C G C A G A A G A C A T T T G G 0 E118 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E119 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 E120 C T C G C A G A A G A C A T T T G G T C A A T G G G A C A C A T T T G C 0 E121 C C C G C G G A C C A C A T T T G G T C A A T G G G A C A C A T T T G C 0 E122 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H101 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H102 C C C G C G G A A C G T G G C C A G C T C G C A G A A G A C A T T T G G 0 H103 C T A G C A A A A G A C A T T T G G T C A A T G G [A] A C A C A T T T G C 0 H104 C C C G C G G A A C A C A T T T G G C T A G C A A A A G A C A T T T G G 0 H105 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H106 C C A A T G G G A C A C A T T T G C C T C G C A G A A G A C A T T T G G 0 H107 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H108 C C C G C G G A C C A C A T T T G G T C A A T G G G A C A C A T T T G C 0 H109 C C C G C G G A C C A C A T T T G G C T A G C A A A A G A C A T T T G G 0 H110 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H111 T C A A T G G A A C A C A T T T G C T C A A T G G [G] A C A C A T T T G C 0 H112 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H113 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H114 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H115 C C C G C G G A C C A C A T T T G G C C C G C G G A [C] C A C A T T T G G 0 H116 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H117 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H118 C C C G C G G A C C A C A T T T G G T C A A T G G A A C A C A T T T G C 0 H119 T C C G C G G A A C A T A G T T G G T C A A T G G A A C A C A T T T G C 0 H120 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 H121 T C A A T G G A A C A C A T T T G C T C A A T G G [G] A C A C A T T T G C 0 H122 C C C G C (A) G (A) (A) G A C A T T T G G T C A A T (G) G (G) (C) C A C A T T T G C 0 X101 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X102 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X103 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X104 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X105 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X106 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X107 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X108 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X109 C T C G C A G A A G A C A T T T G G C T A G C A A A A G A C A T T T G G 0 X110 C C C G C G G A C C A C A T T T G G C C C G C G G A [C] C A C A T T T G G 0 X111 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X112 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X113 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X114 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X115 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X116 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X117 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X118 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X119 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X120 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X121 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X122 C C C G C G G A [C] C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X123 C C C G C G G A C C A C A T T T G G C T C G C A G A A G A C A T T T G G 0 X124 C T C G C A G A A G A C A T T T G G C T C G C A G A A G A C A T T T G G 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 ? ? = = = = = = ? = ? ? G G C C A = ? ? = = = = = = ? = ? ? A T T T G = 0 D002 = ? = = = G = = = C G T G G C C A = = ? = = = A = = = G A C A T T T G = 0 D003 = C = = = G = = = C G T G G C C A ? = T = = = A = = = G A C A T T T G ? 0 D004 = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 D005 = = C G C ? = = = = = T = G = = = G = = A A T ? = = = = = C = T = = = C 0 D006 = = = = = = G = = = = ? = = = = = = = = = = = = A = = = = ? = = = = = = 0 D007 ? = C G C = = = = = G T G G C = = G ? = A A T = = = = = A C A T T = = C 0 D008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D009 = = C = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = 0 D010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D011 = C = = = G = = = C G T G G C C A ? = T = = = A = = = G A C A T T T G ? 0 D012 ? = = = = = G = = = = = = = = = = = ? = = = = = A = = = = = = = = = = = 0 D013 = = = = = = G = = = = = = = = = = = = = = = = = A = = = = = = = = = = = 0 D014 C = = G C = = = C = = = = = = = = G T = = A T = = = A = = = = = = = = C 0 D015 = C = = = = = = = C G T G G C C A = = T = = = = = = = G A C A T T T G = 0 DY01 = C = = = = = = = C G ? G ? C C A = = T = = = = = = = G A ? A ? T T G = 0 DY02 ? = = G C = = = = = G T G G C C A = ? = = A T = = = = = A C A T T T G = 0 DY03 = = C G C = = = = = = T G G = C A G = = A A T = = = = = = C A T = T G C 0 DY04 ? = = = = = = ? = = = C = T = = = ? ? = = = = = = ? = = = T = G = = = ? 