************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 foxc2.phase.inp foxc2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST foxc2.phase.out_freqs : haplotype frequency estimates foxc2.phase.out_pairs : most likely haplotype pairs for each individual foxc2.phase.out_recom : estimates of recombination parameters foxc2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 9 Positions of loci: 110 411 422 533 1437 1599 3650 3714 4381 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file foxc2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 IATGCGCGC 18.000000 2 IATGCGCGT 41.000000 3 IATGCGCAC 15.000000 4 IATGCGTGC 1.000000 5 IATGCTCGC 2.000000 6 IATGTGCGC 87.000000 7 IACGCGCAC 1.000000 8 IGCCCGCGC 5.000000 9 DATGCGCGC 1.000000 10 DGCCCGCGC 1.000000 11 DGCCCTCGC 1.000000 12 DGCCCTTGC 17.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (6,6) D002: (1,3) D003: (5,6) D004: (1,1) D005: (1,6) D006: (6,8) D007: (1,6) D008: (1,3) D009: (6,6) D010: (2,6) D011: (6,6) D012: (6,6) D013: (1,1) D014: (3,6) D015: (1,3) DY01: (3,8) DY02: (6,8) DY03: (1,2) DY04: (1,6) DY05: (6,6) DY06: (1,11) DY07: (6,8) DY08: (6,8) DY09: (1,2) DY10: (6,6) DY11: (6,6) DY12: (6,6) E101: (6,6) E102: (2,6) E103: (6,6) E104: (6,6) E105: (2,9) E106: (2,6) E107: (2,6) E108: (6,6) E109: (6,6) E110: (2,2) E111: (3,6) E112: (2,6) E113: (6,6) E114: (2,6) E115: (2,2) E116: (1,6) E117: (6,6) E118: (6,6) E119: (2,6) E120: (6,6) E121: (3,10) E122: (6,12) H101: (2,6) H102: (2,12) H103: (2,2) H104: (6,12) H105: (6,12) H106: (2,6) H107: (2,12) H108: (2,6) H109: (2,12) H110: (6,6) H111: (2,3) H112: (2,6) H113: (2,12) H114: (2,2) H115: (1,6) H116: (6,6) H117: (1,2) H118: (2,2) H119: (6,6) H120: (6,6) H121: (6,6) H122: (2,6) X101: (2,12) X102: (6,6) X103: (6,12) X104: (2,3) X105: (3,6) X106: (2,6) X107: (2,5) X108: (6,12) X109: (6,6) X110: (2,12) X111: (3,12) X112: (3,6) X113: (7,12) X114: (2,12) X115: (2,6) X116: (1,6) X117: (2,3) X118: (2,6) X119: (1,12) X120: (12,12) X121: (2,4) X122: (3,6) X123: (6,6) X124: (3,6) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 I A T G T G C G C I A T G [T] G C G C 0 D002 I A T G C G C G C I A T G C G C A C 0 D003 I A T G C T C G C I A T G T G C G C 0 D004 I A T G C G C G C I A T G C G C G C 0 D005 I A T G C G C G C I A T G T G C G C 0 D006 I A T G T G C G C I G C C C G C G C 0 D007 I A T G C G C G C I A T G T G C G C 0 D008 I A T G C G C G C I A T G C G C A C 0 D009 I A T G T G C G C I A T G [T] G C G C 0 D010 I A T G C G C G T I A T G T G C G C 0 D011 I A T G T G C G C I A T G [T] G C G C 0 D012 I A T G T G C G C I A T G T G C G C 0 D013 I A T G C G C G C I A T G C G C G C 0 D014 I A T G C G C A C I A T G [T] G C G C 0 D015 I A T G C G C G C I A T G C G C A C 0 DY01 I A T G C G C A C I G C C C G C G C 0 DY02 I A T G [T] G C G C I G C C C G C G C 0 DY03 I A T G C G C G C I A T G C G C G T 0 DY04 I A T G C G C G C I A T G T G C G C 0 DY05 I A T G