************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 thmdn.phase.inp thmdn.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST thmdn.phase.out_freqs : haplotype frequency estimates thmdn.phase.out_pairs : most likely haplotype pairs for each individual thmdn.phase.out_recom : estimates of recombination parameters thmdn.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 9 Positions of loci: 1075 1209 4007 4404 4594 5110 5318 6235 6867 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file thmdn.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GICTGAAAI 4.000000 2 GICTGAAAD 15.000000 3 GICTGAAGI 3.000000 4 GICTGAAGD 14.000000 5 GICTGGAAI 1.000000 6 GICTGGAAD 35.000000 7 GICTGGAGD 2.000000 8 GICGGAAGD 3.000000 9 GITTGACAD 2.000000 10 GDTTGACAD 8.000000 11 GDTTAACAI 2.000000 12 GDTTAACAD 1.000000 13 AICTGAAAD 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (6,13) D003: (1,10) D004: (6,10) D005: (2,6) D006: (2,10) D007: (8,11) D008: (6,8) D009: (6,12) D010: (1,6) D011: (4,6) D012: (6,6) D013: (6,13) D014: (3,7) D015: (3,6) D016: (5,10) D033: (4,13) D034: (6,11) D035: (2,2) D036: (2,6) D037: (4,13) D038: (2,8) D039: (2,4) D040: (2,2) E001: (2,10) E002: (2,4) E003: (4,6) E004: (4,6) E005: (2,6) E006: (2,6) E007: (4,6) E008: (6,10) E009: (4,6) E010: (9,10) E011: (3,6) E012: (4,6) E013: (4,6) E014: (2,6) E015: (6,6) E016: (6,6) E017: (6,6) E018: (4,6) E019: (4,4) E020: (9,10) E021: (2,6) E022: (6,7) E023: (6,6) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G I C T G A A A I G I C T G A A A I 0 D002 G I C T G G A A D A I C T G A A A D 0 D003 G I C T G A A A (I) G D T T G A C A (D) 0 D004 G I C T G G A A D G D T T G A C A D 0 D005 G I C T G [A] A A D G I C T G [G] A A D 0 D006 G I C T G A A A D G [D] T T G A C A D 0 D007 G I C G G A A G (D) G D T T A A C A (I) 0 D008 G I C T G G A A D G I C G G A A G D 0 D009 G I C T G G A A D G D T T A A C A D 0 D010 G I C T G (A) A A I G I C T G (G) A A D 0 D011 G I C T G (A) A G D G I C T G (G) A A D 0 D012 G I C T G G A A D G I C T G G A A D 0 D013 G I C T G G A A D A I C T G A A A D 0 D014 G I C T G (A) A G I G I C T G (G) A G D 0 D015 G I C T G A A (G) (I) G I C T G G A (A) (D) 0 D016 G I C T G G A A (I) G D T T G A C A (D) 0 D033 (G) I C T G A A G D (A) I C T G A A A D 0 D034 G I C T G G A A (D) G D T T A A C A (I) 0 D035 G I C T G A A A D G I C T G A A A D 0 D036 G I C T G A A A [D] G I C T G G A A D 0 D037 (G) I C T G A A G D (A) I C T G A A A D 0 D038 G I C T G A A A D G I C G G A A G D 0 D039 G I C T G A A A D G I C T G A A G D 0 D040 G I C T G A A A D G I C T G A A A D 0 E001 G I C T G A A A D G D T T G A C A D 0 E002 G I C T G A A A D G I C T G A A G D 0 E003 G I C T G (A) A G D G I C T G (G) A A D 0 E004 G I C T G (A) A G D G I C T G (G) A A D 0 E005 G I C T G A A A D G I C T G G A A D 0 E006 G I C T G A A A D G I C T G G A A D 0 E007 G I C T G (A) A G [D] G I C T G (G) A A D 0 E008 G I C T G G A A D G D T T G A C A D 0 E009 G I C T G (A) A G [D] G I C T G (G) A A D 0 E010 G I T T G A C A D G D T T G A C A [D] 0 E011 G I C T G A A (G) (I) G I C T G G A (A) (D) 0 E012 G I C T G (A) A G D G I C T G (G) A A D 0 E013 G I C T G (A) A G D G I C T G (G) A A D 0 E014 G I C T G A A A D G I C T G G A A D 0 E015 G I C T G G A A D G I C T G G A A D 0 E016 G I C T G G A A D G I C T G G A A D 0 E017 G I C T G G A A D G I C T G G A A [D] 0 E018 G I C T G (A) A G [D] G I C T G (G) A A D 0 E019 G I C T G A A G D G I C T G A A G D 0 E020 G I T T G A C A D G D T T G A C A D 0 E021 G I C T G A A [A] D G I C T G G A A D 0 E022 G I C T G G A A D G I C T G G A G D 0 E023 G I C T G G A A D G I C T G G A A D 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 = = = = G = = = A = = = = A = = = 0 D003 = I C = = = A = (I) = D T = = = C = (D) 0 D004 = I C = = G A = = = D T = = A C = = 0 D005 ? ? = ? ? ? ? = ? ? ? = ? ? ? ? = ? 