************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 dutxx.phase.inp dutxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST dutxx.phase.out_freqs : haplotype frequency estimates dutxx.phase.out_pairs : most likely haplotype pairs for each individual dutxx.phase.out_recom : estimates of recombination parameters dutxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 11 Positions of loci: 161 811 1055 1079 2551 3493 7439 10647 10708 13608 13849 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file dutxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 IIAGTGTCCTD 34.000000 2 IIACTGTCCTD 1.000000 3 IICCTATCCTD 4.000000 4 IICCTATCCCD 9.000000 5 IICCGATCCTD 11.000000 6 IDCCTACTCCD 19.000000 7 IDCCTACTCCI 38.000000 8 IDCCTACTTCI 53.000000 9 IDCCTGCCCTD 5.000000 10 IDCCGACCCTD 1.000000 11 DIAGTGTCCTD 15.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (4,5) D002: (1,1) D003: (1,7) D004: (4,5) D005: (5,8) D006: (5,7) D007: (8,9) D008: (6,7) D009: (6,8) D010: (5,5) D011: (4,9) D012: (1,4) D013: (4,6) D014: (8,11) D015: (6,7) DY01: (7,8) DY02: (6,7) DY03: (1,6) DY04: (4,5) DY05: (5,6) DY06: (4,6) DY07: (6,6) DY08: (1,10) DY09: (1,6) DY10: (3,9) DY11: (1,9) DY12: (1,9) E101: (7,11) E102: (8,8) E103: (8,11) E104: (8,8) E105: (7,8) E106: (7,8) E107: (8,8) E108: (7,7) E109: (8,11) E110: (8,8) E111: (8,11) E112: (8,11) E113: (8,8) E114: (8,8) E115: (8,8) E116: (11,11) E117: (8,8) E118: (8,8) E119: (8,8) E120: (8,8) E121: (8,11) E122: (8,11) H101: (1,7) H102: (7,8) H103: (7,8) H104: (1,7) H105: (8,8) H106: (5,7) H107: (7,7) H108: (5,8) H109: (7,8) H110: (1,8) H111: (8,8) H112: (7,8) H113: (8,11) H114: (7,8) H115: (7,8) H116: (8,11) H117: (7,7) H118: (1,7) H119: (8,8) H120: (1,5) H121: (4,8) H122: (7,8) X101: (7,11) X102: (1,7) X103: (1,3) X104: (6,7) X105: (2,7) X106: (1,1) X107: (1,7) X108: (6,7) X109: (1,6) X110: (1,11) X111: (1,7) X112: (1,7) X113: (3,4) X114: (1,7) X115: (1,6) X116: (1,6) X117: (1,7) X118: (1,7) X119: (1,3) X120: (1,1) X121: (1,6) X122: (1,6) X123: (6,11) X124: (1,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 I I C C T A T C C [C] D I I C C [G] A T C C T D 0 D002 I I A G T G T C C T D I I A G T G T C C T D 0 D003 I I A G T G T C C T D I D C C T A C T C C [I] 0 D004 I I C C T A T C C C D I I C C G A T C C T D 0 D005 I I C C G A T C C T D I D C C T A C T T C I 0 D006 I I C C G A T C C T D I D C C T A C T C C I 0 D007 I D C C T A C T T C I I D C C T G C C C T D 0 D008 I D C C T A C T C C [D] I D C C T A C T C C [I] 0 D009 I D C C T A C T C C D I D C C T A C T T C I 0 D010 I I C C G A T C C T D I I C C G A T C C T D 0 D011 I I C C T A T C C [C] D I D C C T G C C C T D 0 D012 I I A G T G T C C T D I I C C T A T C C C D 0 D013 I I C C T A T C C [C] D I D C C T A C T C C D 0 D014 I D C C T A C T T C I D I A G T G T C C T D 0 D015 I D C C T A C T C C D I D C C T A C T C C I 0 DY01 I D C C T A C T C C [I] I D C C T A C T T C I 0 DY02 I D C C T A C T C C D I D C C T A C T C C I 0 DY03 I I A G T G T C C T D I D C C T A C T C C D 0 DY04 I I C C T A T C C C D I I C C G A T C C T D 0 DY05 I I C C G A T C C T D I D C C T A C T C C D 0 DY06 I I C C T A T C C C D I D C C T A C T C C D 0 DY07 I D C C T A C T C C D I D C C T A C T C C D 0 DY08 I