************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 lcmt2.phase.inp lcmt2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST lcmt2.phase.out_freqs : haplotype frequency estimates lcmt2.phase.out_pairs : most likely haplotype pairs for each individual lcmt2.phase.out_recom : estimates of recombination parameters lcmt2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 8 Positions of loci: 625 1898 2549 2867 4371 4741 4863 5254 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file lcmt2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AAGCATAG 43.000000 2 AAGCATAA 1.000000 3 AAGCATCG 14.000000 4 AAGCGTAG 7.000000 5 AATCATAG 13.000000 6 GGGTATAA 87.000000 7 GGGTGTAA 10.000000 8 GGGTGGAA 15.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (4,8) D003: (1,4) D004: (1,6) D005: (7,7) D006: (1,3) D007: (3,8) D008: (3,8) D009: (1,4) D010: (3,3) D011: (3,8) D012: (1,6) D013: (1,1) D014: (6,8) D015: (1,5) DY01: (1,8) DY02: (1,4) DY03: (1,4) DY04: (2,8) DY05: (1,1) DY06: (1,6) DY07: (1,1) DY08: (1,4) DY09: (1,8) DY10: (1,3) DY11: (1,3) DY12: (1,1) E101: (1,6) E102: (5,6) E103: (6,6) E104: (6,6) E105: (6,7) E106: (6,8) E107: (6,7) E108: (6,6) E109: (6,7) E110: (6,8) E111: (6,8) E112: (6,7) E113: (5,6) E114: (6,6) E115: (6,8) E116: (6,6) E117: (6,6) E118: (6,6) E119: (5,6) E120: (6,8) E121: (6,6) E122: (6,8) H101: (1,6) H102: (6,7) H103: (6,6) H104: (1,6) H105: (6,7) H106: (6,6) H107: (6,6) H108: (6,6) H109: (6,6) H110: (6,6) H111: (6,6) H112: (6,6) H113: (6,7) H114: (6,7) H115: (6,6) H116: (5,6) H117: (1,6) H118: (6,6) H119: (6,6) H120: (1,8) H121: (6,6) H122: (4,6) X101: (1,5) X102: (1,6) X103: (1,6) X104: (1,6) X105: (1,5) X106: (6,6) X107: (5,6) X108: (3,6) X109: (3,6) X110: (3,6) X111: (3,6) X112: (1,6) X113: (5,6) X114: (6,6) X115: (1,3) X116: (6,6) X117: (1,6) X118: (1,5) X119: (1,6) X120: (5,6) X121: (1,1) X122: (1,5) X123: (3,5) X124: (1,6) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A A G C A T A G A A G C A T A G 0 D002 A A G C G T A G G G G T G G A A 0 D003 A A G C A T A G A A G C G T A G 0 D004 A A G C A T A G G G G T A T A A 0 D005 G G G T G T A A G G G T G T A A 0 D006 A A G C A T A G A A G C A T C G 0 D007 A A G C A T C G G G G T G G A A 0 D008 A A G C A T C G G G G T G G A A 0 D009 A A G C A T A G A A G C G T A G 0 D010 A A G C A T C G A A G C A T C G 0 D011 A A G C A T C G G G G T G G A A 0 D012 A A G C A T A G G G G T A T A A 0 D013 A A G C A T [A] G A A G C A T A G 0 D014 G G G T A T A A G G G T G G A A 0 D015 A A G C A T A G A A T C A T A G 0 DY01 A A G C A T A G G G G T G G A A 0 DY02 A A G C A T A G A A G C G T A G 0 DY03 A A G C A T A G A A G C G T A G 0 DY04 A A G C (A) (T) A A G G G T (G) (G) A A 0 DY05 A A G C A T A G A A G C A T A G 0 DY06 A A G C A T A G G G G T A T A A 0 DY07 A A G C A T A G A A G C A T A G 0 DY08 A A G C A T A G A A G C G T A G 0 DY09 A A G C A T A G G G G T G G A A 0 DY10 A A G C A T A G A A G C A T C G 0 DY11 A A G C A T A G A A G C A T C G 0 DY12 A A G C A T A G A A G C A T A G 0 E101 A A G C A T A G G G G T A T A A 0 E102 A A T C A T A G G G G T A T A A 0 E103 G G G T A T A A G G G T A T A A 0 E104 G G G T A T A A G G G T A T A A 0 E105 G G G T A T A A G G G T G T A A 0 E106 G G G T A T A A G G G T G G A A 0 E107 G G G T A T A A G G G T G T A A 0 E108 G G G T A T A A G G G T A T A A 0 E109 G G G T A T A A G G G T G T A A 0 E110 G G G T A T A A G G G T G G A A 0 E111 G G G T A T A A G G G T G G A A 0 E112 G G G T A T A A G G G T G T A A 0 E113 A A T C A T A G G G G T A T A A 0 E114 G G G T A T A A G G G T A T A A 0 E115 G G G T A T A A G G G T G [G] A A 0 E116 G G G T A T A A G G G T A T A A 0 E117 G G G T A T A A G G G T A T A A 0 E118 