************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 foxc1.phase.inp foxc1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST foxc1.phase.out_freqs : haplotype frequency estimates foxc1.phase.out_pairs : most likely haplotype pairs for each individual foxc1.phase.out_recom : estimates of recombination parameters foxc1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 10 Positions of loci: 163 1011 3145 4858 5015 5697 6117 6795 6835 6990 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file foxc1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGDTGGGCTI 6.000000 2 CGDTGGGCCI 2.000000 3 CGDTGGGTTI 15.000000 4 CGDTGGGTCI 1.000000 5 CGDTGTGTTI 5.000000 6 CGDTGTGTCI 4.000000 7 CGDTAGGTCD 3.000000 8 CGDTATGTCD 16.000000 9 CGDAATGTCD 31.000000 10 CGITGGGCTI 1.000000 11 CGITGGGCCI 8.000000 12 CGITGGGTTI 5.000000 13 CGITGGGTCI 6.000000 14 CGITGGATCI 1.000000 15 CGITAGGCTI 1.000000 16 CGIAATGTCD 1.000000 17 CTDTGGGCTI 3.000000 18 CTDTGGGCCI 12.000000 19 CTDTGGGTCI 3.000000 20 CTDTGGGTCD 1.000000 21 CTDTGGACCI 1.000000 22 CTDTGTGTCI 2.000000 23 CTDAATGTCD 3.000000 24 CTITGGGTCI 32.000000 25 CTITGGGTCD 2.000000 26 CTITGGATTI 8.000000 27 CTIAATGTCD 3.000000 28 ATDTGTGTCI 14.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (3,18) D003: (3,6) D004: (3,19) D005: (17,17) D006: (4,8) D007: (8,8) D008: (3,22) D009: (8,28) D010: (3,8) D011: (3,17) D012: (6,18) D013: (8,28) D014: (9,28) D015: (8,28) DY01: (8,18) DY02: (1,11) DY03: (5,6) DY04: (8,15) DY05: (3,3) DY06: (1,8) DY07: (5,10) DY08: (5,18) DY09: (8,28) DY10: (28,28) DY11: (5,6) DY12: (1,5) E101: (8,18) E102: (18,18) E103: (3,27) E104: (7,26) E105: (9,24) E106: (9,26) E107: (3,9) E108: (9,24) E109: (3,26) E110: (9,12) E111: (9,28) E112: (3,9) E113: (9,13) E114: (7,24) E115: (8,9) E116: (8,18) E117: (9,23) E118: (9,21) E119: (20,26) E120: (9,23) E121: (9,11) E122: (7,24) H101: (24,24) H102: (9,26) H103: (9,24) H104: (8,26) H105: (12,24) H106: (13,13) H107: (13,25) H108: (3,8) H109: (9,13) H110: (9,13) H111: (9,12) H112: (14,26) H113: (3,25) H114: (1,24) H115: (9,28) H116: (9,18) H117: (3,9) H118: (9,28) H119: (12,24) H120: (9,12) H121: (9,23) H122: (19,26) X101: (9,24) X102: (18,24) X103: (22,24) X104: (24,28) X105: (11,27) X106: (16,27) X107: (11,28) X108: (11,24) X109: (11,18) X110: (11,2) X111: (9,9) X112: (24,24) X113: (24,24) X114: (11,24) X115: (18,24) X116: (9,24) X117: (28,28) X118: (24,24) X119: (24,24) X120: (9,19) X121: (24,24) X122: (2,9) X123: (24,24) X124: (24,24) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C G [D] T G G G C T I C G D T G G G C T I 0 D002 C G D T G G G (T) T I C T D T G G G (C) C I 0 D003 C G D T G (G) G T T I C G D T G (T) G T C I 0 D004 C G D T G G G T T I C T D T G G G T C I 0 D005 C T D T G G G C T I C T D T G G G C T I 0 D006 C G D T G (G) G T C I C G D T A (T) G T C D 0 D007 C G D T A T G T C D C G D T A T G T C D 0 