I A G T G T C C T D I D C C G A C C C T D 0 DY09 I I A G T G T C C T D I D C C T A C T C C D 0 DY10 I I C C T A T C C T D I D C C T G C C C T D 0 DY11 I I A G T G T C C T D I D C C T G C C C T D 0 DY12 I I A G T G T C C T D I D C C T G C C C T D 0 E101 I D C C T A C T C C I D I A G T G T C C T D 0 E102 I D C C T A C T T C I I D C C T A C T T C I 0 E103 I D C C T A C T T C I D I A G T G T C C T D 0 E104 I D C C T A C T T C I I D C C T A C T T C I 0 E105 I D C C T A C T C C I I D C C T A C T T C I 0 E106 I D C C T A C T C C I I D C C T A C T T C I 0 E107 I D C C T A C T T C I I D C C T A C T T C I 0 E108 I D C C T A C T C C I I D C C T A C T C C I 0 E109 I D C C T A C T T C I D I A G T G T C C T D 0 E110 I D C C T A C T T C I I D C C T A C T T C I 0 E111 I D C C T A C T T C I D I A G T G T C C T D 0 E112 I D C C T A C T T C I D I A G T G T C C T D 0 E113 I D C C T A C T T C I I D C C T A C T T C I 0 E114 I D C C T A C T T C I I D C C T A C T T C I 0 E115 I D C C T A C T T C I I D C C T A C T T C I 0 E116 D I A G T G T C C T D D I A G T G T C C T D 0 E117 I D C C T A C T T C I I D C C T A C T T C I 0 E118 I D C C T A C T T C I I D C C T A C T T C I 0 E119 I D C C T A C T T C I I D C C T A C T T C I 0 E120 I D C C T A C T T C I I D C C T A C T T C I 0 E121 I D C C T A C T T C I D I A G T G T C C T D 0 E122 I D C C T A C T T C I D I A G T G T C C T D 0 H101 I I A G T G T C C T D I D C C T A C T C C I 0 H102 I D C C T A C T C C I I D C C T A C T T C I 0 H103 I D C C T A C T C C I I D C C T A C T T C I 0 H104 I I A G T G T C C T D I D C C T A C T C C I 0 H105 I D C C T A C T T C I I D C C T A C T T C I 0 H106 I I C C G A T C C T D I D C C T A C T C C I 0 H107 I D C C T A C T C C I I D C C T A C T C C I 0 H108 I I C C G A T C C T D I D C C T A C T T C I 0 H109 I D C C T A C T C C I I D C C T A C T T C I 0 H110 I I A G T G T C C T D I D C C T A C T T C I 0 H111 I D C C T A C T T C I I D C C T A C T T C I 0 H112 I D C C T A C T C C I I D C C T A C T T C I 0 H113 I D C C T A C T T C I D I A G T G T C C T D 0 H114 I D C C T A C T C C I I D C C T A C T T C I 0 H115 I D C C T A C T C C I I D C C T A C T T C I 0 H116 I D C C T A C T T C I D I A G T G T C C T D 0 H117 I D C C T A C T C C I I D C C T A C T C C I 0 H118 I I A G T G T C C T D I D C C T A C T C C I 0 H119 I D C C T A C T T C I I D C C T A C T T C I 0 H120 I I A G T G T C C T D I I C C G A T C C T D 0 H121 I I C C T A T C C C D I D C C T A C T [T] C I 0 H122 I D C C T A C T C C I I D C C T A C T T C I 0 X101 I D C C T A C T C C I D I A G T G T C C T D 0 X102 I I A G T G T C C T D I D C C T A C T C C I 0 X103 I I A G T G T C C T D I I C C T A T C C T D 0 X104 I D C C T A C T C C D I D C C T A C T C C I 0 X105 I I A C T G T C C T D I D C C T A C T C C I 0 X106 I I A G T G T C C T D I I A G T G T C C T D 0 X107 I I A G T G T C C T D I D C C T A C T C C I 0 X108 I D C C T A C T C C D I D C C T A C T C C I 0 X109 I I A G T G T C C T D I D C C T A C T C C D 0 X110 I I A G T G T C C T D D I A G T G T C C T D 0 X111 I I A G T G T C C T D I D C C T A C T C C I 0 X112 I I A G T G T C C T D I D C C T A C T C C I 0 X113 I I C C T A T C C T D I I C C T A T C C C D 0 X114 I I A G T G T C C T D I D C C T A C T C C I 0 X115 I I A G T G T C