G G G T A T A A G G G T A T A A 0 E119 A A T C A T A G G G G T A T A A 0 E120 G G G T A T A A G G G T G G A A 0 E121 G G G T A T A A G G G T A T A A 0 E122 G G G T A T A A G G G T G G A A 0 H101 A A G C A T A G G G G T A T A A 0 H102 G G G T A T A A G G G T G T A A 0 H103 G G G T A T A A G G G T A T A A 0 H104 A A G C A T A G G G G T A T A A 0 H105 G G G T A T A A G G G T G T A A 0 H106 G G G T A T A A G G G T A T A A 0 H107 G G G T A T A A G G G T A T A A 0 H108 G G G T A T A A G G G T A T A A 0 H109 G G G T A T A A G G G T A T A A 0 H110 G G G T A T A A G G G T A T A A 0 H111 G G G T A T A A G G G T A T A A 0 H112 G G G T A T A A G G G T A T A A 0 H113 G G G T A T A A G G G T G T A A 0 H114 G G G T A T A A G G G T G T A A 0 H115 G G G T A T A A G G G T A T A A 0 H116 A A T C A T A G G G G T A T A A 0 H117 A A G C A T A G G G G T A T A A 0 H118 G G G T A T A A G G G T A T A A 0 H119 G G G T A T A A G G G T A T A A 0 H120 A A G C A T A G G G G T G G A A 0 H121 G G G T A T A A G G G T A T A A 0 H122 A A G C (G) T A G G G G T (A) T A A 0 X101 A A G C A T A G A A T C A T A G 0 X102 A A G C A T A G G G G T A T A A 0 X103 A A G C A T A G G G G T A T A A 0 X104 A A G C A T A G G G G T A T A A 0 X105 A A G C A T A G A A T C A T A G 0 X106 G G G T A T A A G G G T A T A A 0 X107 A A T C A T A G G G G T A T A A 0 X108 A A G C A T C G G G G T A T A A 0 X109 A A G C A T C G G G G T A T A A 0 X110 A A G C A T C G G G G T A T A A 0 X111 A A G C A T C G G G G T A T A A 0 X112 A A G C A T A G G G G T A T A A 0 X113 A A T C A T A G G G G T A T A A 0 X114 G G G T A T A A G G G T A T A A 0 X115 A A G C A T A G A A G C A T C G 0 X116 G G G T A T A A G G G T A T A A 0 X117 A A G C A T A G G G G T A T A A 0 X118 A A G C A T A G A A T C A T A G 0 X119 A A G C A T A G G G G T A T A A 0 X120 A A T C A T A G G G G T A T A A 0 X121 A A G C A T A G A A G C A T A G 0 X122 A A G C A T A G A A T C A T A G 0 X123 A A G C A T C G A A T C A T A G 0 X124 A A G C A T A G G G G T A T A A 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 A A = C = T = G G G = T = G = A 0 D003 = = = = A = = = = = = = G = = = 0 D004 A A = C = = = G G G = T = = = A 0 D005 = = ? = = = = = = = ? = = = = = 0 D006 = = = = = = A = = = = = = = C = 0 D007 A A = C A T C G G G = T G G A A 0 D008 A A ? C A T C G G G ? T G G A A 0 D009 = = = = A = = = = = = = G = = = 0 D010 = = ? = = = = = = = ? = = = = = 0 D011 A A = C A T C G G G = T G G A A 0 D012 A A = C = = = G G G = T = = = A 0 D013 = = = = = = ? ? = = = = = = ? ? 0 D014 = ? = = A T = = = ? = = G G = = 0 D015 = = G = = = ? ? = = T = = = ? ? 0 DY01 A A = C A T = G G G = T G G = A 0 DY02 = = = = A ? ? ? = = = = G ? ? ? 0 DY03 = = = = A = = = = = = = G = = = 0 DY04 A A = C (A) (T) = = G G = T (G) (G) = = 0 DY05 = = = = = = = = = = = = = = = = 0 DY06 A ? = C = = ? ? G ? = T = = ? ? 0 DY07 = = = = = = = = = = = = = = = = 0 DY08 = = = = A = = = = = = = G = = = 0 DY09 A ? = C A T = G G ? = T G G = A 0 DY10 = = = = = = A = = = = = = = C = 0 DY11 = = = = = = A = = = = = = = C = 0 DY12 = = = = ? = = = = = = = ? = = = 0 E101 A A = C = = = G G G = T = = = A 0 E102 A A T C = = = G G G G T = = = A 0 E103 = ? = = = = ? = = ? = = = = ? = 0 E104 = = = = = = = = = = = = = = = = 0 E105 = = = = A = = = = = = = G = = = 0 E106 = = = = A T = = = = = = G G = = 0 E107 = = = = A = = = = = = = G = = = 0 E108 = = = = = = = = = = = = = = = = 0 E109 = = = = A = = = = = = = G = = = 0 E110 = = = = A T = = = = = = G G = = 0 E111 = = = = A T = = = = = = G G = = 0 E112 = = = = A = = = = = = = G = = = 0 E113 A A T C = = = G G G G T = = = A 0 E114 = = = = = = = = = = = = = = = = 0 E115 = = = = A ? ? ? = = = = G ? ? ? 