D008 C G D T G (G) G T T I C T D T G (T) G T C I 0 D009 C G D T A T G T C D A T D T G T G T C I 0 D010 C G D T G G G T T I C G D T A T G T C D 0 D011 C (G) D T G G G T T I C (T) D T G G G C T I 0 D012 C (G) D T G T G T C I C (T) D T G G G C C I 0 D013 C G D T A T G T C D A T D T G T G T C I 0 D014 C G D A A T G T C D A T D T G T G T C I 0 D015 C G D T A T G T C D [A] T D T G T G T C I 0 DY01 C G D T A T G T C D C T D T G G G C C I 0 DY02 C G (D) T G G G C T I C G (I) T G G G C C I 0 DY03 C G D T G T G T T I C G D T G T G T C I 0 DY04 C G (D) T A T G T C D C G (I) T A G G C T I 0 DY05 C G D T G G G T T I C G D T G G G T T I 0 DY06 C G D T G G G C T I C G D T A T G T C D 0 DY07 C G (D) T G T G (T) T I C G (I) T G G G (C) T I 0 DY08 C (G) D T G T G T (T) I C (T) D T G G G C (C) I 0 DY09 C G D T A T G T C D A T D T G T G T C I 0 DY10 A T D T G T G T C I A T D T G T G T C I 0 DY11 C G D T G T G T T I C G D T G T G T C I 0 DY12 C G D T G (G) G C T I C G D T G (T) G T T I 0 E101 C G D T A T G T C D C T D T G G G [C] [C] I 0 E102 C T D T G G G C C I C T D T G G G C C I 0 E103 C (G) (D) T G G G [T] T I C (T) (I) A A T G T C D 0 E104 C G D T A G G T C D C T I T G G A T T I 0 E105 C G D A A T G T C D C T I T G G G [T] C I 0 E106 C G D A A T G T C D C T I T G G A T T I 0 E107 C G D T G G G T T I C G D A A T G T C D 0 E108 C G D A A T G T C D C T I T G G G T C I 0 E109 C G D T G G G T T I C T I T G G [A] T T I 0 E110 C G (D) A A T G T C D C G (I) T G G G T T I 0 E111 C G D A A T G T C D A T D T G T G T C I 0 E112 C G D T G G G T T I C G D A A T G T C D 0 E113 C G D A A T G T C D C G I T G G G T C I 0 E114 C G D T A G G T C D C T I T G G G T C I 0 E115 C G D T A T G T C D C G D A A T G T C D 0 E116 C G D T A T G T C D C T D T G G G C C I 0 E117 C G D A A T G T C D C T D A A T G T C D 0 E118 C G D A A T (G) T C D C T D T G G (A) C C I 0 E119 C T (D) T G G G T C D C T (I) T G G A T T I 0 E120 C G D A A T G T C D C T D A A T G T C D 0 E121 C G D A A T G T C D C G I T G G G C C I 0 E122 C G D T A G G T C D C T I T G G G T C I 0 H101 C T I T G G G T C I C T I T G G G T C I 0 H102 C G D A A T G T C D C T I T G G A T T I 0 H103 C G D A A T G T C D C T I T G G G T C I 0 H104 C G D T A T G T C D C T I T G G A T T I 0 H105 C G I T G G G T T I C T I T G G G T C I 0 H106 C G I T G G G T C I C G I T G G G T C I 0 H107 C (G) I T G G G T C I C (T) I T G G G T C D 0 H108 C G D T G G G T T I C G D T A [T] G T C D 0 H109 C G D A A T G T C D C G I T G G G T C I 0 H110 C G D A A T G T C D C G I T G G G T C I 0 H111 C G (D) A A T G T C D C G (I) T G G G T T I 0 H112 C (G) I T G G A T C I C (T) I T G G A T T I 0 H113 C G (D) T G G G T T I C T (I) T G G G T C D 0 H114 C (G) D T G G G C (T) I C (T) I T G G G T (C) I 0 H115 C G D A A T G T C D [A] T D T G T G T C I 0 H116 C G D A A T G T C D C T D T G G G C C I 0 H117 C G D T G G G T T I C G D A A T G T C D 0 H118 C G D