************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 fcln3.phase.inp fcln3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fcln3.phase.out_freqs : haplotype frequency estimates fcln3.phase.out_pairs : most likely haplotype pairs for each individual fcln3.phase.out_recom : estimates of recombination parameters fcln3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 11 Positions of loci: 741 4235 5459 5782 6419 6564 7935 7992 8349 8455 8720 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fcln3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGICCCIATTA 1.000000 2 GGICAAIGTTA 1.000000 3 GGICAAIGTTG 23.000000 4 GGIGCCIGTTG 4.000000 5 GGDCCCIGTTG 3.000000 6 GGDCCCIGCTG 36.000000 7 GGDCCCDGCTG 1.000000 8 GGDCCCDGCGG 4.000000 9 GAICCCIATTA 4.000000 10 GADCCCIGCTG 13.000000 11 GADCCCDGCGG 1.000000 12 AAICCCIATTA 1.000000 13 AAICCCIGTTA 1.000000 14 AADCCCIGCTG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,4) D002: (7,9) D003: (8,8) D004: (4,5) D005: (6,10) D006: (9,13) D007: (6,10) D008: (2,10) D009: (6,6) D010: (8,10) D011: (6,6) D012: (6,14) D013: (5,9) D014: (4,6) D015: (6,6) D016: (3,4) D033: (5,10) D034: (3,11) D035: (3,6) D036: (6,6) D037: (8,12) D038: (6,6) D039: (3,9) D040: (6,10) E001: (6,6) E002: (3,10) E003: (3,6) E004: (3,3) E005: (6,10) E006: (6,10) E007: (3,3) E008: (6,6) E009: (6,10) E010: (6,6) E011: (6,10) E012: (3,10) E013: (3,6) E014: (3,3) E015: (3,3) E016: (6,6) E017: (6,6) E018: (6,10) E019: (3,6) E020: (3,3) E021: (3,3) E022: (6,6) E023: (3,3) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G G I C C C I A T T A G G I G C C I G T T G 0 D002 G (G) D C C C (D) G C T G G (A) I C C C (I) A T T A 0 D003 G G D C C C D G C G G G G D C C C D G C G G 0 D004 G G I G C C I G T T G G G D C C C I G T T G 0 D005 G G D C C C I G C T G G A D C C C I G C T G 0 D006 (G) A I C C C I A T T A (A) A I C C C I G T T A 0 D007 G G D C C C I G C T G G A D C C C I G C T G 0 D008 G G I C A A I G T T (A) G A D C C C I G C T (G) 0 D009 G [G] D C C C I G C T G G G D C C C I G C T G 0 D010 G (G) D C C C D G C G G G (A) D C C C I G C T G 0 D011 G [G] D C C C I G C T G G G D C C C I G C T G 0 D012 (G) G D C C C I G C T G (A) A D C C C I G C T G 0 D013 G G D C C C I G T T G G A I C C C I A T T A 0 D014 G G I G C C I G T T G G G D C C C I G C T G 0 D015 G G D C C C I G C T G G G D C C C I G C T G 0 D016 G G I C A A I G T T G G G I G C C I G T T G 0 D033 G (G) D C C C I G T T G G (A) D C C C I G C T G 0 D034 G (G) I C A A I G T T G G (A) D C C C D G C G G 0 D035 G G I C A A I G T T G G G D C C C I G C T G 0 D036 G G D C C C I G C T G G G D C C C I G C T G 0 D037 (G) G D C C C D G C G G (A) A I C C C I A T T A 0 D038 G G D C C C I G C T G G G D C C C I G C T G 0 D039 G G I C A A I G T T G G A I C C C I A T T A 0 D040 G G D C C C I G C T G G A D C C C I G C T G 0 E001 G G D C C C I G C T G G G D C C C I G C T G 0 E002 G G I C A A I G T T G G A D C C C I G C T G 0 E003 G G I C A A I G T T G G G D C C C I G C T G 0 E004 G G I C A A I G T T G G G I C A A I G T T G 0 E005 G G D C C C I G C T G G A D C C C I G C T G 0 E006 G G D C C C I G C T G G A D C C C I G C T G 0 E007 G G I C A A I G T T G G G I C A A I G T T G 0 E008 G G D C C C I G C T G G G D C C C I G C T G 0 E009 G G D C C C I G C T G G A D C C C I G C T G 0 E010 G G D C C C I G C T G G G D C C C I G C T G 0 E011 G G D C C C I G C T G G A D C C C I G C T G 0 E012 G G I C A A I G T T G G A D C C C I G C T G 0 E013 G G I C A A I G T T G G G D C C C I G C T G 0 E014 G G I C A A I G T T G G G I C A A I G T T G 0 E015 G G I C A A I G T T G G G I C A A I G T T G 0 E016 G G D C C C I G C T G G G D C C C I G [C] T G 0 E017 G [G] D C C C I G C T G G G D C C C