0 E116 = = ? ? = = = = = = ? ? = = = = 0 E117 = = = = = = = = = = = = = = = = 0 E118 = = ? ? = = ? ? = = ? ? = = ? ? 0 E119 A A T C = = = G G G G T = = = A 0 E120 = = = = A T = = = = = = G G = = 0 E121 = = = = = = = = = = = = = = = = 0 E122 = = = = A T = = = = = = G G = = 0 H101 A A = C = = = G G G = T = = = A 0 H102 = = = = A = = = = = = = G = = = 0 H103 = = ? ? = = = = = = ? ? = = = = 0 H104 A A = C = = = G G G = T = = = A 0 H105 = = = = A = = = = = = = G = = = 0 H106 = = = = = = = = = = = = = = = = 0 H107 = = = = = = = = = = = = = = = = 0 H108 = = = = = = = = = = = = = = = = 0 H109 = = = = = = = = = = = = = = = = 0 H110 = = = = = = = = = = = = = = = = 0 H111 = = = = = = = = = = = = = = = = 0 H112 = = = = = = = = = = = = = = = = 0 H113 = = = = A = = = = = = = G = = = 0 H114 = = = = A = = = = = = = G = = = 0 H115 = = = = = = = = = = = = = = = = 0 H116 A A T C = = = G G G G T = = = A 0 H117 A A = C = = = G G G = T = = = A 0 H118 = = = = = = = = = = = = = = = = 0 H119 = = = = = = = = = = = = = = = = 0 H120 A A = C A T ? ? G G = T G G ? ? 0 H121 = = = = ? = = = = = = = ? = = = 0 H122 A A = C (G) = = G G G = T (A) = = A 0 X101 = = G = = = = = = = T = = = = = 0 X102 A A = C = = = G G G = T = = = A 0 X103 A A = C = = = G G G = T = = = A 0 X104 A A = C = = = G G G = T = = = A 0 X105 = = G = = = = = = = T = = = = = 0 X106 = = = = = = = = = = = = = = = = 0 X107 A ? T C = = = G G ? G T = = = A 0 X108 A A = C = = C G G G = T = = A A 0 X109 A A = C = = C G G G = T = = A A 0 X110 A A = C = = C G G G = T = = A A 0 X111 A A = C = = C G G G = T = = A A 0 X112 A A = C = = = G G G = T = = = A 0 X113 A A T C = = = G G G G T = = = A 0 X114 = = = = = = ? ? = = = = = = ? ? 0 X115 = = = = = = A = = = = = = = C = 0 X116 = = = = = = = = = = = = = = = = 0 X117 A A = C = = = G G G = T = = = A 0 X118 = = G = = = = = = = T = = = = = 0 X119 A A = C = = = G G G = T = = = A 0 X120 A A T C = = = G G G G T = = = A 0 X121 = = = = = = = = = = = = = = = = 0 X122 = = G = = = = = = = T = = = = = 0 X123 = = G = = = C = = = T = = = A = 0 X124 A A = C ? = = G G G = T ? = = A 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 0.99 1.00 1.00 1.00 ? 1.00 1.00 1.00 0.99 1.00 = = = = 1.00 = = = = = ? = = = = = 1.00 1.00 = 1.00 1.00 1.00 0.99 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = = = = ? ? = ? = = 1.00 1.00 = = = = 1.00 = = = ? ? 1.00 1.00 = 1.00 0.99 0.99 = 1.00 = = = = 1.00 ? ? ? = = = = 1.00 = = = 1.00 1.00 = 1.00 0.89 0.88 = = = = = = = = = = 1.00 ? = 1.00 = = ? ? = = = = = = = = = = = = 1.00 = = = 1.00 ? = 1.00 0.99 0.99 = 1.00 = = = = = = 1.00 = = = = = = = 1.00 = = = = = ? = = = 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 0.99 1.00 = = = 1.00 = ? = = = = ? = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = 1.00 = = = 1.00 1.00 0.99 1.00 = = = 1.00 = = = = = = = = = = = = 1.00 ? ? ? = = ? ? = = = = = = = = = = = = = = ? ? = = ? ? 1.00 1.00 0.99 1.00 = = = 1.00 = = = = 1.00 1.00 = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = 1.00 = = = = 1.00 = = = = = ? ? = = = = 1.00 1.00 = 1.00 = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = = = = = = = = = = 1.00 1.00 0.99 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 0.98 0.99 ? ? = = = = ? = = = 1.00 1.00 = 1.00 0.55 = = 1.00 = = 1.00 = = = = = 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = = = = = = = = = = 1.00 ? 0.99 1.00 = = = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 0.99 1.00 = = = 1.00 = = = = = = ? ? = = = = = = 1.00 = = = = = = = = = 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = = 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 0.99 1.00 = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = 0.99 = = = 1.00 = 1.00 1.00 = 1.00 ? = = 1.00 END PHASEPROBS