T G C G C I A T G T G C G C 0 DY06 I A T G C (G) C G C D G C C C (T) C G C 0 DY07 I A T G T G C G C I G C C C G C G C 0 DY08 I A T G T G C G C I G C C C G C G C 0 DY09 I A T G C G C G C I A T G C G C G T 0 DY10 I A T G T G C G C I A T G [T] G C G C 0 DY11 I A T G T G C G C I A T G [T] G C G C 0 DY12 I A T G T G C G C I A T G [T] G C G C 0 E101 I A T G T G C G C I A T G T G C G C 0 E102 I A T G C G C G T I A T G T G C G C 0 E103 I A T G T G C G C I A T G T G C G C 0 E104 I A T G T G C G C I A T G T G C G C 0 E105 (I) A T G C G C G T (D) A T G C G C G C 0 E106 I A T G C G C G T I A T G [T] G C G C 0 E107 I A T G C G C G T I A T G T G C G C 0 E108 I A T G T G C G C I A T G T G C G C 0 E109 I A T G T G C G C I A T G T G C G C 0 E110 I A T G C G C G T I A T G C G C G T 0 E111 I A T G C G C A C I A T G T G C G C 0 E112 I A T G C G C G T I A T G T G C G C 0 E113 I A T G T G C G C I A T G T G C G C 0 E114 I A T G C G C G T I A T G [T] G C G C 0 E115 I A T G C G C G T I A T G C G C G T 0 E116 I A T G C G C G C I A T G T G C G C 0 E117 I A T G T G C G C I A T G T G C G C 0 E118 I A T G T G C G C I A T G T G C G C 0 E119 I A T G C G C G T I A T G T G C G C 0 E120 I A T G T G C G C I A T G T G C G C 0 E121 I A T G C G C (A) C D G C C C G C (G) C 0 E122 I A T G T G C G C D G C C C T T G C 0 H101 I A T G C G C G T I A T G T G C G C 0 H102 I A T G C G C G T D G C C C T T G C 0 H103 I A T G C G C G T I A T G C G C G T 0 H104 I A T G T G C G C D G C C C T T G C 0 H105 I A T G T G C G C D G C C C T T G C 0 H106 I A T G C G C G T I A T G T G C G C 0 H107 I A T G C G C G T D G C C C T T G C 0 H108 I A T G C G C G T I A T G [T] G C G C 0 H109 I A T G C G C G T D G C C C T T G C 0 H110 I A T G T G C G C I A T G T G C G C 0 H111 I A T G C G C G T I A T G C G C A C 0 H112 I A T G C G C G T I A T G T G C G C 0 H113 I A T G C G C G T D G C C C T T G C 0 H114 I A T G C G C G T I A T G C G C G T 0 H115 I A T G C G C G C I A T G T G C G C 0 H116 I A T G T G C G C I A T G [T] G C G C 0 H117 I A T G C G C G C I A T G C G C G T 0 H118 I A T G C G C G T I A T G C G C G T 0 H119 I A T G T G C G C I A T G T G C G C 0 H120 I A T G T G C G C I A T G T G C G C 0 H121 I A T G T G C G C I A T G T G C G C 0 H122 I A T G C G C G T I A T G T G C G C 0 X101 I A T G C G C G T D G C C C T T G C 0 X102 I A T G T G C G C I A T G [T] G C G C 0 X103 I A T G T G C G C D G C C C T T G C 0 X104 I A T G C G C G T I A T G C G C A C 0 X105 I A T G C G C A C I A T G T G C G C 0 X106 I A T G C G C G T I A T G T G C G C 0 X107 I A T G C G C G T I A T G C T C G C 0 X108 I A T G T G C G C D G C C C T T G C 0 X109 I A T G T G C G C I A T G T G C G C 0 X110 I A T G C G C G T D G C C C T T G C 0 X111 I A T G C G C A C D G C C C T T G C 0 X112 I A T G C G C A C I A T G T G C G C 0 X113 I A C G C G C A C D G C C C T T G C 0 X114 I A T G C G C G T D G C C C T T G C 0 X115 I A T G C G C G T I A T G T G C G C 0 X116 I A T G C G