A A T G T C D A T D T G T G T C I 0 H119 C G I T G G G T T I C T I T G G G T C I 0 H120 C G (D) A A T G T C D C G (I) T G G G T T I 0 H121 C G D A A T G T C D C T D A A T G T C D 0 H122 C T (D) T G [G] G T C I C T (I) T G G A T T I 0 X101 C G D A A T G T C D C T [I] T G G G T C I 0 X102 C T D T G G G C C I C T [I] T G G G T C I 0 X103 C T D T G T G T C I C T [I] T G G G T C I 0 X104 C T I T G G G T C I [A] T D T G T G T C I 0 X105 C (G) I T G G G C C I C (T) I A A T G T C D 0 X106 C G I A A T G T C D C T I A A T G T C D 0 X107 C G I T G G G C C I A T D T G T G T C I 0 X108 C (G) [I] T G G G C C I C (T) [I] T G G G T C I 0 X109 C G [I] T G G G C C I C [T] D T G G G C C I 0 X110 C G [I] T G G G C C I C G [D] T G G G C C I 0 X111 C G D A A T G T C D C G D A A T G T C D 0 X112 C T I T G G G T C I C T I T G G G T C I 0 X113 C T I T G G G T C I C [T] I T G G G T C I 0 X114 C G I T G G G C C I C T I T G G G T C I 0 X115 C [T] [D] T G G G C C I C [T] [I] T G G G T C I 0 X116 C G D A A T G T C D C [T] [I] T G G G T C I 0 X117 A T D T G T G T C I A T D T G T G T C I 0 X118 C T I T G G G T C I C T [I] T G G G T C I 0 X119 C T I T G G G T C I C T [I] T G G G T C I 0 X120 C G D A A T G T C D C T D T G G G T C I 0 X121 C T I T G G G T C I C T [I] T G G G T C I 0 X122 C G D T G G G C C I C G D A A T G T C D 0 X123 C T I T G G G T C I C T [I] T G G G T C I 0 X124 C T I T G G G T C I C T [I] T G G G T 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 = G = = = = = (T) T = = T = = = = = (C) C = 0 D003 = = = = = (G) ? = T = = = = = = (T) ? = C = 0 D004 = G = = = = ? = T = = T = = = = ? = C = 0 D005 = = = = = = = = = = = = = = = = = = = = 0 D006 = = = = G (G) = = = ? = = = = A (T) = = = ? 0 D007 = = = = = = = = = = = = = = = = = = = = 0 D008 = G = = = (G) = = T = = T = = = (T) = = C = 0 D009 C G = = A = = = = D A T = = G = = = = I 0 D010 = = = = G G = = T I = = = = A T = = C D 0 D011 ? (G) = = = = = T = = ? (T) = = = = = C = = 0 D012 = (G) = = = T ? T = = = (T) = = = G ? C = = 0 D013 C G = = A = = = = D A T = = G = = = = I 0 D014 C G = A A = = = = D A T = T G = = = = I 0 D015 ? G = = A = = = = D ? T = = G = = = = I 0 DY01 = G = = A T = T = D = T = = G G = C = I 0 DY02 ? = (D) = = = = = T = ? = (I) = = = = = C = 0 DY03 ? = = = = = = = T = ? = = = = = = = C = 0 DY04 = = (D) = = T = T C D = = (I) = = G = C T I 0 DY05 = = = = = = ? = = = = = = = = = ? = = = 0 DY06 = = = = G G = C T I = = = = A T = T C D 0 DY07 = = (D) = = T ? (T) = = = = (I) = = G ? (C) = = 0 DY08 = (G) = = = T = T (T) = = (T) = = = G = C (C) = 0 DY09 C G = = A = = = = D A T = = G = = = = I 0 DY10 = = = = = = = = = = = = = = = = = = = = 0 DY11 = = = = = = ? = T = = = = = = = ? = C = 0 DY12 = = = = = (G) = C = = = = = = = (T) = T = = 0 E101 = G = = A T = ? ? D = T = = G G = ? ? I 0 E102 = = = = = ? = = = = = = = = = ? = = = = 0 E103 ? (G) (D) T G G = ? T I ? (T) (I) A A T = ? C D 0 E104 = G D = A = G ? C D = T I = G = A ? T I 0 E105 = G D A A T = ? = D = T I T G G = ? = I 0 E106 ? G D A A T G = C D ? T I T G G A = T I 0 E107 = = = T G G = = T I = = = A A T = = C D 0 E108 = G D A A T = = = D = T I T G G = = = I 0 E109 ? G D = = = ? = = = ? T I = = = ? = = = 0 E110 = = (D) A A T = = C D = = (I) T G G = = T I 0 E111 C G = A A = = = = D A T = T G = = = = I 0 E112 = = = T G G = = T I = = = A A T = = C D 0 E113 = = D A A T = = = D = = I T G G = = = I 0 E114 = G D = A = = = = D = T I = G = = = = I 0 E115 = = = T = = = = = = = = = A = = = = = = 0 E116 ? G = = A T = T = D ? T = = G G = C = I 0 E117 = G = = = ? ? = = = = T = = = ? ? = = = 0 E118 = G = A A T (G) T = D = T = T G G (A) C = I 0 E119 = = (D) = = = G = C D = = (I) = = = A = T I 0 E120 = G = = = = = = = = = T = = = = = = = = 0 E121 = = D A A T = T = D = = I T G G = C = I 0 E122 = G D = A = = = = D = T I = G = = = = I 0 H101 = = = = = = = = = = = = = = = = = = = = 0 H102 = G D A A T G = C D = T I T G G A = T I 0 H103 ? G D A A T ? = = D ? T I T G G ? = = I 0 H104 = G D = A T G = C D = T I = G G A = T I 0 H105 = G = = = = = = T = = T = = = = = = C = 0 H106 = = = = = = = = = = = = = = = = = = = = 0 H107 = (G) = = = = = = = I = (T) = = = = = = = D 0 H108 = = = = G ? = = T I = = = = A ? = = C D 0 H109 = = D A A T = = = D = = I T G G = = = I 0 H110 = = D A A T = = = ? = = I T G G = = = ? 0 H111 = = (D) A A T = = C D = = (I) T G G = = T I 0 H112 ? (G) = = = = = = C = ? (T) = = = = = = T = 0 H113 = G (D) = = = = = T I = T (I) = = = = = C D 0 H114 ? (G) D = = = = C (T) = ? (T) I = = = = T (C) = 0 H115 ? G = A A = = = = D ? T = T G = = = = I 0 H116 = G = A A T = T = D = T = T G G = C = I 0 H117 = = = T G G = = T I = = = A A T = = C D 0 H118 C G = A A = = = = D A T = T G = = = = I 0 H119 = G = = = = = = T = = T = = = = = = C = 0 H120 = = (D) A A T = = C D = = (I) T G G = = T I 0 H121 = G = = = = = = = = = T = = = = = = = = 0 H122 = = (D) = = ? G = C = = = (I) = = ? A = T = 0 X101 = G ? A A T = = = D = T ? T G G = = = I 0 X102 ? = ? = = = = C = = ? = ? = = = = T = = 0 X103 = = ? = = T = = = = = = ? = = G = = = = 0 X104 ? = I = = G = = = = ? = D = = T = = = = 0 X105 ? (G) = T G G = C = I ? (T) = A A T = T = D 0 X106 = G = = = = = = = = = T = = = = = = = = 0 X107 C G I = = G = C = = A T D = = T = T = = 0 X108 = (G) ? = = = = C = = = (T) ? = = = = T = = 0 X109 = ? ? = = = = = = = = ? ? = = = = = = = 0 X110 = = ? = = = = = = = = = ? = = = = = = = 0 X111 = = = = = = = = = = = = = = = = = = = = 0 X112 = = = = = = = = = = = = = = = = = = = = 0 X113 ? ? = = = = ? = = = ? ? = = = = ? = = = 0 X114 ? G = = = = = C = = ? T = = = = = T = = 0 X115 = ? ? = = = = C = = = ? ? = = = = T = = 0 X116 = ? ? A A T = = = D = ? ? T G G = = = I 0 X117 = ? ? = = = = = = = = ? ? = = = = = = = 0 X118 = = ? = = = = = = ? = = ? = = = = = = ? 