************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ikbep.phase.inp ikbep.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ikbep.phase.out_freqs : haplotype frequency estimates ikbep.phase.out_pairs : most likely haplotype pairs for each individual ikbep.phase.out_recom : estimates of recombination parameters ikbep.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 18 Positions of loci: 552 735 2059 3201 4160 4567 5035 5568 5571 5572 5578 6824 7114 7525 8843 9081 9259 9416 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ikbep.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCCTACCCAAITCGGATD 33.000000 2 GCCTACCCAAITCGGATI 4.000000 3 GCCTACCCAAITCGGACD 3.000000 4 GCCTACCCAAITCGGGTD 3.000000 5 GCCTACCTGGDTCGGATD 13.000000 6 GCCTACCTGGDTCGAATD 4.000000 7 GCCTACCTGGDCTGGATD 1.000000 8 GCCTACCTGGDCTGGGTD 1.000000 9 GCCTACTCAAITCGGATD 2.000000 10 GCCCACCTGGDTCGGATD 2.000000 11 GCCCACCTGGDCTGGATD 9.000000 12 GCCCACCTGGDCTGGGTD 2.000000 13 GCCCACCTGGDCTTGATD 1.000000 14 GCCCATCTGGDCTGGATD 3.000000 15 GCCCGCCTGGDCTTGATD 4.000000 16 GCGCACCCAAITCGGATD 1.000000 17 GCGCGCCTGGDCTGGGTD 1.000000 18 GCGCGCCTGGDCTTGGTD 2.000000 19 AGCTACCTGGDTCGGATD 4.000000 20 AGCTACCTGGDTCGGGTD 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (1,1) D003: (5,9) D004: (1,19) D005: (1,3) D006: (1,2) D007: (1,2) D008: (2,10) D009: (5,11) D010: (1,4) D011: (1,3) D012: (1,11) D013: (9,19) D014: (4,17) D015: (1,5) D016: (1,1) D033: (1,5) D034: (1,1) D035: (1,3) D036: (1,1) D037: (1,1) D038: (1,19) D039: (1,1) D040: (1,2) E001: (1,1) E002: (15,18) E003: (5,13) E004: (5,15) E005: (5,19) E006: (1,18) E007: (5,11) E008: (11,11) E009: (12,20) E010: (14,16) E011: (5,14) E012: (6,11) E013: (6,15) E014: (1,6) E015: (8,12) E016: (1,11) E017: (4,15) E018: (5,5) E019: (5,11) E020: (1,14) E021: (6,11) E022: (1,7) E023: (5,10) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T D 0 D002 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T D 0 D003 G C C T A C (C) T G G D T C G G A T D G C C T A C (T) C A A I T C G G A T D 0 D004 G C C T A C C C A A I T C G G A T D A G C T A C C T G G D T C G G A T D 0 D005 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A C D 0 D006 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T I 0 D007 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T I 0 D008 G C C (T) A C C C A A I T C G G A T (I) G C C (C) A C C T G G D T C G G A T (D) 0 D009 G C C T A C C T G G D T C G G A T D G C C C A C C T G G D [C] [T] G G A T D 0 D010 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G G T D 0 D011 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A C D 0 D012 G C C T A C C C A A I T C G G A T D G C C C A C C T G G D C T G G A T D 0 D013 (G) (C) C T A C (T) C A A I T C G G A T D (A) (G) C T A C (C) T G G D T C G G A T D 0 D014 G C C T A C C C A A I T C G G G T D G C G C G C C T G G D C T G G G T D 0 D015 G C C T A C C C A A I T C G G A T D G C C T A C C T G G D T C G G A T D 0 D016 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T D 0 D033 G C C T A C C C A A I T C G G A T D G C C T A C C T G G D T C G G A T D 0 D034 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T D 0 D035 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A C D 0 D036 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T D 0 D037 G C C T A C C [C] [A] [A] [I] T C G G A T D G C C T A C C C A A I T C G G A T D 0 D038 G C C T A C C C A A I T C G G A T D A G C T A C C T G G D T C G G A T D 0 D039 G C C T A C C [C] [A] [A] [I] T C G G A T D G C C T A C C C A A I T C G G A T D 0 D040 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T I 0 E001 