************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 apex2.phase.inp apex2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST apex2.phase.out_freqs : haplotype frequency estimates apex2.phase.out_pairs : most likely haplotype pairs for each individual apex2.phase.out_recom : estimates of recombination parameters apex2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 9 Positions of loci: 1769 1793 2533 4414 4923 8552 9664 10528 10802 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file apex2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCTDATGCT 79.000000 2 GCTDATGTT 45.000000 3 GCTDACGTT 10.000000 4 GCTDCTGCT 20.000000 5 GCTDCTGTT 4.000000 6 GCTIACGTT 2.000000 7 GCCDATGCT 14.000000 8 GCCDATGTT 2.000000 9 GCCDCCGTT 1.000000 10 CGTIATTTG 9.000000 11 CGCIATTTG 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,4) D002: (10,10) D003: (3,3) D004: (1,7) D005: (2,2) D006: (1,1) D007: (3,3) D008: (1,1) D009: (1,4) D010: (10,10) D011: (10,11) D012: (1,11) D013: (2,11) D014: (3,6) D015: (2,2) DY01: (3,4) DY02: (1,1) DY03: (10,10) DY04: (2,3) DY05: (2,2) DY06: (1,3) DY07: (1,2) DY08: (1,4) DY09: (1,4) DY10: (10,10) DY11: (3,9) DY12: (4,11) E101: (2,4) E102: (2,5) E103: (1,2) E104: (2,2) E105: (1,2) E106: (1,7) E107: (4,7) E108: (2,4) E109: (1,7) E110: (1,2) E111: (1,7) E112: (1,7) E113: (1,4) E114: (1,7) E115: (2,7) E116: (1,4) E117: (1,7) E118: (5,7) E119: (1,4) E120: (1,7) E121: (1,1) E122: (1,4) H101: (2,4) H102: (2,8) H103: (1,2) H104: (1,4) H105: (1,1) H106: (2,2) H107: (2,4) H108: (1,2) H109: (1,1) H110: (1,2) H111: (1,1) H112: (1,2) H113: (1,7) H114: (1,4) H115: (1,1) H116: (2,5) H117: (1,2) H118: (1,1) H119: (1,1) H120: (1,1) H121: (1,1) H122: (1,1) X101: (1,7) X102: (1,1) X103: (2,4) X104: (2,6) X105: (1,3) X106: (1,1) X107: (1,1) X108: (1,4) X109: (2,2) X110: (1,2) X111: (2,2) X112: (2,7) X113: (2,8) X114: (2,5) X115: (1,1) X116: (2,2) X117: (1,4) X118: (1,2) X119: (1,1) X120: (2,2) X121: (1,1) X122: (1,1) X123: (1,1) X124: (1,2) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G C T D A T G C T G C T D C T G C T 0 D002 C G T I A T T T G C G T I A T T T G 0 D003 G C T D A C G T T G C T D A C G T T 0 D004 G C T D A T G C T G C C D A T G C T 0 D005 G C T D A T G T T G C T D A T G T T 0 D006 G C T D A T G C T G C T D A T G C T 0 D007 G C T D A C G T T G C T D A C G T T 0 D008 G C T D A T G C T G C T D A T G C T 0 D009 G C T D A T G C T G C T D C T G C T 0 D010 C G [T] I A T T T G C G T I A T T T G 0 D011 C G T I A T T T G C G C I A T T T G 0 D012 G C (T) D A T G C T C G (C) I A T T T G 0 D013 G C (T) D A T G T T C G (C) I A T T T G 0 D014 G C T D A C G T T G C T I A C G T T 0 D015 G C T D A T G T T G C T D A T G T T 0 DY01 G C T D (A) C G T T G C T D (C) T G C T 0 DY02 G C T D [A] T G C T G C T D A T G C T 0 DY03 C G T I A T T T G C G T I A T T T G 0 DY04 G C T D A T G T T G C T D A C G T T 0 DY05 G C T D A T G T T G C T D A T G T T 0 DY06 G C T D A T G C T G C T D A C G T T 