************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 gpr81.phase.inp gpr81.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST gpr81.phase.out_freqs : haplotype frequency estimates gpr81.phase.out_pairs : most likely haplotype pairs for each individual gpr81.phase.out_recom : estimates of recombination parameters gpr81.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 12 Positions of loci: 866 1273 1280 4390 4894 5007 5022 5729 5803 7835 7971 7981 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file gpr81.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GIACCACTGAGA 1.000000 2 GIACCCCCGAGG 20.000000 3 GIATCAGTGAGG 2.000000 4 GIATTAGTGAGG 1.000000 5 GIATTAGTGTAG 1.000000 6 GIATTAGCGTAG 3.000000 7 GIGCCAGTGAGA 1.000000 8 GIGCCCCCGAGG 2.000000 9 GIGTCAGTGAGG 3.000000 10 GIGTCAGCGAGG 1.000000 11 GIGTCCCTGTAG 2.000000 12 GIGTTAGTGAGG 5.000000 13 GIGTTAGTAAGG 16.000000 14 GIGTTAGTATAG 1.000000 15 GIGTTAGCGAGG 1.000000 16 GDACCACTGAGA 9.000000 17 GDACCAGTGAGA 1.000000 18 GDACCCCCGAGG 1.000000 19 GDATTAGTGAGG 2.000000 20 GDATTAGTAAGG 1.000000 21 AIATCACTGTAG 1.000000 22 AIATCACCGTAG 1.000000 23 AIATCCCTGTAG 2.000000 24 AIATCCGTGTAG 2.000000 25 AIATTAGTGTGG 1.000000 26 AIATTAGTGTAG 2.000000 27 AIATTAGTATAG 10.000000 28 AIGTTAGTATAG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (12,16) DY02: (16,26) DY03: (27,27) DY04: (2,10) DY05: (3,21) DY06: (13,13) DY07: (14,16) DY08: (16,16) DY09: (1,4) DY10: (17,27) DY11: (13,27) DY12: (27,28) DY13: (2,24) DY14: (12,27) DY15: (25,27) DY16: (7,27) DY17: (12,16) DY18: (18,27) DY19: (13,13) DY20: (2,24) DY21: (2,26) DY22: (16,27) DY23: (3,16) DY24: (13,16) E101: (2,15) E102: (13,20) E103: (13,13) E104: (6,5) E105: (2,2) E106: (2,2) E107: (2,6) E108: (2,19) E109: (2,13) E110: (2,12) E111: (2,9) E112: (6,8) E113: (2,23) E114: (2,11) E115: (8,9) E116: (13,13) E117: (2,19) E118: (2,22) E119: (2,12) E120: (13,13) E121: (2,9) E122: (11,23) E123: (13,13) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G I G T [T] A G T G A G G G D A C C A C T G A G A 0 DY02 G D A C C A C T G A G A A I A T T A G T G T A G 0 DY03 A I A T T A G T A T A G A I A T T A G T A T A G 0 DY04 G I (A) C C C C C G A G G G I (G) T C A G C G A G G 0 DY05 (G) I A T C A G T G A G G (A) I A T C A C T G T A G 0 DY06 G I G T T A G T A A G G G I G T T A G T A A G G 0 DY07 G I G T T A G T A T A G G D A C C A C T G A G A 0 DY08 G D A C C A C T G A G A G D A C C A C T G A G A 0 DY09 G I A C C A C T G A G A G I A T T A G T G A G G 0 DY10 (G) (D) A C C A G T G A G A (A) (I) A T T A G T A T A G 0 DY11 G I G T T A G T A A G G A I A T T A G T A T A G 0 DY12 A I A T T A G T A T A G A I G T T A G T A T A G 0 DY13 G I A C C C C C G A G G A I A T C C G T G T A G 0 DY14 G I G T T A G T (G) A G G A I A T T A G T (A) T A G 0 DY15 A I A T T A G T (G) T G G A I A T T A G T (A) T A G 0 DY16 (G) I (G) C C A G T G A G A (A) I (A) T T A G T A T A G 0 DY17 G I G T T A G T G A G G G D