C T D I D C C T A C T C C D 0 X116 I I A G T G T C C T D I D C C T A C T C C D 0 X117 I I A G T G T C C T D I D C C T A C T C C I 0 X118 I I A G T G T C C T D I D C C T A C T C C I 0 X119 I I A G T G T C C T D I I C C T A T C C T D 0 X120 I I A G T G T C C T D I I A G T G T C C T D 0 X121 I I A G T G T C C T D I D C C T A C T C C D 0 X122 I I A G T G T C C T D I D C C T A C T C C D 0 X123 I D C C T A C T C C D D I A G T G T C C T D 0 X124 I I A G T G T C C T D I D C C T A C T 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 = = = = = = = = = = = = = = = = = = = = = = 0 D003 = I A ? = G T C = T ? = D C ? = A C T = C ? 0 D004 = = = = T = = = = C = = = = = G = = = = T = 0 D005 = I = = G = T C C T D = D = = T = C T T C I 0 D006 = I = = G = T C = T D = D = = T = C T = C I 0 D007 = = = = = A = T T C I = = = = = G = C C T D 0 D008 = = ? ? = = = = = = ? = = ? ? = = = = = = ? 0 D009 = = = = = = = = C = D = = = = = = = = T = I 0 D010 = = = = = = = = = = = = = = = = = = = = = = 0 D011 = I = = = A T = = ? = = D = = = G C = = ? = 0 D012 = = A G = G = = = T = = = C C = A = = = C = 0 D013 = I = = = = T C = ? = = D = = = = C T = ? = 0 D014 I D C C = A C T T C I D I A G = G T C C T D 0 D015 = = = = = = = = = = D = = = = = = = = = = I 0 DY01 = = = = = = = = C = ? = = = = = = = = T = ? 0 DY02 = = = = = = = = = = D = = = = = = = = = = I 0 DY03 = I A G = G T C = T = = D C C = A C T = C = 0 DY04 = = = = T = = = = C = = = = = G = = = = T = 0 DY05 = I ? ? G = T C = T = = D ? ? T = C T = C = 0 DY06 = I = = = = T C ? = = = D = = = = C T ? = = 0 DY07 = = = = = = = = = = = = = = = = = = = = = = 0 DY08 = I ? ? T G T = = = = = D ? ? G A C = = = = 0 DY09 = I A G = G T C = T = = D C C = A C T = C = 0 DY10 = I = = = A T = = = = = D = = = G C = = = = 0 DY11 = I A G = = T = = = = = D C C = = C = = = = 0 DY12 = I A G = = T = = = = = D C C = = C = = = = 0 E101 I D C C = A C T = C I D I A G = G T C = T D 0 E102 = = = = = = = = = = = = = = = = = = = = = = 0 E103 I D C C = A C T T C I D I A G = G T C C T D 0 E104 = = = = = = = = = = = = = = = = = = = = = = 0 E105 = = = = = = = = C = = = = = = = = = = T = = 0 E106 = = = = = = = = C = = = = = = = = = = T = = 0 E107 = = = = = = = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = = = = = = = = = = = = = = = 0 E109 I D C C = A C T T C I D I A G = G T C C T D 0 E110 = = = = = = = = = = = = = = = = = = = = = = 0 E111 I D C C = A C T T C I D I A G = G T C C T D 0 E112 I D C C = A C T T C I D I A G = G T C C T D 0 E113 = = = = = = = = = = = = = = = = = = = = = = 0 E114 = = = = ? = = = = = = = = = = ? = = = = = = 0 E115 ? ? = = = = = = = = = ? ? = = = = = = = = = 0 E116 = = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = = = = = = = = = = = = = = = = = 0 E118 = = = = = = = = = = = = = = = = = = = = = = 0 E119 = = = = = ? = = = = = = = = = = ? = = = = = 0 E120 = = = = = = = = = = = = = = = = = = = = = = 0 E121 I D C C = A C T T C I D I A G = G T C C T D 0 E122 I D C C ? A C T T ? I D I A G ? G T C C ? D 0 H101 = I A G = G T C = T D = D C C = A C T = C I 0 H102 = = = = = = = = C = = = = = = = = = = T = = 0 H103 = = = = = = = = C = = = = = = = = = = T = = 0 H104 = I A G = G T C = T D = D C C = A C T = C I 0 H105 = = = = = = = = = = = = = = = = = = = = = = 0 