0 DY05 = = = = = = = A = = = = = = = = = = = = = = = = = G = = = = = = = = = = 0 DY06 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY07 C T = G C A A = = G = = = = = = = G T C = A T G G = = C = = = = = = = C 0 DY08 C = = = = = = = = = = C = T = = = = T = = = = = = = = = = T = G = = = = 0 DY09 (C) = = = = = = = = ? G T G ? C C A = (T) = = = = = = = = ? A C A ? T T G = 0 DY10 ? ? = = = A A ? = G = C = T = = = = ? ? = = = G G ? = C = T = G = = = = 0 DY11 C T C G C = = = = G = = = = = = = G T C A A T = = = = C = = = = = = = C 0 DY12 C T = G C A A = = G = = = = = = = ? T C = A T G G = = C = = = = = = = ? 0 E101 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 E105 = = = = = = = ? = = = = = ? ? = = = = = = = = = = ? = = = = = ? ? = = = 0 E106 = ? = = = G = = C C = = = = = = = = = ? = = = A = = A G = = = = = = = = 0 E107 C = C G C ? = A C = = = = = = = = G T = A A T ? = G A = = = = = = = = C 0 E108 = = = = = = = = = = = = = = = ? = ? = = = = = = = = = = = = = = = ? = ? 0 E109 C = C G C ? = A C = = = = = = = = G T = A A T ? = G A = = = = = = = = C 0 E110 C T C G C ? = A = G = = = = = = = G T C A A T ? = G = C = = = = = = = C 0 E111 ? T C G C A = A = G = = = = = = = G ? C A A T G = G = C = = = = = = = C 0 E112 = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 E113 = ? = = = G = = ? C = = = = = = = = = ? = = = A = = ? G = = = = = = = = 0 E114 = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 E115 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 E116 ? = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = ? = = = = = = 0 E117 = (C) = = = = = G = = = = = = = = = = = (T) = = = = = A = = = = = = = = = = 0 E118 = = = ? ? ? ? = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = 0 E119 = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 E120 C T C G C A = A = G = = = = = = = G T C A A T G = G = C = = = = = = = C 0 E121 C = C G C = = A C = = = = = = = = ? T = A A T = = G A = = = = = = = = ? 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H101 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 H102 = C = = = G = = = C G T G G C C A ? = T = = = A = = = G A C A T T T G ? 0 H103 C T = G C A A ? = G = = = = = = = G T C = A T G G ? = C = = = = = = = C 0 H104 = C C = = G G = = C = = = = = = = = = T A = = A A = = G = = = = = = = = 0 H105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H106 = C A A T G = G = C = = = = = = = C = T C G C A = A = G = = = = = = = G 0 H107 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 H108 C = C G C = = A C = = = = = = = = G T = A A T = = G A = = = = = = = = C 0 H109 = ? C = = ? G = C C = = = = = = = = = ? A = = ? A = A G = = = = = = = = 0 H110 = C = = = G = = C C = = = = = = = ? = T = = = A = = A G = = = = = = = ? 0 H111 = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 H112 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 H113 = ? = ? ? G = = C C = = = = = = = = = ? = ? ? A = = A G = = = = = = = = 0 H114 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 H115 = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 H116 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 H117 = C = = = G = = C C = = = ? ? = = ? = T = = = A = = A G = = = ? ? = = ? 0 H118 ? = C G C = = = C = = = = = = = = ? ? = A A T = = = A = = = = = = = = ? 0 H119 = = C G C = = = = = = T = G = = = G = = A A T = = = = = = C = T = = = C 0 H120 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 H121 = = = ? = = = ? = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = 0 H122 C = C G C (A) = (A) (A) G = = = = = = = G T = A A T (G) = (G) (C) C = = = = = = = C 0 X101 = C = = = ? = = C C = = = = = = = = = T = = = ? = = A G = = = = = = = = 0 X102 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 X103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X104 = C = = = G = = C C = = = = = = = ? = T = = = A = = A G = = = = = = = ? 0 X105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X106 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = 0 X107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X108 = C = = = G = = C C = = = = = = = = = T = = = A = = A G = = = = = = = = 0 X109 = = C = = = G = ? = = = = = = = = = = = A = = = A = ? = = = = = = = = = 0 X110 ? = = = = = = = ? = ? = = = = = = = ? = = = = = = = ? = ? = = = = = = = 0 X111 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X112 = ? = = = = = = = = = = = = = = = ? = ? = = = = = = = = = = = = = = = ? 0 X113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X114 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = 0 X115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X117 = ? = = = G = = C C = ? = = = = = = = ? = = = A = = A G = ? = = = = = = 0 X118 ? ? = = = = = = = = ? = = = = = = = ? ? = = = = = = = = ? = = = = = = = 0 X119 = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? ? = = = = = = = 0 X120 = ? = = = = = = = ? ? = = = = = = ? = ? = = = = = = = ? ? = = = = = = ? 0 X121 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = 0 X122 = C = = = G = = ? C ? = = = = = = = = T = = = A = = ? G ? = = = = = = = 0 X123 = C = = = G = = C C ? = = = = = = ? = T = = = A = = A G ? = = = = = = ? 0 X124 = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? ? = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? 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