A C C A C T G A G A 0 DY18 G (D) A C C C C C G A G G A (I) A T T A G T A T A G 0 DY19 G I G T T A G T A A G G G I G T T A G T A A G G 0 DY20 G I A C C C C C G A G G A I A T C C G T G T A G 0 DY21 G I A C C C C C G A G G A I A T T A G T G T A G 0 DY22 G [D] A C C A C T G A G A [A] I A T T A G T A T A G 0 DY23 G I A T C A G T G A G G G D A C C A C T G A G A 0 DY24 G I G T T A G T A A G G G D A C C A C T G A G A 0 E101 G I (A) C C C C C G A G G G I (G) T T A G C G A G G 0 E102 G I G T T A G T A A G G G D A T T A G T A A G G 0 E103 G I G T T A G T A A G G G I G T T A G T A A G G 0 E104 G I A T T A G [C] G T A G G I A T [T] A [G] [T] [G] T A G 0 E105 G I A C C C C C G A G G G I A C C C C C G A G G 0 E106 G I A C C C C C G A G G G I A C C C C C G A G G 0 E107 G I A C C C C C G A G G G I A T T A G C G T A G 0 E108 G (I) A C C C C C G A G G G (D) A T T A G T G A G G 0 E109 G I A C C C C C G A G G G I G T T A G T [A] A G G 0 E110 G I A C C C C C G A G G G I G T T A G T G A G G 0 E111 G I (A) C C C C C G A G G G I (G) T C A G T G A G G 0 E112 G I (A) T T A G C G T A G G I (G) C C C C C G A G G 0 E113 G I A C C C C C G A G G A I A T C C C T G T A G 0 E114 G I A C C C C C G A G G G I G T C C C T G T A G 0 E115 G I G C C C C C G A G G G I G T C A G T G A G G 0 E116 G I G T T A G T A A G G G I G T T A G T A A G G 0 E117 G (I) A C C C C C G A G G G (D) A T T A G T G A G G 0 E118 G I A C C C C C G A G G A I A T C A C C G T A G 0 E119 G I A C C C C C G A G G G I G T T A G T G A G G 0 E120 G I G T T A G T A A G G G I G T T A G T A A G G 0 E121 G I (A) C C C C C G A G G G I (G) T C A G T G A G G 0 E122 G I G T C C C T G T A G A I A T C C C T G T A G 0 E123 G I G T T A G T A A G G G I G T T A G T A A G G 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 DY01 = I G T ? ? ? = = = = G = D A C ? ? ? = = = = A 0 DY02 G D = C C = C = = A G A A I = T T = G = = T A G 0 DY03 = = = = = = = = = = = = = = = = = = = = = = = = 0 DY04 = = (A) C = C C = = = = = = = (G) T = A G = = = = = 0 DY05 (G) = = = = = G = = A G = (A) = = = = = C = = T A = 0 DY06 = = = = ? = = = = = = = = = = = ? = = = = = = = 0 DY07 = I G T T = G = A T A G = D A C C = C = G A G A 0 DY08 = = = = = = = = = = = = = = = = = = = = = = = = 0 DY09 = = = C C = C = = = = A = = = T T = G = = = = G 0 DY10 (G) (D) = C C = = = G A G A (A) (I) = T T = = = A T A G 0 DY11 G = G = = = = ? = A G = A = A = = = = ? = T A = 0 DY12 = = A = ? = = = = = = = = = G = ? = = = = = = = 0 DY13 G = = C = = C C = A G = A = = T = = G T = T A = 0 DY14 G ? G = = ? = ? (G) A G = A ? A = = ? = ? (A) T A = 0 DY15 = = = = = = = = (G) = G = = = = = = = = = (A) = A = 0 DY16 (G) = (G) C C = = = G A G A (A) = (A) T T = = = A T A G 0 DY17 = I G T T = G = = = = G = D A C C = C = = = = A 0 DY18 G (D) = C C C C C G A G = A (I) = T T A G T A T A = 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 G = = C = = C C = A G = A = = T = = G T = T A = 0 DY21 G = = C C C C C = A G = A = = T T A