0 DY07 G C T D A T G C T G C T D A T G T T 0 DY08 G C T D A T G C T G C T D C T G C T 0 DY09 G C T D A T G C T G C T D C T G C T 0 DY10 C G T I A T T T G C G T I A T T T G 0 DY11 G C (T) D A C G T T G C (C) D C C G T T 0 DY12 G C T D C T G C T C G C I A T T T G 0 E101 G C T D (A) T G T T G C T D (C) T G C T 0 E102 G C T D A T G T T G C T D C T G T T 0 E103 G C T D A T G C T G C T D A T G T T 0 E104 G C T D A T G T T G C T D A T G T T 0 E105 G C T D A T G C T G C T D A T G T T 0 E106 G C T D A T G C T G C C D A T G C T 0 E107 G C T D C T G C T G C C D A T G C T 0 E108 G C T D (A) T G T T G C T D (C) T G C T 0 E109 G C T D A T G C T G C C D A T G C T 0 E110 G C T D A T G C T G C T D A T G T T 0 E111 G C T D A T G C T G C C D A T G C T 0 E112 G C T D A T G C T G C C D A T G C T 0 E113 G C T D A T G C T G C T D C T G C T 0 E114 G C T D A T G C T G C C D A T G C T 0 E115 G C (T) D A T G T T G C (C) D A T G C T 0 E116 G C T D A T G C T G C T D C T G C T 0 E117 G C T D A T G C T G C C D A T G C T 0 E118 G C T D C T G (T) T G C C D A T G (C) T 0 E119 G C T D A T G C T G C T D C T G C T 0 E120 G C T D A T G C T G C C D A T G C T 0 E121 G C T D [A] T G C T G C T D A T G C T 0 E122 G C T D A T G C T G C T D C T G C T 0 H101 G C T D (A) T G T T G C T D (C) T G C T 0 H102 G C T D A T G T T G C C D A T G T T 0 H103 G C T D A T G C T G C T D A T G T T 0 H104 G C T D A T G C T G C T D C T G C T 0 H105 G C T D A T G C T G C T D A T G C T 0 H106 G C T D A T G T T G C T D A T G T T 0 H107 G C T D (A) T G T T G C T D (C) T G C T 0 H108 G C T D A T G C T G C T D A T G T T 0 H109 G C T D A T G C T G C T D A T G C T 0 H110 G C T D A T G C T G C T D A T G T T 0 H111 G C T D A T G C T G C T D A T G C T 0 H112 G C T D A T G C T G C T D A T G T T 0 H113 G C T D A T G C T G C C D A T G C T 0 H114 G C T D A T G C T G C T D C T G C T 0 H115 G C T D A T G C T G C T D A T G C T 0 H116 G C T D A T G T T G C T D C T G T T 0 H117 G C T D A T G C T G C T D A T G T T 0 H118 G C T D A T G C T G C T D A T G C T 0 H119 G C T D A T G C T G C T D A T G C T 0 H120 G C T D A T G C T G C T D A T G C T 0 H121 G C T D A T G C T G C T D A T G C T 0 H122 G C T D A T G C T G C T D A T G C T 0 X101 G C T D A T G C T G C C D A T G C T 0 X102 G C T D A T G C T G C T D A T G C T 0 X103 G C T D (A) T G T T G C T D (C) T G C T 0 X104 G C T D A T G T T G C T I A C G T T 0 X105 G C T D A T G C T G C T D A C G T T 0 X106 G C T D A T G C T G C T D A T G C T 0 X107 G C T D A T G C T G C T D A T G C T 0 X108 G C T D A T G C T G C T D C T G C T 0 X109 G C T D A T G T T G C T D A T G T T 0 X110 G C T D A T G C T G C T D A T G T T 0 X111 G C T D A T G T T G C T D A T G T T 0 X112 G C (T) D A T G T T G C (C) D A T G C T 0 X113 G C T D A T G T T G C C D A T G T T 0 X114 G C T D A T G T T G C T D C T G T T 0 X115 G C T D A T G C T G C T D A T G C T 0 X116 G C T D A T G T T G C T D A T G T T 0 X117 G C T D A T G C T G C T D C T G C T 0 X118 G C T D A T G C T G C T D A T G T T 