I G C T G 0 E018 G G D C C C I G C T G G A D C C C I G C T G 0 E019 G G I C A A I G T T G G G D C C C I G C T G 0 E020 G G I C A A I G T T G G G I C A A I G T T G 0 E021 G G I C A A I G T T G G G I C A A I G T T G 0 E022 G G D C C C I G C T G G G D C C C I G C T G 0 E023 G G I C A A I G T T G G G I C A A I G T T 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 D001 = = = ? = = = A = = A = = = ? = = = G = = G 0 D002 = (G) D = = = (D) G C = G = (A) I = = = (I) A T = A 0 D003 = = = = = = = = = = = = = = = = = = = = = = 0 D004 = = I G = = = = = = = = = D C = = = = = = = 0 D005 = G = = = = = = = = = = A = = = = = = = = = 0 D006 (G) = = = = = = A = = = (A) = = = = = = G = = = 0 D007 = G = = = = = = = = = = A = = = = = = = = = 0 D008 = G I = A A = = T = (A) = A D = C C = = C = (G) 0 D009 = ? = = = = = = = = = = ? = = = = = = = = = 0 D010 = (G) = = = = D = = G = = (A) = = = = I = = T = 0 D011 = ? = = = = = = = = = = ? = = = = = = = = = 0 D012 (G) G = = = = = = = = = (A) A = = = = = = = = = 0 D013 = G D = = = = G = = G = A I = = = = A = = A 0 D014 = = I G = = = = T = = = = D C = = = = C = = 0 D015 = = = = = = = = = = = = = = = = = = = = = = 0 D016 = = = C ? ? = = = = = = = = G ? ? = = = = = 0 D033 = (G) = = = = = = T = = = (A) = = = = = = C = = 0 D034 = (G) I = A A I = T T = = (A) D = C C D = C G = 0 D035 = = I = A A = = T ? ? = = D = C C = = C ? ? 0 D036 = = = = = = = = = = = = = = = = = = = = = = 0 D037 (G) G D = = = D G C G G (A) A I = = = I A T T A 0 D038 = = = = = = = = = = = = = = = = = = = = = = 0 D039 = G = = A A = G = = G = A = = C C = A = = A 0 D040 = G = = = = = = = = = = A = = = = = = = = = 0 E001 = = = = = = = = = = = = = = = = = = = = = = 0 E002 = G I = A A = = T = = = A D = C C = = C = = 0 E003 = = I = A A = = T = = = = D = C C = = C = = 0 E004 = = = = = = = = = = = = = = = = = = = = = = 0 E005 = G = = = = = = = = = = A = = = = = = = = = 0 E006 = G = = = = = = = = = = A = = = = = = = = = 0 E007 = = = = = = = = = = = = = = = = = = = = = = 0 E008 = = = = = = = = = = = = = = = = = = = = = = 0 E009 = G = = = = = = = = = = A = = = = = = = = = 0 E010 = = = = = = = = = = = = = = = = = = = = = = 0 E011 = G = = = = = = = = = = A = = = = = = = = = 0 E012 = G I = A A = = T = = = A D = C C = = C = = 0 E013 = = I = A A = = T = = = = D = C C = = C = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = 0 E015 = = = = = = = = = = = = = = = = = = = = = = 0 E016 = = = = = = = = ? = = = = = = = = = = ? = = 0 E017 = ? = = = = = = = = = = ? = = = = = = = = = 0 E018 = G = = = = = = = = = = A = = = = = = = = = 0 E019 = = I = A A = = T = = = = D = C C = = C = = 0 E020 = = = = = = = = = = = = = = = = = = = = = = 0 E021 = = = = = = = = = = = = = = = = = = = = = = 0 E022 = = = = = = = = = = = = = = = = = = = = = = 0 E023 = = = = = = = = = = = = = = = = = = = = = = 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 = 0.84 1.00 = = = 0.56 1.00 1.00 = 1.00 = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = 0.54 = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = 0.92 1.00 = 1.00 1.00 = = 1.00 = 0.56 = ? = = = = = = = = = = 0.65 = = = = 1.00 = = 1.00 = = ? = = = = = = = = = 0.62 1.00 = = = = = = = = = = 0.92 1.00 = = = = 1.00 = = 1.00 = = 1.00 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = 1.00 ? ? = = = = = = 0.83 = = = = = = 1.00 = = = 0.67 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 ? ? = = = = = = = = = = = 0.77 0.92 1.00 = = = 1.00 0.97 1.00 1.00 1.00 = = = = = = = = = = = = 0.97 = = 1.00 1.00 = 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = 0.92 1.00 = 1.00 1.00 = = 1.00 = = = = 1.00 = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 0.92 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