C G C I A T G T G C G C 0 X117 I A T G C G C G T I A T G C G C A C 0 X118 I A T G C G C G T I A T G [T] G C G C 0 X119 I A T G C G C G C D G C C C T T G C 0 X120 D G C C C T T G C D G C C C T T G C 0 X121 I A T G C G (C) G T I A T G C G (T) G C 0 X122 I A T G C G C A C I A T G T G C G C 0 X123 I A T G T G C G C I A T G T G C G C 0 X124 I A T G C G C A C I A T G T G C G C 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 = = = ? = = = G = = = = ? = = = A = 0 D003 = = = = C T = = = = = = = T G = = = 0 D004 = = = ? = = = = = = = = ? = = = = = 0 D005 = = = = C = = = = = = = = T = = = = 0 D006 = A T G T = = = = = G C C C = = = = 0 D007 = = = ? C = = = = = = = ? T = = = = 0 D008 = = = ? = = = G = = = = ? = = = A = 0 D009 = = = = ? ? = = = = = = = ? ? = = = 0 D010 = = = = C = = = T = = = = T = = = C 0 D011 = = = = ? ? = = = = = = = ? ? = = = 0 D012 = = = = = = = = = = = = = = = = = = 0 D013 = = = = = = = = = = = = = = = = = = 0 D014 = = = = ? ? = A = = = = = ? ? = G = 0 D015 = = = = = = = G = = = = = = = = A = 0 DY01 = A T G = = = A = = G C C = = = G = 0 DY02 = A T G ? ? = = = = G C C ? ? = = = 0 DY03 = = = = = = = = C = = = = = = = = T 0 DY04 = = = = C = = = = = = = = T = = = = 0 DY05 = = = = = = = = = = = = = = = = = = 0 DY06 I A T G = (G) = = = D G C C = (T) = = = 0 DY07 = A T G T = = = = = G C C C = = = = 0 DY08 = A T G T = = = = = G C C C = = = = 0 DY09 = = = = = = = = C = = = = = = = = T 0 DY10 = = = = ? ? = = = = = = = ? ? = = = 0 DY11 = = = = ? = = = = = = = = ? = = = = 0 DY12 = = = = ? ? = = = = = = = ? ? = = = 0 E101 = = = = = = = = = = = = = = = = = = 0 E102 = = = = C = = = T = = = = T = = = C 0 E103 = = = = = = = = = = = = = = = = = = 0 E104 ? = = = = = = = = ? = = = = = = = = 0 E105 (I) = = = = = = = T (D) = = = = = = = C 0 E106 = = = = ? ? = = T = = = = ? ? = = C 0 E107 = = = = C = = = T = = = = T = = = C 0 E108 = = = = = = = = = = = = = = = = = = 0 E109 = = = = = = = = = = = = = = = = = = 0 E110 = = = = = = = = = = = = = = = = = = 0 E111 = = = = C = = A = = = = = T = = G = 0 E112 = = = = C = = = T = = = = T = = = C 0 E113 = = = = = = = = = = = = = = = = = = 0 E114 = = = = ? = = = T = = = = ? = = = C 0 E115 = = = = = = = = = = = = = = = = = = 0 E116 = = = = C = = = = = = = = T = = = = 0 E117 = = = = = = = = = = = = = = = = = = 0 E118 = = = = = = = = = = = = = = = = = = 0 E119 = = = = C = = = T = = = = T = = = C 0 E120 = = = = = = = = = = = = = = = = = = 0 E121 I A T G = = = (A) = D G C C = = = (G) = 0 E122 I A T G T G C = = D G C C C T T = = 0 H101 = = = = C = = = T = = = = T = = = C 0 H102 I A T G = G C = T D G C C = T T = C 0 H103 = = = = = = = = = = = = = = = = = = 0 H104 I A T G T G C = = D G C C C T T = = 0 H105 I A T G T G C = = D G C C C T T = = 0 H106 = = = = C = = = T = = = = T = = = C 0 H107 I A T ? = G C = T D G C ? = T T = C 0 H108 = = = = ? ? = = T = = = = ? ? = = C 0 H109 I A T G = G C = T D G C C = T T = C 0 H110 = = = = = = = = = = = = = = = = = = 