G T = T A = 0 DY22 ? ? = ? C = C = G A G A ? ? = ? T = G = A T A G 0 DY23 ? I = T = = G = = = = G ? D = C = = C = = = = A 0 DY24 ? I G ? T = G = A = = G ? D A ? C = C = G = = A 0 E101 = = (A) C C C C = = = = = = = (G) T T A G = = = = = 0 E102 = I G = = = = = = = = = = D A = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = = = = ? ? ? ? ? = = = = = = = ? ? ? ? ? = = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = = = C C C C = = A G = = = = T T A G = = T A = 0 E108 = (I) = C C C C C = = = = = (D) = T T A G T = = = = 0 E109 = = A C C ? C ? ? = = = = = G T T ? G ? ? = = = 0 E110 = = A C C C C C = = = = = = G T T A G T = = = = 0 E111 = = (A) C = C C C = = = = = = (G) T = A G T = = = = 0 E112 = = (A) T T A G = = T A = = = (G) C C C C = = A G = 0 E113 G = = C = = = C = ? ? ? A = = T = = = T = ? ? ? 0 E114 = = A C = = = C = ? ? ? = = G T = = = T = ? ? ? 0 E115 = = = C = C C C = ? ? ? = = = T = A G T = ? ? ? 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = (I) = C C C C C = = = = = (D) = T T A G T = = = = 0 E118 G = = C = C = = = A G = A = = T = A = = = T A = 0 E119 = = A C C C C C = = = = = = G T T A G T = = = = 0 E120 = = = = ? ? ? = = = = = = = = = ? ? ? = = = = = 0 E121 = = (A) C = C C C = = = = = = (G) T = A G T = = = = 0 E122 G = G = = = = ? ? = = = A = A = = = = ? ? = = = 0 E123 = = = = = = = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.98 0.98 1.00 ? ? ? = = = = 1.00 0.99 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = = = = 0.88 1.00 = 1.00 1.00 = = = = = 0.81 = = = = = 0.94 = = 1.00 1.00 = = = = = ? = = = = = = = = 0.97 0.97 1.00 1.00 = 1.00 = 1.00 0.99 0.99 1.00 = = = = = = = = = = = = = = = 0.99 1.00 = 1.00 = = = = 0.99 0.86 0.84 = 1.00 1.00 = = = 1.00 0.99 0.99 1.00 0.98 = 0.98 = = = = ? = 1.00 1.00 = = = 1.00 = ? = = = = = = = 0.98 = = 1.00 = = 0.93 1.00 = 1.00 1.00 = 0.99 ? 0.94 = = ? = ? 0.51 0.99 0.99 = = = = = = = = = 0.51 = 1.00 = 0.83 = 0.72 1.00 1.00 = = = 1.00 0.99 0.99 1.00 = 0.96 0.96 1.00 1.00 = 1.00 = = = = 1.00 0.92 0.82 = 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.99 = = = = = = = = = = = = = 0.98 = = 1.00 = = 0.93 1.00 = 1.00 1.00 = 0.99 = = 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 = = 0.97 = = = = 1.00 ? 0.99 0.99 ? 1.00 = 1.00 = 1.00 = = 1.00 = = 0.89 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = 0.98 0.98 = = 0.84 = 1.00 1.00 1.00 1.00 1.00 = = = = = = 0.97 1.00 1.00 ? 1.00 ? ? = = = = = 0.90 1.00 1.00 1.00 1.00 1.00 = = = = = = 0.85 1.00 = 1.00 1.00 1.00 = = = = = = 0.58 1.00 1.00 1.00 1.00 = = 0.94 0.94 = 1.00 = = 1.00 = = = 0.98 = ? ? ? = = 0.95 1.00 = = = 1.00 = ? ? ? = = = 0.96 = 1.00 1.00 0.99 = ? ? ? = = = = = = = = = = = = = 0.84 = 1.00 1.00 1.00 1.00 1.00 = = = = 0.92 = = 0.99 = 0.93 = = = 0.96 0.96 = = = 0.91 1.00 1.00 1.00 1.00 1.00 = = = = = = = = ? ? ? = = = = = = = 0.85 1.00 = 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = = = ? ? = = = = = = = = = = = = = = = END PHASEPROBS