************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 csft2.phase.inp csft2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST csft2.phase.out_freqs : haplotype frequency estimates csft2.phase.out_pairs : most likely haplotype pairs for each individual csft2.phase.out_recom : estimates of recombination parameters csft2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 16 Positions of loci: 69 545 1310 2586 3148 3247 3347 3371 3477 3606 3928 4400 4660 4706 5723 5768 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file csft2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGCGGACIACTAGAAC 2.000000 2 CGCGGACIACTAGAGT 1.000000 3 CGCGGACIACTGGAGC 22.000000 4 CGCGGATIACCAGGAT 2.000000 5 CGCGGATIACTAGAAT 2.000000 6 CGCGGATIACTAGGAC 1.000000 7 CGCGGATIACTGGGAC 1.000000 8 CGCGGGTIACCAGGAT 2.000000 9 CGCGCACIACTGGAGC 5.000000 10 TAAGGATIACTGGAGC 23.000000 11 TAAGGATIATCAGGAC 20.000000 12 TAAGGATDACTATGAT 3.000000 13 TAAGGATDGCTAGGAC 1.000000 14 TAAGGGTIACTGGAGC 4.000000 15 TAAACATDGCTAGGAC 1.000000 16 TAAACATDGCTAGGGT 3.000000 17 TGAGGATIACCAGGAC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,11) D002: (3,11) D003: (6,10) D004: (7,8) D005: (11,16) D006: (4,9) D007: (3,14) D008: (1,14) D009: (3,12) D010: (9,10) D011: (10,16) D012: (3,16) D013: (3,11) D014: (4,11) D015: (1,9) D016: (8,11) D033: (11,12) D034: (9,9) D035: (11,11) D036: (12,13) D037: (10,11) D038: (2,14) D039: (11,15) D040: (10,11) E001: (3,11) E002: (10,10) E003: (3,10) E004: (3,10) E005: (11,11) E006: (10,10) E007: (3,10) E008: (5,10) E009: (5,11) E010: (3,10) E011: (3,10) E012: (10,11) E013: (3,10) E014: (3,10) E015: (3,3) E016: (3,10) E017: (3,11) E018: (3,11) E019: (3,10) E020: (14,17) E021: (3,10) E022: (3,10) E023: (10,11) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C G C G G A C I A C T G G A G C T A A G G A T I A T C A G G A C 0 D002 C G C G G A C I A C T G G A G C T A A G G A T I A T C A G G A C 0 D003 C G C G G A T I A C T A G G A C T A A G G A T I A C T G G A G C 0 D004 C G C G G (A) T I A C T (G) G G A C C G C G G (G) T I A C C (A) G G A T 0 D005 T A A G G A T I A T C A G G A C T A A A C A T D G C T A G G G T 0 D006 C G C G G A T I A C C A G G A T C G C G C A C I A C T G G A G C 0 D007 C G C G G (A) C I A C T G G A G C T A A G G (G) T I A C T G G A G C 0 D008 C G C G G (A) C I A C T A G A A C T A A G G (G) T I A C T G G A G C 0 D009 C G C G G A C I A C T G G A G C T A A G G A T D A C T A T G A T 0 D010 C G C G C A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 D011 T A A G G A T I A C T G G A G C T A A A C A T D G C T A G G [G] [T] 0 D012 C G C G G A C I A C T G G A G C T A A A C A T D G C T A G G G T 0 D013 C G C G G A C I A C T G G A G C T A A G G A T I A T C A G G A C 0 D014 C G C G G A T I A C C A G G A T T A A G G A T I A T C A G G A C 0 D015 C G C G (G) A C I A C T A G A A C C G C G (C) A C I A C T G G A G C 0 D016 C G C G G (G) T I A C C A G G A T T A A G G (A) T I A T C A G G A C 0 D033 T A A G G A T I A T C A G G A C T A A G G A T D A C T A T G A T 0 D034 C G C G C A C I A C T G G A G C C G C G C A C I A C T G G A G C 0 D035 T A A G G A T I A T C A G G A C T A A G G A T I A T C A G G A C 0 D036 T A A G G A T D A C T A T G A T T A A G G A T D G C T A G G A C 0 D037 T A A G G A T I A C T G G A G C T A A G G A T I A T C A G G A C 0 D038 C G C G G (A) C I A C T (A) G A G (T) T A A G G (G) T I A C T (G) G A G (C) 0 D039 T A A G G A T I A T C A G G A C T A A A C A T D G C T A G G A C 0 D040 T A A G G A T I A C T G G A G C T A A G G A T I A T C A G G A C 0 E001 C G C G G A C I A C T G G A G C T A A G G A T I A T C A G G A C 0 E002 T A A G G A T I A C T G G A G C T A A G G A T I A C T G G A G C 0 E003 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E004 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E005 T A A G G A T I A T C A G G A C T A A G G A T I A T C A G G A C 0 E006 T A A G G A T I A C T G G A G C T A A G G A T I A C T G G A G C 0 E007 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E008 C G C G G A T I A C T A G A A T T A A G G A T I A C T G G A G C 0 E009 C G C G G A T I A C T A G A A T T A A G G A T I A T C A G G A C 0 E010 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E011 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E012 T A A G G A T I A C T G G A G C T A A G G A T I A T C A G G A C 0 E013 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E014 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E015 C G C G G A C I A C T G G A G C C G C G G A C I A C T G G A G C 0 E016 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E017 C G C G G A C I A C T G G A G C T A A G G A T I A T C A G G A C 0 E018 C G C G G A C I A C T G G A G C T A A G G A T I A T C A G G A C 0 E019 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E020 T (A) A G G (G) T I A C T G G A G C T (G) A G G (A) T I A C C A G G A C 0 E021 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E022 C G C G G A C I A C T G G A G C T A A G G A T I A C T G G A G C 0 E023 T A A G G A T I A C T G G A G C T A A G G A T I A T C A G G A C 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 C G C = = = C = = C T ? = A G = T A A = = = T = = T C ? = G A = 0 D002 C G C = = = C = = C T G = A ? ? T A A = = = T = = T C A = G ? ? 