************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 hspa1.phase.inp hspa1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST hspa1.phase.out_freqs : haplotype frequency estimates hspa1.phase.out_pairs : most likely haplotype pairs for each individual hspa1.phase.out_recom : estimates of recombination parameters hspa1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 6 Positions of loci: 322 2943 5008 5265 5591 5766 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file hspa1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGGTGI 70.000000 2 GGGTAI 1.000000 3 GGATGI 4.000000 4 GGATGD 21.000000 5 GTGTGI 16.000000 6 TGGTGI 8.000000 7 TGGTAI 42.000000 8 TGGCGI 28.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,7) D002: (1,1) D003: (1,8) D004: (3,4) D005: (1,1) D006: (1,7) D007: (1,1) D008: (1,3) D009: (1,6) D010: (4,5) D011: (1,4) D012: (5,7) D013: (1,1) D014: (1,5) D015: (1,4) DY01: (4,5) DY02: (1,5) DY03: (1,5) DY04: (4,5) DY05: (1,5) DY06: (1,4) DY07: (5,6) DY08: (4,5) DY09: (3,5) DY10: (1,4) DY11: (1,5) DY12: (5,5) E101: (7,8) E102: (7,7) E103: (1,7) E104: (7,8) E105: (1,8) E106: (1,8) E107: (8,8) E108: (7,8) E109: (8,8) E110: (6,7) E111: (1,7) E112: (7,8) E113: (1,8) E114: (1,8) E115: (7,8) E116: (7,8) E117: (1,1) E118: (7,8) E119: (1,1) E120: (6,7) E121: (1,8) E122: (6,8) H101: (7,7) H102: (1,4) H103: (1,7) H104: (6,8) H105: (1,7) H106: (1,1) H107: (1,4) H108: (1,1) H109: (1,1) H110: (1,6) H111: (5,7) H112: (1,1) H113: (1,4) H114: (7,7) H115: (1,8) H116: (7,8) H117: (1,1) H118: (1,7) H119: (3,7) H120: (1,1) H121: (1,7) H122: (1,4) X101: (5,7) X102: (2,4) X103: (7,7) X104: (1,4) X105: (1,6) X106: (7,7) X107: (1,8) X108: (1,8) X109: (4,8) X110: (4,8) X111: (1,1) X112: (1,8) X113: (4,4) X114: (1,4) X115: (1,7) X116: (7,7) X117: (1,8) X118: (1,1) X119: (1,7) X120: (1,7) X121: (7,8) X122: (1,7) X123: (4,7) X124: (7,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G G G T G I T G G T [A] I 0 D002 G [G] G T G I G G G T G I 0 D003 G G G T G I T G G C G I 0 D004 G G A T G I G G A T G D 0 D005 G [G] G T G I G G G T G I 0 D006 G G G T G I T G G T [A] I 0 D007 G G G T G I G G G T G I 0 D008 G G G T G I G G A T G I 0 D009 G G G T G I T G G T G I 0 D010 G G A T G D G T G T G I 0 D011 G G G T G I G G A T G D 0 D012 G T G T G I T G G T A I 0 D013 G [G] G T G I G G G T G I 0 D014 G G G T G I G T G T G I 0 D015 G G G T G I G G A T G D 0 DY01 G G A T G D G T G T G I 0 DY02 G G G T G I G T G T G I 0 DY03 G G G T G I G T G T G I 0 DY04 G G A T G D G T G T G I 0 DY05 G G G T G I G T G T G I 0 DY06 G G G T G I G G A T G D 0 DY07 G T G T G I T G G T G I 0 DY08 G G A T G D G T G T G I 0 DY09 G G A T G I G T G T G I 0 DY10 G G G T G I G G A T G D 0 DY11 G G G T G I G T G T G I 0 DY12 G T G T G I G T G T G I 0 E101 T G G T A I T G G C G I 0 E102 T G G T A I T G G T A I 0 E103 G G G T G I T G G T A I 0 E104 T G G T A I T G G C G I 0 E105 G G G T G I T G G C G I 0 E106 G G G T G I T G G C G I 0 E107 T G G C G I T G G C G I 0 