0 X119 = = ? = = = = = = = = = ? = = = = = = = 0 X120 = G = A A T = = = D = T = T G G = = = I 0 X121 = = ? = = = ? = = = = = ? = = = ? = = = 0 X122 ? = = T G G = C = I ? = = A A T = T = D 0 X123 ? = ? = = = = = = = ? = ? = = = = = = = 0 X124 = = ? = = = = = = = = = ? = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = ? = = = = = = = = 0.98 = = = = = 0.80 0.94 = = = = = = 0.80 ? = 1.00 = = 0.93 = = = = ? = 1.00 = = = = = = = = = = = = = = = 0.98 0.66 = = = ? = = = = = = = = = = = 0.95 = = = 0.58 = = 0.99 = 1.00 1.00 = = 1.00 = = = = 1.00 = = = = 1.00 0.91 = = 1.00 1.00 ? 0.89 = = = = = 1.00 = = = 0.79 = = = 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 = 0.99 = = 1.00 1.00 = 1.00 = 1.00 ? = 0.88 = = = = = 1.00 = ? = = = = = = = 1.00 = = = 0.81 = = 0.92 = 0.99 0.99 1.00 = = = = = = ? = = = = = = = 1.00 0.97 = 1.00 1.00 1.00 = = 0.84 = = 0.99 ? 0.80 = = = 0.78 = = = 0.99 = 0.96 0.58 = 1.00 1.00 = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = ? = 1.00 = = = = = = 0.86 = 1.00 = = = 0.96 = = 1.00 0.95 = ? ? 1.00 = = = = = ? = = = = ? 0.68 0.51 1.00 1.00 1.00 = ? 0.99 1.00 = 0.99 0.99 = 1.00 = 1.00 ? 1.00 1.00 = 0.91 0.94 1.00 1.00 1.00 = ? = 1.00 ? 0.98 0.98 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 = 0.95 0.97 1.00 1.00 1.00 = = = 1.00 ? 0.95 0.96 = = = ? = = = = = 0.80 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 = = 0.96 1.00 1.00 1.00 = = = 1.00 = 0.99 0.99 = 1.00 = = = = 1.00 = = = 1.00 = = = = = = ? 0.98 = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = ? ? = = = = 0.92 = 1.00 1.00 1.00 0.52 1.00 = 1.00 = = 0.76 = = = 0.99 = 1.00 0.95 = 1.00 = = = = = = = = = = 0.94 1.00 1.00 1.00 = 1.00 = 1.00 = 0.98 0.99 = 1.00 = = = = 1.00 = = = = = = = = = = = 0.98 0.98 1.00 1.00 1.00 0.99 = 1.00 1.00 ? 0.95 0.97 1.00 1.00 1.00 ? = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 0.96 = = = = = = 1.00 = = = = = = = = = = = = 0.51 = = = = = = = 1.00 = = = = 1.00 ? = = 1.00 1.00 = = 0.96 1.00 1.00 1.00 = = = 1.00 = = 0.96 1.00 1.00 1.00 = = = ? = = 0.80 1.00 1.00 1.00 = = 1.00 1.00 ? 0.80 = = = = = = 1.00 = = 0.94 0.69 = = = = = 1.00 0.96 ? 0.68 0.97 = = = = 0.91 0.78 = ? 0.95 = 1.00 1.00 = = = = 1.00 = 0.93 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 = 0.95 = = = = = = 1.00 = = = 0.80 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = 0.85 = = ? 1.00 = 1.00 = = 0.94 ? 1.00 1.00 1.00 = = = 1.00 ? = ? = = = = 0.98 = = = = ? = = 0.97 = = = = ? = 1.00 = = 0.99 = = = = ? 0.80 = 1.00 1.00 1.00 = 0.99 = 1.00 = 1.00 = = = = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 = = = 0.76 ? = = = = 1.00 = = = ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = ? = = = ? 0.95 = = = = = 1.00 = = = ? ? = = = = 0.93 = = = ? ? 1.00 1.00 1.00 = = = 1.00 = ? ? = = = = = = = = = ? = = = = = = ? = = ? = = = = = = = = 0.91 = 1.00 1.00 1.00 = = = 1.00 = = ? = = = ? = = = ? = = 1.00 1.00 1.00 = 1.00 = 1.00 ? = ? = = = = = = = = = ? = = = = = = = END PHASEPROBS