0 D003 C G C = = = = = = = = A = G A = T A A = = = = = = = = G = A G = 0 D004 = = = = = (A) = = = = T (G) = = = C = = = = = (G) = = = = C (A) = = = T 0 D005 = = = G ? = = I A ? C = = = A C = = = A ? = = D G ? T = = = G T 0 D006 = = = = G = T = = = C A = G A T = = = = C = C = = = T G = A G C 0 D007 C G C = = (A) C = = = = = = = = = T A A = = (G) T = = = = = = = = = 0 D008 C G C = = (A) C = = = = A = = A = T A A = = (G) T = = = = G = = G = 0 D009 C G C = ? ? C I = ? = G G A G C T A A = ? ? T D = ? = A T G A T 0 D010 C G ? = C = C = = = = = = = ? ? T A ? = G = T = = = = = = = ? ? 0 D011 = = = G ? = = I A ? = G = A ? ? = = = A ? = = D G ? = A = G ? ? 0 D012 ? G C G ? ? C I A ? = G = A = C ? A A A ? ? T D G ? = A = G = T 0 D013 C G C = = = C = = C T G = A G = T A A = = = T = = T C A = G A = 0 D014 ? G C = = = = = = C = = = = = T ? A A = = = = = = T = = = = = C 0 D015 = = = = (G) = = = = = = A = = A = = = = = (C) = = = = = = G = = G = 0 D016 C G ? = = (G) = = = C = = = = = T T A ? = = (A) = = = T = = = = = C 0 D033 = = = = = ? = I = ? C = G = = C = = = = = ? = D = ? T = T = = T 0 D034 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D035 ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 D036 = = = = = = = = A = = = T = = T = = = = = = = = G = = = G = = C 0 D037 ? = = = = = = = = C T G = A G = ? = = = = = = = = T C A = G A = 0 D038 ? G C = = (A) C = = = = (A) = = = (T) ? A A = = (G) T = = = = (G) = = = (C) 0 D039 = = = G ? ? = I A ? C = = = = = = = = A ? ? = D G ? T = = = = = 0 D040 = = = = = = = = = C T G = A G = = = = = = = = = = T C A = G A = 0 E001 ? G C = = = C = = C T G = A G = ? A A = = = T = = T C A = G A = 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E003 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E004 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E008 C G ? = = = = = = = = A = = A T T A ? = = = = = = = = G = = G C 0 E009 C G C = = = = = = C T = = A = T T A A = = = = = = T C = = G = C 0 E010 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E011 C G ? = = = C = = = = = = ? = = T A ? = = = T = = = = = = ? = = 0 E012 ? = = = = = = = = C T G = A G = ? = = = = = = = = T C A = G A = 0 E013 ? G C = = = C = = = = = = = = = ? A A = = = T = = = = = = = = = 0 E014 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 C G C ? = = C = = = = = = = = = T A A ? = = T = = = = = = = = = 0 E017 C G C = = = C = = C T G = A G = T A A = = = T = = T C A = G A = 0 E018 C G C = = = C = = C T G = A ? = T A A = = = T = = T C A = G ? = 0 E019 C G C ? = = C = = = = = = = = = T A A ? = = T = = = = = = = = = 0 E020 = (A) = = = (G) = = = = T G = A G = = (G) = = = (A) = = = = C A = G A = 0 E021 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E022 C G C = = = C = = = = = = = = = T A A = = = T = = = = = = = = = 0 E023 = = = = = = = = = C T G = A G = = = = = = = = = = T C A = G A = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.99 0.99 0.99 = = = 0.99 = = 1.00 1.00 ? = 1.00 1.00 = 0.99 0.99 0.99 = = = 0.99 = = 1.00 1.00 1.00 = 1.00 ? ? 0.94 0.94 0.94 = = = = = = = = 0.95 = 1.00 1.00 = = = = = = 0.78 = = = = 1.00 0.69 = = = 0.99 = = = 1.00 ? = = 1.00 1.00 ? 1.00 = = = 1.00 1.00 = = = = 0.98 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 0.82 1.00 = = = = = = = = = 1.00 1.00 1.00 = = 0.83 1.00 = = = = 0.93 = = 0.91 = 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 0.99 0.99 = = = 0.99 = = 1.00 1.00 1.00 = 1.00 1.00 = ? 1.00 1.00 = = = = = = 1.00 = = = = = 1.00 = = = = 0.88 = = = = = = 0.99 = = 0.99 = 1.00 1.00 ? = = 0.72 = = = 0.99 = = = = = 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 = = 0.77 1.00 = = = = 0.73 = = = 0.67 = = = 0.95 ? ? = 1.00 1.00 ? 1.00 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 = ? 0.99 0.99 = = = 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 = = = = = = = = = 0.99 0.99 0.99 = = = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 0.99 0.99 0.99 = = = 0.99 = = 1.00 1.00 1.00 = 1.00 ? = 1.00 1.00 1.00 ? = = 1.00 = = = = = = = = = = 0.59 = = = 0.58 = = = = 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 = END PHASEPROBS