E108 T G G T A I T G G C G I 0 E109 T G G C G I T G G C G I 0 E110 T G G T G I T G G T A I 0 E111 G G G T G I T G G T A I 0 E112 T G G T A I T G G C G I 0 E113 G G G T G I T G G C G I 0 E114 G G G T G I T G G C G I 0 E115 T G G T A I T G G C G I 0 E116 T G G T A I T G G C G I 0 E117 G G G T G I G G G T G I 0 E118 T G G T A I T G G C G I 0 E119 G G G T G I G G G T G I 0 E120 T G G T G I T G G T A I 0 E121 G G G T G I T G G C G I 0 E122 T G G T G I T G G C G I 0 H101 T G G T A I T G G T A I 0 H102 G G G T G I G G A T G D 0 H103 G G G T G I T G G T A I 0 H104 T G G T G I T G G C G I 0 H105 G G G T G I T G G T A I 0 H106 G G G T G I G G G T G I 0 H107 G G G T G I G G A T G D 0 H108 G G G T G I G G G T G I 0 H109 G G G T G I G G G T G I 0 H110 G G G T G I T G G T G I 0 H111 G T G T G I T G G T A I 0 H112 G G G T G I G G G T G I 0 H113 G G G T G I G G A T G D 0 H114 T G G T A I T G G T A I 0 H115 G G G T G I T G G C G I 0 H116 T G G T A I T G G C G I 0 H117 G G G T G I G G G T G I 0 H118 G G G T G I T G G T A I 0 H119 G G A T G I T G G T A I 0 H120 G [G] G T G I G G G T G I 0 H121 G G G T G I T G G T A I 0 H122 G G G T G I G G A T G D 0 X101 G T G T G I T G G T A I 0 X102 G G G T (A) I G G A T (G) D 0 X103 T G G T A I T G G T A I 0 X104 G G G T G I G G A T G D 0 X105 G G G T G I T G G T G I 0 X106 T G G T A I T G G T A I 0 X107 G G G T G I T G G C G I 0 X108 G G G T G I T G G C G I 0 X109 G G A T G D T G G C G I 0 X110 G G A T G D T G G C G I 0 X111 G [G] G T G I G G G T G I 0 X112 G G G T G I T G G C G I 0 X113 G G A T G D G G A T G D 0 X114 G G G T G I G G A T G D 0 X115 G G G T G I T G G T A I 0 X116 T G G T A I T G G T A I 0 X117 G G G T G I T G G C G I 0 X118 G G G T G I G G G T G I 0 X119 G G G T G I T G G T A I 0 X120 G G G T G I T G G T A I 0 X121 T G G T A I T G G C G I 0 X122 G G G T G I T G G T A I 0 X123 G G A T G D T G G T A I 0 X124 T G G T A I T G G T A 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 G ? = = ? ? T ? = = ? ? 0 D002 = ? = = ? ? = ? = = ? ? 0 D003 G = = T = = T = = C = = 0 D004 = = = = = I = = = = = D 0 D005 = ? = = = = = ? = = = = 0 D006 G = = = ? ? T = = = ? ? 0 D007 = = = = = = = = = = = = 0 D008 = = G = = = = = A = = = 0 D009 G = = = = = T = = = = = 0 D010 = G A = = D = T G = = I 0 D011 = = G = = I = = A = = D 0 D012 G T = = G = T G = = A = 0 D013 = ? = = = = = ? = = = = 0 D014 = G = = = = = T = = = = 0 D015 = = G = = I = = A = = D 0 DY01 = G A = = D = T G = = I 0 DY02 = G = = ? ? = T = = ? ? 0 DY03 = G = = = = = T = = = = 0 DY04 = G A = = D = T G = = I 0 DY05 = G = = = = = T = = = = 0 DY06 = = G = = I = = A = = D 0 DY07 G T = = = = T G = = = = 0 DY08 = G A = = D = T G = = I 0 DY09 = G A = = = = T G = = = 0 DY10 = = G = = I = = A = = D 0 DY11 = G = = = = = T = = = = 0 DY12 = = = = = = = = = = = = 0 E101 = = = T A = = = = C G = 0 E102 = = = = = = = = = = = = 0 E103 G = = = G = T = = = A = 0 E104 = = = T A = = = = C G = 0 E105 G = = T = = T = = C = = 0 E106 G = = T = = T = = C = = 0 E107 = = = = = = = = = = = = 