************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 plaua.phase.inp plaua.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST plaua.phase.out_freqs : haplotype frequency estimates plaua.phase.out_pairs : most likely haplotype pairs for each individual plaua.phase.out_recom : estimates of recombination parameters plaua.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 21 Positions of loci: 82 211 835 2291 3123 3271 3272 3369 3479 3855 3995 4490 4625 4642 4773 5634 7358 8061 8734 9170 9609 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file plaua.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GTCATGDGAGCCCCCCCICTG 9.000000 2 GTCCCGDGGACCCATCCICTG 1.000000 3 GTCCTGDGAGCCCCCCCICTG 2.000000 4 GCACCGDAGGCCCACCCICTG 9.000000 5 GCACCGDAGGTCCACCCICTG 13.000000 6 GCACCGDAGGTCCACTCICTG 1.000000 7 GCACCTIGGGCCTACTTDAGA 1.000000 8 TTACCGDGGGCCCACCCIATG 3.000000 9 TTACCGDGGGCCCACCTDAGG 1.000000 10 TTACCGDGGGTCCACCCICTG 1.000000 11 TTACCGDGGACCCATCCICTG 7.000000 12 TTACCGIGGGCCTACCTDAGA 1.000000 13 TTACCGIGGGCCTACTTDAGA 1.000000 14 TTACCTIGGGCCTACCTDAGA 8.000000 15 TTACCTIGGGCCTACTTDAGA 32.000000 16 TTACCTIGGGCTTACCTDAGA 3.000000 17 TTACCTIGGGTCTACTTDAGA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,15) D002: (3,14) D003: (15,16) D004: (4,4) D005: (15,16) D006: (1,11) D007: (1,16) D008: (1,5) D009: (8,14) D010: (12,13) D011: (4,11) D012: (1,1) D013: (14,15) D014: (7,15) D015: (11,15) D016: (1,4) D033: (1,4) D034: (3,4) D035: (1,4) D036: (14,15) D037: (4,15) D038: (4,14) D039: (8,14) D040: (15,15) E001: (15,15) E002: (5,15) E003: (6,15) E004: (5,5) E005: (15,15) E006: (15,15) E007: (5,15) E008: (15,15) E009: (8,2) E010: (15,15) E011: (5,11) E012: (15,15) E013: (11,15) E014: (5,15) E015: (10,15) E016: (5,15) E017: (5,14) E018: (5,14) E019: (5,9) E020: (11,11) E021: (5,17) E022: (5,15) E023: (15,15) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G T C A T G D G A G C C C C C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 D002 G T C C T G D G A G C C C C C C C I C T G T T A C C T I G G G C C T A C C T D A G A 0 D003 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C T T A C C T D A G A 0 D004 G C A C C G D A G G C C C A C C C I C T G G C A C C G D A G G C C C A C C C I C T G 0 D005 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C T T A C C T D A G A 0 D006 G T C A T G D G A G C C C C C C C I C T G T T A C C G D G G A C C C A T C C I C T G 0 D007 G T C A T G D G A G C C C C C C C I C T G T T A C C T I G G G C T T A C C T D A G A 0 D008 G T C A T G D G A G C C C C C C C I C T G G C A C C G D A G G T C C A C C C I C T G 0 D009 T T A C C G D G G G C C C A C C C I A T G T T A C C [T] I G G G C C T A C C T D A G A 0 D010 T T A C C G I G G G C C T A C C T D A G A T T A C C G I G G G C C T A C T T D A G A 0 D011 G C A C C G D A G G C C C A C C C I C T G T T A C C G D G G A C C C A T C C I C T G 0 D012 G T C A T G D G A G C C C C C C C I C T G G T C A T G D G A G C C C C C C C I C T G 0 D013 T T A C C T I G G G C C T A C C T D A G A T T A C C T I G G G C C T A C T T D A G A 0 D014 G C A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 D015 T T A C C G D G G A C C C A T C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 D016 G T C A T G D G A G C C C C C C C I C T G G C A C C G D A G G C C C A C C C I C T G 0 D033 G T C A T G D G A G C C C C C C C I C T G G C A C C G D A G G C C C A C C C I C T G 0 D034 G T C C T G D G A G C C C C C C C I C T G G C A C C G D A G G C C C A C C C I C T G 0 D035 G T C A T G D G A G C C C C C C C I C T G G C A C C G D A G G C C C A C C C I C T G 0 D036 T T A C C T I G G G C C T A C C T D A G A T T A C C T I G G G C C T A C T T D A G A 0 D037 G C A C C G D A G G C C C A C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 D038 G C A C C G D A G G C C C A C C C I C T G T T A C C T I G G G C C T A C C T D A G A 0 D039 T T A C C G D G G G C C C A C C C I A T G T T A C C T I G G G C C T A C C T D A G A 0 D040 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E001 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E002 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E003 G C A C C G D A G G T C C A C T C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E004 G C A C C G D A G G T C C A C C C I C T G G C A C C G D A G G T C C A C C C I C T G 0 E005 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E006 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E007 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E008 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E009 (T) T (A) C C G D G G G C C C A C C C I A T G (G) T (C) C C G D G G A C C C A T C C I C T G 0 E010 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E011 G C A C C G D A G G T C C A C C C I C T G T T A C C G D G G A C C C A T C C I C T G 0 E012 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 0 E013 T T A C C G D G G A C C C A T C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E014 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E015 T T A C C G D G G G (T) C C A C C C I C T G T T A C C T I G G G (C) C T A C T T D A G A 0 E016 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E017 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C C T D A G A 0 E018 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C C T D A G A 0 E019 (G) (C) A C C G D (A) G G (T) C C A C C C I C T G (T) (T) A C C G D (G) G