0 X119 G C T D A T G C T G C T D A T G C T 0 X120 G C T D A T G T T G C T D A T G T T 0 X121 G C T D A T G C T G C T D A T G C T 0 X122 G C T D A T G C T G C T D A T G C T 0 X123 G C T D A T G C T G C T D A T G C T 0 X124 G C T D A T G C T G C T D A T G T T 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 = = = = A = = = = = = = = C = = = = 0 D002 = = = = ? = = = = = = = = ? = = = = 0 D003 = = = = = = = = = = = = = = = = = = 0 D004 ? ? T = = = = = = ? ? C = = = = = = 0 D005 = = = = = = = = = = = = = = = = = = 0 D006 = = = = = = = = = = = = = = = = = = 0 D007 = = = = = = = = = = = = = = = = = = 0 D008 = = = = = = = = = = = = = = = = = = 0 D009 = = = = A = = = = = = = = C = = = = 0 D010 = = ? = = = = = = = = ? = = = = = = 0 D011 = = T = = = = = = = = C = = = = = = 0 D012 G C (T) D = = G C T C G (C) I = = T T G 0 D013 G C (T) D = = G = T C G (C) I = = T = G 0 D014 = = = D = = = = = = = = I = = = = = 0 D015 = = ? = = = = = = = = ? = = = = = = 0 DY01 = = = = (A) C = T = = = = = (C) T = C = 0 DY02 = = = = ? = = = = = = = = ? = = = = 0 DY03 = = = = ? = = = = = = = = ? = = = = 0 DY04 = = = = = T = = = = = = = = C = = = 0 DY05 = = ? = = = = = = = = ? = = = = = = 0 DY06 = = = = = T = C = = = = = = C = T = 0 DY07 = = = = = = = C = = = = = = = = T = 0 DY08 = = = = A = = = = = = = = C = = = = 0 DY09 = = = = A = = = = = = = = C = = = = 0 DY10 = = = = = = = = = = = = = = = = = = 0 DY11 = = (T) = A = = = = = = (C) = C = = = = 0 DY12 G C T D C = G C T C G C I A = T T G 0 E101 = = = = (A) = = T = = = = = (C) = = C = 0 E102 = = = = A = = = = = = = = C = = = = 0 E103 ? ? = = = = = C = ? ? = = = = = T = 0 E104 = = = = = = = = = = = = = = = = = = 0 E105 = = = = ? = = C = = = = = ? = = T = 0 E106 ? = T = ? = = = = ? = C = ? = = = = 0 E107 = = T = C = = = = = = C = A = = = = 0 E108 = = = = (A) = = T = = = = = (C) = = C = 0 E109 ? ? T = = = = = = ? ? C = = = = = = 0 E110 = = = = ? = = C = = = = = ? = = T = 0 E111 ? ? T = = = = = = ? ? C = = = = = = 0 E112 = = T = = = = = = = = C = = = = = = 0 E113 = = = = A = = = = = = = = C = = = = 0 E114 = = T = ? = = = = = = C = ? = = = = 0 E115 = = (T) = = = = T = = = (C) = = = = C = 0 E116 = = = = A = = = = = = = = C = = = = 0 E117 = = T = = = = = = = = C = = = = = = 0 E118 = = T = C = = (T) = = = C = A = = (C) = 0 E119 = = = = A = = = = = = = = C = = = = 0 E120 = = T = = = = = = = = C = = = = = = 0 E121 = = = = ? = = = = = = = = ? = = = = 0 E122 = = = = A = = = = = = = = C = = = = 0 H101 = = = = (A) = = T = = = = = (C) = = C = 0 H102 = = T = = = = = = = = C = = = = = = 0 H103 = = ? = = = = C = = = ? = = = = T = 0 H104 = = = = A = = = = = = = = C = = = = 0 H105 = = ? = = = = = = = = ? = = = = = = 0 H106 = = ? = = = = = = = = ? = = = = = = 0 H107 = = = = (A) = = T = = = = = (C) = = C = 0 H108 = = = = = = ? C = = = = = = = ? T = 0 H109 = = = = = = = = = = = = = = = = = = 0 H110 = = = = = = = C = = = = = = = = T = 0 H111 = = = = = = = = = = = = = = = = = = 0 H112 = = = = = = = C = = = = = = = = T = 0 H113 = = T = = = = = = = = C = = = = = = 0 H114 = = = = A = = = = = = = = C = = = = 0 H115 = = = = = = = = = = = = = = = = = = 0 H116 = = = = A = ? = = = = = = C = ? = = 0 H117 = = = = = = = C = = = = = = = = T = 0 H118 = = = = = = = = = = = = = = = = = = 0 H119 = = = = = = = = = = = = = = = = = = 0 H120 = = = = = = = = = = = = = = = = = = 0 H121 = = = = = = = = = = = = = = = = = = 0 H122 = = = = = = = = = = = = = = = = = = 0 X101 = = T = = = = = = = = C = = = = = = 0 X102 = = = = = = = = ? = = = = = = = = ? 0 X103 = = = = (A) = = T = = = = = (C) = = C = 0 X104 = = = D = T = = = = = = I = C = = = 0 X105 = = = = = T = C = = = = = = C = T = 0 X106 = = = = = = = = = = = = = = = = = = 0 X107 = = = = = = = = = = = = = = = = = = 0 X108 = = = = A = = = = = = = = C = = = = 0 X109 = = = = ? = = = = = = = = ? = = = = 0 X110 = = = = = = = C = = = = = = = = T = 0 X111 = = = = = = = = = = = = = = = = = = 0 X112 ? ? (T) = = = = T = ? ? (C) = = = = C = 0 X113 = = T = = = = = = = = C = = = = = = 0 X114 = = = = A = = = = = = = = C = = = = 0 X115 = = = = = = = = = = = = = = = = = = 0 X116 = = = = = = = = = = = = = = = = = = 0 X117 = = = = A = = = = = = = = C = = = = 0 X118 = = = = = = ? C ? = = = = = = ? T ? 0 X119 = = = = = = = = = = = = = = = = = = 0 X120 = = = = = = = = = = = = = = = = = = 0 X121 = = ? = = = = = = = = ? = = = = = = 0 X122 = = = = = = = = = = = = = = = = = = 0 X123 = = = = = = = = = = = = = = = = = = 0 X124 = = = = = = = C = = = = = = = = 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 0.70 1.00 = = 1.00 1.00 1.00 1.00 1.00 0.81 1.00 = = 1.00 = 1.00 = = = 1.00 = = = = = = = ? = = = = = = = = = = 0.87 1.00 = 1.00 = = = = = ? = = = = = = = = ? = = = = = = = = = 1.00 = = = = = ? = = = = = = = = = = = 0.99 = 1.00 = = = = = = = = 1.00 = = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = 0.61 = 1.00 = = = = 1.00 1.00 0.98 1.00 0.99 = 1.00 1.00 1.00 = = = = 0.64 = = 1.00 = = = = = 1.00 = = = = ? ? = = = = = 1.00 = = = = = = = = = = = = = = ? = = 1.00 = ? = 1.00 = ? = = = = = = 0.98 = 1.00 = = = = = = = = 0.64 = = 1.00 = ? ? 1.00 = = = = = = = = = = ? = = 1.00 = ? ? 1.00 = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = 1.00 = ? = = = = = = 0.66 = = = = 1.00 = = = = = 1.00 = = = = = = 1.00 = = = = = = = = 0.99 = 0.98 = = 0.56 = = = = = 1.00 = = = = = = 1.00 = = = = = = = = = = ? = = = = = = = = 1.00 = = = = = = = = 0.64 = = 1.00 = = = 1.00 = = = = = = = = ? = = = = 1.00 = = = = = 1.00 = = = = = = ? = = = = = = = = ? = = = = = = = = = = 0.64 = = 1.00 = = = = = = = ? 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = ? = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = ? = = = = 0.64 = = 1.00 = = = = 1.00 = 1.00 = = = = = = = = 0.99 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = ? = = = = = = = = = = = 1.00 = = = = = = = = = = ? ? 0.67 = = = = 1.00 = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = ? 1.00 ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = END PHASEPROBS