************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ilk21.phase.inp ilk21.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ilk21.phase.out_freqs : haplotype frequency estimates ilk21.phase.out_pairs : most likely haplotype pairs for each individual ilk21.phase.out_recom : estimates of recombination parameters ilk21.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 15 Positions of loci: 783 2821 3404 3421 4294 4308 5250 6223 7199 7537 7757 8427 8869 9467 11022 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ilk21.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ICCGCCACTCCCCTT 10.000000 2 ICCGCCGCCCCCCTT 25.000000 3 ICTGCCACTCCCCTT 5.000000 4 ITCGCCACTCCCCCT 10.000000 5 ITCGCCACTTCCCTT 1.000000 6 ITTGCCACTCCCCTT 1.000000 7 ITTGCTACTCCCCTT 4.000000 8 ITTGCTACTCCCCTC 8.000000 9 DTCGCCACTTCCCTT 2.000000 10 DTCGCCACTTTTTCT 1.000000 11 DTCGCCAATTTTTCT 5.000000 12 DTCGGCACTTTTTCT 2.000000 13 DTCGGCACTTTTTTT 5.000000 14 DTCTCCACTCCCCCT 14.000000 15 DTCTCCACTCCCCTT 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: (7,7) D003: (2,2) D004: (3,5) D005: (1,13) D006: (1,9) D007: (1,4) D008: (3,11) D009: (4,11) D010: (3,13) D011: (2,11) D012: (1,4) D013: (1,12) D014: (2,14) D015: (1,13) D016: (1,14) D033: (4,9) D034: (1,13) D035: (10,14) D036: (2,3) D037: (11,11) D038: (4,13) D039: (7,12) D040: (4,7) E001: (8,15) E002: (2,2) E003: (2,2) E004: (2,4) E005: (2,14) E006: (2,8) E007: (2,14) E008: (2,2) E009: (2,2) E010: (2,8) E011: (6,8) E012: (2,8) E013: (8,14) E014: (8,14) E015: (2,14) E016: (14,14) E017: (8,14) E018: (1,3) E019: (2,14) E020: (2,14) E021: (2,4) E022: (2,4) E023: (2,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 I C C G C C A C T C C C C T T I T C G C C A C T C C C C C T 0 D002 I T T G C T A C T C C C C T T I T T G C T A C T C C C C T T 0 D003 I C C G C C G C C C C C C T T I C C G C C G C C C C C C T T 0 D004 I (C) (T) G C C A C T C C C C T T I (T) (C) G C C A C T T C C C T T 0 D005 I C C G C C A C T C C C C T T D T C G G C A C T T T T T T T 0 D006 I C C G C C A C T C C C C T T D T C G C C A C T [T] C C C T T 0 D007 I C C G C C A C T C C C C T T I T C G C C A C T C C C C C T 0 D008 I C T G C C A C T C C C C T T D T C G C C A A T T T T T C T 0 D009 I T C G C C A C T C C C C C T D T C G C C A A T T T T T C T 0 D010 I C T G C C A C T C C C C T T D T C G G C A C T T T T T T T 0 D011 I C C G C C G C C C C C C T T D T C G C C A A T T T T T C T 0 D012 I C C G C C A C T C C C C T T I T C G C C A C T C C C C C T 0 D013 I C C G C C A C T C C C C (T) T D T C G G C A C T T T T T (C) T 0 D014 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C T 0 D015 I C C G C C A C T C C C C T T D T C G G C A C T T T T T [T] T 0 D016 I C C G C C A C T C C C C T T D T C T C C A C T C C C C C T 0 D033 (I) T C G C C A C T C C C C [C] T (D) T C G C C A C T T C C C T T 0 D034 I C C G C C A C T C C C C T T D T C G G C A C T T T T T T T 0 D035 D T C G C C A C T T T T T C T D T C T C C A C T C C C C C T 0 D036 I C C G C C G C C C C C C T T I C T G C C A C T C C C C T T 0 D037 D T C G C C A A T T T T T C T D T C G C C A A T T T T T C T 0 D038 I T C G C C A C T C C C C C T D T C G G C A C T T T T T [T] T 0 D039 I T T G C T A C T C C C C (T) T D T C G G C A C T T T T T (C) T 0 D040 I T C G C C A C T C C C C C T I T T G C T A C T C C C C [T] T 0 E001 I T T G C T A C T C C C C T C D T C T C C A C T C C C C T T 0 E002 I C C G C C G C C C C C C T T I C C G C C G C C C C C C T T 0 E003 I C C G C C G C C C C C C T T I C C G C C G C C C C C C T T 0 E004 I C C G C C G C C C C C C T T I T C G C C A C T C C C C C T 0 E005 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C T 0 E006 I C C G C C G C C C C C C T T I T T G C T A C T C C C C T C 0 E007 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C T 0 E008 I C C G C C G C C C C C C T T I C C G C C G C C C C C C T T 0 E009 I C C G C C G C C C C C C T T I C C G C C G C C C C C C T T 0 E010 I C C G C C G C C C C C C T T I T T G C T A C T C C C C T C 0 E011 I T T G C C A C T C C C C [T] T I T T G C T A C T C C C C T C 0 E012 I C C G C C G C C C C C C T T I T T G C T A C T C C C C T C 0 E013 I T T G C T A C T C C C C T C D T C T C C A C T C C C C C T 0 E014 I T T G C T A C T C C C C T C D T C T C C A C T C C C C C T 0 E015 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C T 0 E016 D T C T C C A C T C C C C C T D T C T C C A C T C C C C C T 0 E017 I T T G C T A C T C C C C T C D T C T C C A C T C C C C C T 0 E018 I C C G C C A C T C C C C T T I C T G C C A C T C C C C T T 0 E019 