G (C) C C A C C T D A G G 0 E020 T T A C C G D G G A C C C A T C C I C T G T T A C C G D G G A C C C A T C C I C T G 0 E021 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G T C T A C T T D A G A 0 E022 G C A C C G D A G G T C C A C C C I C T G T T A C C T I G G G C C T A C T T D A G A 0 E023 T T A C C T I G G G C C T A C T T D A G A T T A C C T I G G G C C T A C T T D A G A 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 G = C A T G D = A = = = C C = C C I C T G T = A C C T I = G = = = T A = T T D A G A 0 D002 G = C = T G D = A = = = C C = = C I C T G T = A = C T I = G = = = T A = = T D A G A 0 D003 = = = = = = = = = = = C = = = T = = = = = = = = = = = = = = = = T = = = C = = = = = 0 D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D005 = = = = = = = = = = = C = = = T = = = = = = = = = = = = = = = = T = = = C = = = = = 0 D006 G = C A T = = = A G = = = C C = = = = = = T = A C C = = = G A = = = A T = = = = = = 0 D007 G = C A T G D = A = = C C C = = C I C T G T = A C C T I = G = = T T A = = T D A G A 0 D008 = T C A T = = G A = C = = C = = = = = = = = C A C C = = A G = T = = A = = = = = = = 0 D009 = = = = ? ? ? = = = = = C = = = ? I = T G = = = = ? ? ? = = = = = T = = = ? D = G A 0 D010 = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = T = = = = = 0 D011 G C = = = = = A = G = = = = C = = = = = = T T = = = = = G = A = = = = T = = = = = = 0 D012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D013 = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = T = = = = = 0 D014 G C = = = = = = = = = = = = = = ? = = = = T T = = = = = = = = = = = = = = ? = = = = 0 D015 = = = = = G D = = A = = C = T C C I C T G = = = = = T I = = G = = T = C T T D A G A 0 D016 = T C A T = = G A = = = = C = = = = = = = = C A C C = = A G = = = = A = = = = = = = 0 D033 = T C A T = = G A = = = = C = = ? = = = = = C A C C = = A G = = = = A = = ? = = = = 0 D034 = T C = T = = G A = = = = C = = = = = = = = C A = C = = A G = = = = A = = = = = = = 0 D035 = T C A T = = G A = = = = C = = = = = = = = C A C C = = A G = = = = A = = = = = = = 0 D036 = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = T = = = = = 0 D037 G C = = = G D A = = = = C = = C C I C T G T T = = = T I G = = = = T = = T T D A G A 0 D038 G C = = = G D A = = = = C = = = C I C T G T T = = = T I G = = = = T = = = T D A G A 0 D039 = = = = = G D = = = = = C = = = C I = T G = = = = = T I = = = = = T = = = T D = G A 0 D040 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E001 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 G C = = = G D A = = T = C = = C C I C T G T T = = = T I G = = C = T = = T T D A G A 0 E003 G C = = = G D A = = T = C = = = C I C T G T T = = = T I G = = C = T = = = T D A G A 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 G C = = = G D A = = T = C = = C C I C T G T T = = = T I G = = C = T = = T T D A G A 0 E008 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 E009 (T) = (A) = = = = = = G = = ? ? C = ? = A = ? (G) = (C) = = = = = = A = = ? ? T = ? = C = ? 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 G C = = = = = A = G T = = = C = = = = = = T T = = = = = G = A C = = = T = = = = = = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = = = G D = = A = = C = T C C I C T G = = = = = T I = = G = = T = C T T D A G A 0 E014 G C = = = G D A = = T = C = = C C I C T G T T = = = T I G = = C = T = = T T D A G A 0 E015 = = = = = G D = = = (T) = C = = C C I C T G = = = = = T I = = = (C) = T = = T T D A G A 0 E016 G C = = = G D ? = = T = C = = C C I C T G T T = = = T I ? = = C = T = = T T D A G A 0 E017 G C = = = G D A = = T = C = = = C I C T G T T = = = T I G = = C = T = = = T D A G A 0 E018 G C = = = G D A = = T = C = = = C I C T G T T = = = T I G = = C = T = = = T D A G A 0 E019 (G) (C) = = = = = (A) = = (T) = = = = = C I C T = (T) (T) = = = = = (G) = = (C) = = = = = T D A G = 0 E020 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = 0 E021 G C = = = G D A = = = = C = = C ? I C T G T T = = = T I G = = = = T = = T ? D A G A 0 E022 G C = = = G D A = = T = C = = C C I C T G T T = = = T I G = = C = T = = T T D A G A 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 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 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.99 = = = 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 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 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 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 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 = = = 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 0.95 = 1.00 = = 0.98 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 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 0.96 = 1.00 = = 0.98 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = ? = = = = = = = = = = 0.50 = 0.50 = = = = = = 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 = = = 1.00 1.00 1.00 = = 0.96 = 1.00 = = 0.98 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = 0.74 = 1.00 = = 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 ? = = 0.95 = 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 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 0.87 0.87 = = = = = 0.87 = = 0.87 = = = = = 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 = = 0.95 = 1.00 = = 0.98 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = ? END PHASEPROBS