0 D006 ? ? C = = = A = = ? ? T = = = C = = 0 D007 = I C G G = A G (D) = D T T A = C A (I) 0 D008 = = = T = G = A = = = = G = A = G = 0 D009 = I C = G G A = = = D T = A A C = = 0 D010 = = = = = (A) = = I = = = = = (G) = = D 0 D011 = = ? = = (A) = G = = = ? = = (G) = A = 0 D012 = = = = = = = = = = = = = = = = = = 0 D013 G = = = = G = = = A = = = = A = = = 0 D014 = = = = = (A) = = I = = = = = (G) = = D 0 D015 = = = = = A = (G) (I) = = = = = G = (A) (D) 0 D016 = I C = = G A = (I) = D T = = A C = (D) 0 D033 (G) = = = = = = G = (A) = = = = = = A = 0 D034 = I C = G G A = (D) = D T = A A C = (I) 0 D035 = = = = = = = = = = = = = = = = = = 0 D036 = = = = = A = = ? = = = = = G = = ? 0 D037 (G) = = = = = = G = (A) = = = = = = A = 0 D038 = = = T = = = A = = = = G = = = G = 0 D039 = = = = = = = A = = = = = = = = G = 0 D040 = = = = = = = = = = = = = = = = = = 0 E001 = I C = = = A = = = D T = = = C = = 0 E002 = = = = = = = A = = = = = = = = G = 0 E003 = = = = = (A) = G = = = = = = (G) = A = 0 E004 = = = = = (A) = G = = = = = = (G) = A = 0 E005 = = = = = A = = = = = = = = G = = = 0 E006 = = = = = A = = = = = = = = G = = = 0 E007 = = = = = (A) = G ? = = = = = (G) = A ? 0 E008 = I C = = G A = = = D T = = A C = = 0 E009 ? ? = = = (A) = G ? ? ? = = = (G) = A ? 0 E010 = I = = = = = = ? = D = = = = = = ? 0 E011 = = = = = A = (G) (I) = = = = = G = (A) (D) 0 E012 = = = = = (A) = G = = = = = = (G) = A = 0 E013 = = = = = (A) = G = = = = = = (G) = A = 0 E014 = = = = = A = = = = = = = = G = = = 0 E015 = = = = = = = = = = = = = = = = = = 0 E016 = = = = = = = = = = = = = = = = = = 0 E017 = = = = = = = = ? = = = = = = = = ? 0 E018 = = = = = (A) = G ? = = = = = (G) = A ? 0 E019 = = = = = = = = = = = = = = = = = = 0 E020 = I = = = = = ? = = D = = = = = ? = 0 E021 = = = = = A = ? = = = = = = G = ? = 0 E022 = = = = = = = A = = = = = = = = G = 0 E023 = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = 0.93 = = = = 1.00 = = = = 1.00 1.00 = = = 1.00 = 0.65 = 1.00 1.00 = = 1.00 1.00 = = ? ? = ? ? ? ? = ? ? ? 1.00 = = = 1.00 = = = 1.00 1.00 0.97 1.00 = 1.00 1.00 0.84 = = = 0.97 = 1.00 = 0.97 = = 1.00 1.00 = 0.94 1.00 1.00 = = = = = = = 0.73 = = 1.00 = = ? = = 0.85 = 1.00 = = = = = = = = = = 0.94 = = = = 1.00 = = = = = = = = 0.61 = = 1.00 = = = = = 0.90 = 0.85 0.71 = 1.00 1.00 = = 1.00 1.00 = 0.50 0.88 = = = = = = 1.00 = = 1.00 1.00 = 0.99 1.00 1.00 = 0.78 = = = = = = = = = = = = = = 1.00 = = ? 0.88 = = = = = = 1.00 = = = = 0.93 = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = = = 1.00 = = = = = = 0.85 = 1.00 = = = = = = 0.85 = 1.00 = = = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = 0.84 = 1.00 ? = 1.00 1.00 = = 1.00 1.00 = = ? ? = = = 0.84 = 0.98 ? = 1.00 = = = = = = ? = = = = = 0.91 = 0.86 0.69 = = = = = 0.85 = 1.00 = = = = = = 0.85 = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0.84 = 1.00 ? = = = = = = = = = = 1.00 = = = = = ? = = = = = = 1.00 = ? = = = = = = = = 1.00 = = = = = = = = = = END PHASEPROBS