************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 cebpb.phase.inp cebpb.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cebpb.phase.out_freqs : haplotype frequency estimates cebpb.phase.out_pairs : most likely haplotype pairs for each individual cebpb.phase.out_recom : estimates of recombination parameters cebpb.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 10 Positions of loci: 220 586 587 1643 2876 2884 3077 3693 4446 4962 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cebpb.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AGCCADDCTT 43.000000 2 AGCCTIDTCT 7.000000 3 AGCCTIDTCC 3.000000 4 AGCTADDCTT 3.000000 5 AGCTTIDTCT 3.000000 6 ATTTADDCTT 18.000000 7 ATTTADDTCT 1.000000 8 ATTTADICTT 4.000000 9 GGCCTIDTCT 12.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,2) D002: (6,9) D003: (5,9) D004: (1,9) D005: (1,5) D006: (1,6) D007: (2,9) D008: (1,9) D009: (9,9) D010: (1,2) D011: (1,3) D012: (1,7) D013: (1,4) D014: (1,6) D015: (1,2) D016: (1,9) D033: (6,9) D034: (1,2) D035: (1,3) D036: (1,9) D037: (1,1) D038: (1,9) D039: (1,2) D040: (2,3) E001: (1,8) E002: (1,1) E003: (1,1) E004: (1,6) E005: (1,6) E006: (1,4) E007: (1,1) E008: (6,6) E009: (1,6) E010: (1,6) E011: (1,5) E012: (6,6) E013: (1,8) E014: (1,6) E015: (1,6) E016: (1,6) E017: (1,6) E018: (1,8) E019: (1,9) E020: (6,8) E021: (1,1) E022: (1,4) E023: (1,6) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A G C C A D D C T T A G C C T I D T C T 0 D002 A [T] [T] T A D D C T T G G C C T I D T C T 0 D003 (A) G C T T I D T C T (G) G C C T I D T C T 0 D004 A G C C A D D C T T G G C C T I D T C T 0 D005 A G C (C) A D D C T T A G C (T) T I D T C T 0 D006 A G C C A D D C T T A [T] [T] T A D D C T T 0 D007 A G C C T I D T C T G G C C T I D T C T 0 D008 A G C C A D D C T T G G C C T I D T C T 0 D009 G G C C T I D T C T G G C C T I D T C T 0 D010 A G C C A D D C T T A G C C T I D T C T 0 D011 A G C C A D D C T T A G C C T I D T C C 0 D012 A G C C A D D (C) (T) T A T T T A D D (T) (C) T 0 D013 A G C C A D D C T T A G C T A D D C T T 0 D014 A G C C A D D C T T A T T T A D D C T T 0 D015 A G C C A D D C T T A G C C T I D T C T 0 D016 A G C C A D D C T T G G C C T I D T C T 0 D033 A T T T A D D C T T G G C C T I D T C T 0 D034 A G C C A D D C T T A G C C T I D T C T 0 D035 A G C C A D D C T T A G C C T I D T C C 0 D036 A G C C A D D C T T G G C C T I D T C T 0 D037 A G C C A D D C T T A G C C A D D C T T 0 D038 A G C C A D D C T T G G C C T I D T C T 0 D039 A G C C A D D C T T A G C C T I D T C T 0 D040 A G C C T I D T C T A G C C T I D T C C 0 E001 A G C C A D D C T T A T T T A D I C T T 0 E002 A G C C A D D C T T A G C C A D D C T T 0 E003 A G C C A D D C T T A G C C A D D C T T 0 E004 A G C C A D D C T T A T T T A D D C T T 0 E005 A G C C A D D C T T A T T T A D D C T T 0 E006 A G C C A D D C T T A G C T A D D C T T 0 E007 A G C C A D D C T T A G C C A D D C T T 0 E008 A T T T A D D C T T A T T T A D D C T T 0 E009 A G C C A D D C T T A T T T A D D C T T 0 E010 A G C C A D D C T T A T T T A D D C T T 0 E011 A G C (C) A D D C T T A G C (T) T I D T C T 0 E012 A T T T A D D C T T A T T T A D D C T T 0 E013 A G C C A D D C T T A T T T A D I C T T 0 E014 A G C C A D D C T T A T T T A D D C T T 0 E015 A G C C A D D C T T A T T T A D D