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C T 0 E020 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C T 0 E021 I C C G C C G C C C C C C T T I T C G C C A C T C C C C C T 0 E022 I C C G C C G C C C C C C T T I T C G C C A C T C C C C C T 0 E023 I C C G C C G C C C C C C T T D T C T C C A C T C C C C C 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 = C = = = = = = ? ? ? = = T = = T = = = = = = ? ? ? = = C = 0 D002 = = = = = = = = ? = = = = = = = = = = = = = = ? = = = = = = 0 D003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D004 = (C) (T) = = = = = ? C = = = = = = (T) (C) = = = = = ? T = = = = = 0 D005 I C = = C = = = ? ? ? C C = = D T = = G = = = ? ? ? T T = = 0 D006 I C = = = = = = ? ? ? = = = = D T = = = = = = ? ? ? = = = = 0 D007 ? ? = = = = = = = ? = = ? T = ? ? = = = = = = = ? = = ? C = 0 D008 I C T = = = ? C ? ? C C C T = D T C = = = ? A ? ? T T T C = 0 D009 I = = = = = = C = C C C ? ? = D = = = = = = A = T T T ? ? = 0 D010 I C T = C = = = = C C C C = = D T C = G = = = = T T T T = = 0 D011 I C = = = = G C C C C C C T = D T = = = = A A T T T T T C = 0 D012 = C = = = = = = = = = = = T ? = T = = = = = = = = = = = C ? 0 D013 I C = = C = = = = C C C C (T) ? D T = = G = = = = T T T T (C) ? 0 D014 I C = G = = G = C = = = = T = D T = T = = A = T = = = = C = 0 D015 I C = = C = = = = C C C C ? ? D T = = G = = = = T T T T ? ? 0 D016 I C = G = = = = = = = = = T = D T = T = = = = = = = = = C = 0 D033 (I) = = = = = = = = C = = = ? = (D) = = = = = = = = T = = = ? = 0 D034 I C = = C = ? = = C C C C = = D T = = G = ? = = T T T T = = 0 D035 = = = G = = = = = T T T T = ? = = = T = = = = = C C C C = ? 0 D036 = = C = = = G = C = = = = = = = = T = = = A = T = = = = = = 0 D037 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? = 0 D038 I = = = C = = = = C C C ? ? = D = = = G = = = = T T T ? ? = 0 D039 I = T = C T = = = C C C C (T) = D = C = G C = = = T T T T (C) = 0 D040 = = C = = C = = = = = = ? ? = = = T = = T = = = = = = ? ? = 0 E001 I = T G = T = = = = = = = = C D = C T = C = = = = = = = = T 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 = C ? ? = = G = C = = = = T = = T ? ? = = A = T = = = = C = 0 E005 I C = G = = G = C = = = = T = D T = T = = A = T = = = = C = 0 E006 = C C = = C G = C = = = ? ? T = T T = = T A = T = = = ? ? C 0 E007 I C = G = = ? = C = = = = T = D T = T = = ? = T = = = = C = 0 E008 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = ? ? = 0 E009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 = C C = = C G = C = = = = = T = T T = = T A = T = = = = = C 0 E011 = = = = = C = = = = = = = ? T = = = = = T = = = = = = = ? C 0 E012 = C C = = C G = C = = = = = T = T T = = T A = T = = = = = C 0 E013 I = T G = T = = = = = = = ? C D = C T = C = = = = = = = ? T 0 E014 I = T G = T = = = = = = = T C D = C T = C = = = = = = = C T 0 E015 I C = G = = G = C = = = = T = D T = T = = A = T = = = = C = 0 E016 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? = 0 E017 I = T G = T = = = = = = = T C D = C T = C = = = = = = = C T 0 E018 = = C = = = = = = = = = = = = = = T = = = = = = = = = = = = 0 E019 I C = G = = G = C = = = = ? = D T = T = = A = T = = = = ? = 0 E020 I C = G = = ? = C = = = = T = D T = T = = ? = T = = = = C = 0 E021 = C ? ? = = G = C = = = = T = = T ? ? = = A = T = = = = C = 0 E022 = C ? ? = = G = C = = = = T = = T ? ? = = A = T = = = = C = 0 E023 I C = G = = G = C = = = = T = D T = T = = A = T = = = = C = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.98 = = = = = = ? ? ? = = 1.00 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = 0.85 0.87 = = = = = ? 0.98 = = = = = 1.00 1.00 = = 1.00 = = = ? ? ? 1.00 1.00 = = 0.98 0.99 = = = = = = ? ? ? = = = = ? ? = = = = = = = ? = = ? 0.98 = 1.00 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 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 0.98 = = 1.00 = = = = 1.00 1.00 1.00 1.00 0.62 ? 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 = = = = = = = = = 0.99 = 0.65 = = = = = = = = 0.98 = = = ? = 1.00 1.00 = = 1.00 = ? = = 1.00 1.00 1.00 1.00 = = = = = 0.99 = = = = = 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 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 0.60 = = = 1.00 = = 1.00 = = = = = = ? ? = 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 = = 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 = = = = = 0.91 = = = = = = = ? 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 0.99 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 = = = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 = = = = 1.00 = END PHASEPROBS