H106 = I ? ? G = T C = T D = D ? ? T = C T = C I 0 H107 = = = = = = = = = = = = = = = = = = = = = = 0 H108 = I ? ? G = T C C T D = D ? ? T = C T T C I 0 H109 = = = = = = = = C = = = = = = = = = = T = = 0 H110 = I A G = G T C C T D = D C C = A C T T C I 0 H111 = = = = ? = = = = = = = = = = ? = = = = = = 0 H112 = = = = = = = = C = = = = = = = = = = T = = 0 H113 I D C C = A C T T C I D I A G = G T C C T D 0 H114 = = = = = = = = C = = = = = = = = = = T = = 0 H115 = = = = = = = = C = = = = = = = = = = T = = 0 H116 I D C C = A C T T C I D I A G = G T C C T D 0 H117 = = = = = = = = = = = = = = = = = = = = = = 0 H118 = I A G = G T C = T D = D C C = A C T = C I 0 H119 = = = = = = = = = = = = = = = = = = = = = = 0 H120 = = A G T G = = = = = = = C C G A = = = = = 0 H121 = I = = = = T C ? = D = D = = = = C T ? = I 0 H122 = = = = = = = = C = = = = = = = = = = T = = 0 X101 I D C C = A C T = C I D I A G = G T C = T D 0 X102 = I A G = G T C = T D = D C C = A C T = C I 0 X103 = = A G = G = = = = = = = C C = A = = = = = 0 X104 = = = = = = = = = = D = = = = = = = = = = I 0 X105 = I A = = G T C = T D = D C = = A C T = C I 0 X106 = = = = = = = = = = = = = = = = = = = = = = 0 X107 = I A G = G T C = T D = D C C = A C T = C I 0 X108 = = = = = = = = = = D = = = = = = = = = = I 0 X109 = I A G = G T C = T = = D C C = A C T = C = 0 X110 I = = = = = = = = = = D = = = = = = = = = = 0 X111 = I A G = G T C = T D = D C C = A C T = C I 0 X112 = I A G = G T C = T D = D C C = A C T = C I 0 X113 = = = = = ? = = ? T = = = = = = ? = = ? C = 0 X114 = I A G = G T C = T D = D C C = A C T = C I 0 X115 = I A G = G T C = T = = D C C = A C T = C = 0 X116 = I A G = G T C = T = = D C C = A C T = C = 0 X117 = I A G = G T C = T D = D C C = A C T = C I 0 X118 = I ? ? ? G T C = T D = D ? ? ? A C T = C I 0 X119 = = A G = ? = = = = = = = C C = ? = = = = = 0 X120 = = = = = = = = = = = = = = = = = = = = = = 0 X121 = I A G = G T C = T = = D C C = A C T = C = 0 X122 = I A G = G T C = T = = D C C = A C T = C = 0 X123 I D C C = A C T = C = D I A G = G T C = T = 0 X124 = I A G = G T C = T D = D C C = A C T = C I 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 = 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = ? = = = 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = 1.00 1.00 = ? = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = 1.00 = = = = = = = = 1.00 = ? = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = 1.00 = = 1.00 ? ? 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 1.00 ? = = = = = = = = = = = = = = 1.00 ? ? 1.00 1.00 1.00 = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = ? = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 ? 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = 1.00 ? ? 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = 1.00 ? ? 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = ? = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = = = = = 1.00 = = = = 1.00 1.00 ? = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = ? = = ? 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 ? ? ? 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = ? = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 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