C T T 0 E016 A G C C A D D C T T A T T T A D D C T T 0 E017 A G C C A D D C T T A T T T A D D C T T 0 E018 A G C C A D D C T T A T T T A D I C T T 0 E019 A G C C A D D C T T G G C C T I D T C T 0 E020 A T T T A D D C T T A T T T A D I C T T 0 E021 A G C C A D D C T T A G C C A D D C T T 0 E022 A G C C A D D C T T A G C T A D D C T T 0 E023 A G C C A D D C T T A T T T A D D C T T 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 D = C T = = = = = T I = T C = 0 D002 A ? ? T A D = C T = G ? ? C T I = T C = 0 D003 (A) = = T = = = = = = (G) = = C = = = = = = 0 D004 A ? ? = A D = C T = G ? ? = T I = T C = 0 D005 = = = (C) A D = C T = = = = (T) T I = T C = 0 D006 = ? ? C = = = = = = = ? ? T = = = = = = 0 D007 A = ? = = = = = = = G = ? = = = = = = = 0 D008 A = ? = A D = C T = G = ? = T I = T C = 0 D009 = = = = = = = = = = = = = = = = = = = = 0 D010 = = = = A D = C T = = = = = T I = T C = 0 D011 = = = = A D = C T T = = = = T I = T C C 0 D012 = G C C = = = (C) (T) = = T T T = = = (T) (C) = 0 D013 = = = C = = = = = = = = = T = = = = = = 0 D014 = G C C = = = = = = = T T T = = = = = = 0 D015 = = = = A D = C T = = = = = T I = T C = 0 D016 A = = = A D = C T = G = = = T I = T C = 0 D033 A T T T A D = C T = G G C C T I = T C = 0 D034 = = = = A D = C T = = = = = T I = T C = 0 D035 = = = = A D = C T T = = = = T I = T C C 0 D036 A = = = A D = C T = G = = = T I = T C = 0 D037 = = = = = = = = = = = = = = = = = = = = 0 D038 A = = = A D = C T = G = = = T I = T C = 0 D039 = = = = A D = C T = = = = = T I = T C = 0 D040 = = = = = = = = = T = = = = = = = = = C 0 E001 = G C C = = D = = = = T T T = = I = = = 0 E002 = = = = = = = = = = = = = = = = = = = = 0 E003 = = = = = = = = = = = = = = = = = = = = 0 E004 = G C C = = = = = = = T T T = = = = = = 0 E005 = G C C = = = = = = = T T T = = = = = = 0 E006 = = = C = = = = = = = = = T = = = = = = 0 E007 = = = = = = = = = = = = = = = = = = = = 0 E008 = = = = = = = = = = = = = = = = = = = = 0 E009 = G C C = = = = = = = T T T = = = = = = 0 E010 = G C C = = = = = = = T T T = = = = = = 0 E011 = = = (C) A D = C T = = = = (T) T I = T C = 0 E012 = = = = = = = = = = = = = = = = = = = = 0 E013 = G C C = = D = = = = T T T = = I = = = 0 E014 = G C C = = = = = = = T T T = = = = = = 0 E015 = G C C = = = = = = = T T T = = = = = = 0 E016 = G C C = = = = = = = T T T = = = = = = 0 E017 = G C C = = = = = = = T T T = = = = = = 0 E018 = G C C = = D = = = = T T T = = I = = = 0 E019 A = ? = A D = C T = G = ? = T I = T C = 0 E020 = = = = = = D = = = = = = = = = I = = = 0 E021 = = = = = = = = = = = = = = = = = = = = 0 E022 = = = C = = = = = = = = = T = = = = = = 0 E023 = G C C = = = = = = = T T T = = = = = = 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 ? ? 0.95 1.00 1.00 = 1.00 1.00 = 0.80 = = 1.00 = = = = = = 1.00 ? ? = 1.00 1.00 = 1.00 1.00 = = = = 0.51 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 0.98 = 1.00 1.00 1.00 = = = 0.51 0.51 = = = = 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 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 1.00 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = = = 0.52 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 1.00 = = = = = = = 1.00 1.00 1.00 = = 0.97 = = = 1.00 = ? = 1.00 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = END PHASEPROBS