G C C T A C C C A A I T C G G A T D G C C T A C C C A A I T C G G A T D 0 E002 G C C C G C C T G G D C T T G A T D G C G C G C C T G G D C T T G G T D 0 E003 G C C (T) A C C T G G D T C G G A T D G C C (C) A C C T G G D C T T G A T D 0 E004 G C C T A C C T G G D T C G G A T D G C C C G C C T G G D C T T G A T D 0 E005 G C C T A C C T G G D T C G G A T D A G C T A C C T G G D T C G G A T D 0 E006 G C C T A C C [C] [A] [A] [I] T C G G A T D G C G C G C C T G G D C T T G G T D 0 E007 G C C T A C C T G G D T C G G A T D G C C C A C C T G G D C T G G A T D 0 E008 G C C C A C C T G G D C T G G A T D G C C C A C C T G G D C T G G A T D 0 E009 G C C C A C C T G G D C T G G G T D A G C T A C C T G G D T C G G G T D 0 E010 G C C C A T C T G G D C T G G A T D G C G C A C C C A A I T C G G A T D 0 E011 G C C T A C C T G G D T C G G A T D G C C [C] A T C T G G D C T G G A T D 0 E012 G C C T A C C T G G D T C G (A) A T D G C C C A C C T G G D C T G (G) A T D 0 E013 G C C T A C C T G G D T C G A A T D G C C C G C C T G G D C T T G A T D 0 E014 G C C T A C C C A A I T C G G A T D G C C T A C C T G G D T C G A A T D 0 E015 G C C T A C C T G G D C T G G G T D G C C C A C C T G G D C T G G G T D 0 E016 G C C T A C C C A A I T C G G A T D G C C C A C C T G G D C T G G A T D 0 E017 G C C T A C C C A A I T C G G (G) T D G C C C [G] C C T G G D C T T G (A) T D 0 E018 G C C T A C C T G G D T C G G A T D G C C T A C C T G G D T C G G A T D 0 E019 G C C T A C C T G G D T C G G A T D G C C C A C C T G G D C T G G A T D 0 E020 G C C T A C C C A A I T C G G A T D G C C C A T C T G G D C T G G A T D 0 E021 G C C T A C C T G G D T C G (A) A T D G C C C A C C T G G D C T G (G) A T D 0 E022 G C C T A C C C A A I T C G G A T D G C C T A C C T G G D C T G G A T D 0 E023 G C C T A C C T G G D T C G G A T D G C C C A C C T G G D T C G G A T 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D003 = = = = = = (C) T G G D = ? = = = = = = = = = = = (T) C A A I = ? = = = = = 0 D004 G C = = = = = C A A I = = = = = = = A G = = = = = T G G D = = = = = = = 0 D005 = = ? = = = = = = = = = ? ? = = T = = = ? = = = = = = = = = ? ? = = C = 0 D006 = = ? = = = = = = = = = = = = = = D = = ? = = = = = = = = = = = = = = I 0 D007 = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = I 0 D008 = = = (T) = = = C A A I = ? = = = = (I) = = = (C) = = = T G G D = ? = = = = (D) 0 D009 = = = T = = = = = = = ? ? = = = = = = = = C = = = = = = = ? ? = = = = = 0 D010 = = = = = = ? = = = = = = ? = A = = = = = = = = ? = = = = = = ? = G = = 0 D011 = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = C = 0 D012 = = = T = = = C A A I T C = ? ? = = = = = C = = = T G G D C T = ? ? = = 0 D013 (G) (C) = = = = (T) C A A I = = = = = = = (A) (G) = = = = (C) T G G D = = = = = = = 0 D014 = = C T A = = C A A I T C = = = = = = = G C G = = T G G D C T = = = = = 0 D015 = = = = = = ? C A A I = = = ? = = = = = = = = = ? T G G D = = = ? = = = 0 D016 = = = = = = ? = = = = = = = ? = = = = = = = = = ? = = = = = = = ? = = = 0 D033 ? ? = = = = = C A A I = = = ? ? = = ? ? = = = = = T G G D = = = ? ? = = 0 D034 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = 0 D035 = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = C = 0 D036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = = ? = = = = ? ? ? ? = = = = = = = = = ? = = = = ? ? ? ? = = = = = = = 0 D038 G C = = = = = C A A I = = ? = = = = A G = = = = = T G G D = = ? = = = = 0 D039 = = = = = = ? ? ? ? ? = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = 0 D040 = = = = = ? = = = = = = = = = = = D = = = = = ? = = = = = = = = = = = I 0 E001 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 = = C = = = = = = = = = = = = A = = = = G = = = = = = = = = = = = G = = 0 E003 = = = (T) = = = = = = = T C G = = = = = = = (C) = = = = = = = C T T = = = = 0 E004 = = = T A = = = = = = T C G = = = = = = = C G = = = = = = C T T = = = = 0 E005 G C = = = = ? = = = = = ? ? = = = = A G = = = = ? = = = = = ? ? = = = = 0 E006 = = C T A = ? ? ? ? ? T C G = A = = = = G C G = ? ? ? ? ? C T T = G = = 0 E007 = = = T = = ? = = = = T C = ? ? = = = = = C = = ? = = = = C T = ? ? = = 0 E008 = = = = = = ? = = = = = = ? ? = = ? = = = = = = ? = = = = = = ? ? = = ? 0 E009 G C = C = = = = = = = C T = = = = = A G = T = = = = = = = T C = = = = = 0 E010 = = C = = T = T G G D C T = = = = = = = G = = C = C A A I T C = = = = = 0 E011 = = = ? = C = = = = = T C = = = = = = = = ? = T = = = = = C T = = = = = 0 E012 = = = T = = = = = = = T C = (A) = = = = = = C = = = = = = = C T = (G) = = = 0 E013 = = ? T A = = = = = = T C G A = = = = = ? C G = = = = = = C T T G = = = 0 E014 = = = = = = = C A A I = = ? G = = = = = = = = = = T G G D = = ? A = = = 0 E015 = = = T = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = 0 E016 = = = T = ? = C A A I T C ? = = = = = = = C = ? = T G G D C T ? = = = = 0 E017 = = = T ? = = ? ? ? ? T C G = (G) = = = = = C ? = = ? ? ? ? C T T = (A) = = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 = = = T = = = = = = = T C = = = = = = = = C = = = = = = = C T = = = = = 0 E020 = = = T = C = C A A I T C = = = = = = = = C = T = T G G D C T = = = = = 0 E021 = = ? T = = = = = = = T C = (A) = = = = = ? C = = = = = = = C T = (G) = = = 0 E022 = = = = ? ? ? C A A I T C ? = = = = = = = = ? ? ? T G G D C T ? = = = = 0 E023 = = = T = = = = = = = = = = ? = = = = = = C = = = = = = = = = = ? = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.69 1.00 1.00 1.00 1.00 = ? = = = = = 0.93 0.93 = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = ? = = = = = = = = = ? ? = = 1.00 = = = ? = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = 0.89 = = = 1.00 1.00 1.00 1.00 = ? = = = = 0.87 = = = 0.98 = = = = = = = ? ? = = = = = = = = = = = ? = = = = = = ? = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = ? ? = = 0.89 0.89 = = = = 0.72 1.00 1.00 1.00 1.00 = = = = = = = = = 0.93 0.93 0.93 = = 1.00 1.00 1.00 1.00 0.99 0.99 = = = = = = = = = = = ? 1.00 1.00 1.00 1.00 = = = ? = = = = = = = = = ? = = = = = = = ? = = = ? ? = = = = = 1.00 1.00 1.00 1.00 = = = ? ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? ? = = = = = = = 0.92 0.92 = = = = = 1.00 1.00 1.00 1.00 = = ? = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = ? = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = 0.95 = = = = = = = = = = = = 1.00 = = = = = 0.78 = = = = = = = 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 = 0.96 = = = = = 0.96 = = ? = = = = 1.00 1.00 = ? ? = = = = = = = = ? = = = = = = ? ? = = ? 0.96 0.96 = 0.99 = = = = = = = 0.98 0.98 = = = = = = = 0.90 = = 0.95 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = ? = 0.98 = = = = = 1.00 1.00 = = = = = = = = 0.99 = = = = = = = 1.00 1.00 = 0.85 = = = = = ? 1.00 1.00 = = = = = = 1.00 1.00 1.00 0.93 = = = = = = = = = = 1.00 1.00 1.00 1.00 = = ? 0.93 = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = ? = 1.00 1.00 1.00 1.00 1.00 1.00 ? = = = = = = = 1.00 ? = = ? ? ? ? 1.00 1.00 1.00 = 0.59 = = = = = = = = = = = = = = = = = = = = = = = 0.96 = = = = = = = 1.00 1.00 = = = = = = = = 0.97 = 0.96 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = ? 0.99 = = = = = = = 1.00 1.00 = 0.85 = = = = = = = ? ? ? 1.00 1.00 1.00 1.00 0.94 0.94 ? = = = = = = = 1.00 = = = = = = = = = = ? = = = END PHASEPROBS