0 E108 = = = T A = = = = C G = 0 E109 = = = = = = = = = = = = 0 E110 = = = = G = = = = = A = 0 E111 G = = = G = T = = = A = 0 E112 = = = T A = = = = C G = 0 E113 G = = T = = T = = C = = 0 E114 G = = T = = T = = C = = 0 E115 = = = T A = = = = C G = 0 E116 = = = T A = = = = C G = 0 E117 = = = = = = = = = = = = 0 E118 = = = T A = = = = C G = 0 E119 = = = = = = = = = = = = 0 E120 = = = = G = = = = = A = 0 E121 G = = T = = T = = C = = 0 E122 = = = T = = = = = C = = 0 H101 = = = = = = = = = = = = 0 H102 = = G = = I = = A = = D 0 H103 G = = = G = T = = = A = 0 H104 = = = T = = = = = C = = 0 H105 G = = = G = T = = = A = 0 H106 = = = = = = = = = = = = 0 H107 = = G = = I = = A = = D 0 H108 = = = = = = = = = = = = 0 H109 = = = = = = = = = = = = 0 H110 G = = = = = T = = = = = 0 H111 G T = = G = T G = = A = 0 H112 = = = = = = = = = = = = 0 H113 = = G = = I = = A = = D 0 H114 = = = = = = = = = = = = 0 H115 G = = T = = T = = C = = 0 H116 = = = T A = = = = C G = 0 H117 = = = = = = = = = = = = 0 H118 G = = = G = T = = = A = 0 H119 G = A = G = T = G = A = 0 H120 = ? = = = = = ? = = = = 0 H121 G = = = G = T = = = A = 0 H122 = = G = = I = = A = = D 0 X101 G T = = G = T G = = A = 0 X102 = = G = (A) I = = A = (G) D 0 X103 = = = = = = = = = = = = 0 X104 = = G = = I = = A = = D 0 X105 G = = = = = T = = = = = 0 X106 = = = = = = = = = = = = 0 X107 G = = T = = T = = C = = 0 X108 G = = T = = T = = C = = 0 X109 G = A T = D T = G C = I 0 X110 G = A T = D T = G C = I 0 X111 = ? = = = = = ? = = = = 0 X112 G = = T = = T = = C = = 0 X113 = = = = = = = = = = = = 0 X114 = = G = = I = = A = = D 0 X115 G = = = G = T = = = A = 0 X116 = = = = = = = = = = = = 0 X117 G = = T = = T = = C = = 0 X118 = = = = = = = = = = = = 0 X119 G = = = G = T = = = A = 0 X120 G = = = G = T = = = A = 0 X121 = = = T A = = = = C G = 0 X122 G = = = G = T = = = A = 0 X123 G = A = G D T = G = A I 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 = ? = = = = 1.00 = = = ? ? = = = = = = = = 1.00 = = = 1.00 = = = = = = 0.98 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = ? = = = = = 1.00 = = = = = = 1.00 = = 1.00 = 0.98 1.00 = = 1.00 = 1.00 = = ? ? = 1.00 = = = = = 0.98 1.00 = = 1.00 = 1.00 = = = = = = 1.00 = = 1.00 0.97 1.00 = = = = = 0.98 1.00 = = 1.00 = 0.97 1.00 = = = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = = = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 = = = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 = = 1.00 = = = = = 1.00 1.00 = = = = 1.00 1.00 = = = = = = = = = = 1.00 1.00 = = = = = = = = = = = 1.00 = 1.00 = = 1.00 = = = = = 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 = 0.98 = 1.00 = = ? = = = = 1.00 = = = 1.00 = = = 1.00 = = 1.00 1.00 0.99 = = 1.00 = = = 1.00 = 0.78 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = 1.00 = = 1.00 = = 1.00 = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = ? = = = = 1.00 = = 1.00 = = = = = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = = = 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