0 H111 = = = = = = = G T = = = = = = = A C 0 H112 = = = = C = = = T = = = = T = = = C 0 H113 I A T G = G C = T D G C C = T T = C 0 H114 = = = = = = = = = = = = = = = = = = 0 H115 = = = = C = = = = = = = = T = = = = 0 H116 = = = = ? ? = = = = = = = ? ? = = = 0 H117 = = = = = = = = C = = = = = = = = T 0 H118 = = = = = = = = = = = = = = = = = = 0 H119 = = = = = = = = = = = = = = = = = = 0 H120 = = = = = = = = = = = = = = = = = = 0 H121 = = = = = = = = = = = = = = = = = = 0 H122 = = = = C = = = T = = = = T = = = C 0 X101 I A T G = G C = T D G C C = T T = C 0 X102 = = = = ? ? = = = = = = = ? ? = = = 0 X103 I A T G T G C = = D G C C C T T = = 0 X104 = = = = = = = G T = = = = = = = A C 0 X105 = = = = C = = A = = = = = T = = G = 0 X106 = = = = C = = = T = = = = T = = = C 0 X107 = = = = = G = = T = = = = = T = = C 0 X108 I A T G T G C = = D G C C C T T = = 0 X109 = = = = = = = = = = = = = = = = = = 0 X110 I A T G ? ? C = T D G C C ? ? T = C 0 X111 I A T G = G C A = D G C C = T T G = 0 X112 = = = = C = = A = = = = = T = = G = 0 X113 I A = G = G C A = D G = C = T T G = 0 X114 I A T G = G C = T D G C C = T T = C 0 X115 = = = = C = = = T = = = = T = = = C 0 X116 = = = = C = = = = = = = = T = = = = 0 X117 = = = = = = = G T = = = = = = = A C 0 X118 = = = = ? ? = = T = = = = ? ? = = C 0 X119 I A T G = G C = = D G C C = T T = = 0 X120 = = = = = = = = = = = = = = = = = = 0 X121 = = = = = = (C) = T = = = = = = (T) = C 0 X122 = = = = C = = A = = = = = T = = G = 0 X123 = = = = = = = = = = = = = = = = = = 0 X124 = = = = C = = A = = = = = T = = G = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = ? ? ? = = = = = = ? = = = 1.00 = = = = = 0.98 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 1.00 1.00 = 0.57 = = = = 1.00 1.00 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = 1.00 = = = = ? ? = = = = = = = ? = = = = = = = = ? ? = = = = = = = = = = = = = = = = 0.99 = = = 1.00 = = = = = = = = = ? = = = = = = = = 0.50 = = = = = = = 1.00 = = = = ? ? = = 1.00 = = = = 0.99 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = 1.00 = = = = = 0.99 = = = 1.00 = = = = = = = = = = = = = ? = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = 1.00 = = = = = = = = = 0.94 1.00 1.00 1.00 = = = 0.79 = 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 = = = = = = 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 = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = 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 = = = = 0.99 = = 1.00 = = = = = 0.99 = = = 1.00 = = = = = 0.98 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = 1.00 1.00 1.00 1.00 ? ? 1.00 = 0.98 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 = 0.99 = = = = 0.99 = = = 1.00 = = = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = = ? ? = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = 0.74 = 1.00 = = = = 0.99 = = 1.00 = = = = = = = = = = = = = = 0.99 = = 1.00 = END PHASEPROBS