************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 ilk13.phase.inp ilk13.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ilk13.phase.out_freqs : haplotype frequency estimates ilk13.phase.out_pairs : most likely haplotype pairs for each individual ilk13.phase.out_recom : estimates of recombination parameters ilk13.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 20 Positions of loci: 293 299 492 693 1090 1159 2319 2346 2553 2963 3697 3727 3848 4329 4384 4481 4553 6297 6576 6760 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ilk13.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AIACAACGCCACGGCGCGCG 2.000000 2 AIACAACGCCGCGGCGCGCG 39.000000 3 AIACAACGCCGTAGCGCGCG 2.000000 4 AIACAACGCCGTAAAGTGCG 1.000000 5 AIACAACGCCGTAAAGTGCA 3.000000 6 AIACAACGCCGTAAAGTACG 1.000000 7 AIACAACGTCGTGGAGCGCG 1.000000 8 AIACAACGTCGTGGAGCGTG 1.000000 9 AIACAACGTCGTGGAGTGCG 5.000000 10 AIACAACGTCGTGGACCGCG 1.000000 11 AIACAACCCCGTGGACCGTG 1.000000 12 AIACAAAGCCGCGGCGCGCG 1.000000 13 AIACAAAGCCGCGGCGCGCA 2.000000 14 AIACAAAGTTGCGGCGCGCA 1.000000 15 AIACAAACCCGCGGCGCGCG 1.000000 16 AIACGACGTCGTGGAGCGCG 2.000000 17 AIACGACGTTACGGCGCGCG 2.000000 18 AIATAACGCCATGGCGCGCG 1.000000 19 AIATAACGTCGTGGAGTGCG 1.000000 20 AIGCAACGCCGTAAAGTGCG 1.000000 21 AIGCAAACCCGCGGCGCGCG 1.000000 22 ADGTAACGCCGTGGAGCGCG 1.000000 23 ADGTAACGCCGTGGACCGCG 1.000000 24 ADGTAACGCCGTAGACCGCG 1.000000 25 ADGTAGCCCCGTGGCGCGCG 1.000000 26 ADGTAGCCCCGTGGACCGTG 1.000000 27 ADGTAGCCCCGTAAAGTGCA 1.000000 28 ADGTAGACCCGTGGACCGTG 4.000000 29 CIACAACGTTGCGGCGCGCG 1.000000 30 CIATAACGCCGCGGCGCGCG 3.000000 31 CIATAACGCCGTAACGCGCG 1.000000 32 CIATAACGCCGTAACGTACG 1.000000 33 CIATAACGCCGTAAAGTGCG 1.000000 34 CIATAACGCCGTAAAGTGCA 1.000000 35 CIATAACGCCGTAAAGTACG 3.000000 36 CIGCAACGCCGCGGCGCGCG 1.000000 37 CIGCAACGCCGTGGAGCGCG 1.000000 38 CIGCAAACCCGTGGAGCGCG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (17,30) D002: (18,9) D003: (5,19) D004: (9,17) D005: (14,38) D006: (9,28) D007: (16,37) D008: (11,25) D009: (2,2) D010: (2,16) D011: (2,27) D012: (3,24) D013: (1,23) D014: (2,28) D015: (2,28) D016: (2,9) D033: (13,21) D034: (2,36) D035: (8,20) D036: (9,22) D037: (7,26) D038: (2,10) D039: (2,29) D040: (12,28) E001: (4,35) E002: (2,33) E003: (2,2) E004: (2,2) E005: (35,35) E006: (2,34) E007: (2,2) E008: (2,5) E009: (2,32) E010: (13,31) E011: (2,2) E012: (1,6) E013: (2,2) E014: (2,2) E015: (2,2) E016: (2,2) E017: (2,2) E018: (2,2) E019: (2,2) E020: (3,15) E021: (2,30) E022: (2,30) E023: (2,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A I A (C) G A C G T T A C G G C G C G C G [C] I A (T) A A C G C C G C G G C G C G C G 0 D002 [A] I A (T) A A C G C C (A) T G G C G C G C G A I A (C) A A C G T C (G) T G G A G T G C G 0 D003 A I A (C) A A C G C C G T A A A G T G C A A I A (T) A A C G T C G T G G A G T G C G 0 D004 A I A C A A C G T C G T G G A G T G C G A I A C G A C G T T A C G G C G C G C G 0 D005 (A) I (A) C A A A G (T) (T) G (C) G G (C) G C G C (A) (C) I (G) C A A A C (C) (C) G (T) G G (A) G C G C (G) 0 D006 A I A C A A C G T C G T G G A G T G C G A D G T A G A C C C G T G G A C C G T G 0 D007 A I A C G A C G T C G T G G A G C G C G C I G C A A [C] [G] C C G T G G A G C G C G 0 D008 A I A C A A C C C C G T G G (A) (C) C G (T) G A D G T A G C C C C G T G G (C) (G) C G (C) G 0 D009 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 D010 A I A C A A C G C C G C G G C G C G C G A I A C G A C G T C G T G G A G C G C G 0 D011 A (I) (A) (C) A (A) C (G) C C G C G G C G C G C G A (D) (G) (T) A (G) C (C) C C G T A A A G T G C [A] 0 D012 A I A C A A C G C C G T A G (C) (G) C G C G A D G T A A C G C C G T A G (A) (C) C G C G 0 D013 A (I) (A) (C) A A C G C C (A) (C) G G (C) (G) C G C G A (D) (G) (T) A A C G C C (G) (T) G G (A) (C) C G C G 0 D014 A I A C A A C G C C G C G G C G C G C G A D G T A G A C C C G T G G A C C G T G 0 D015 A I A C A A C G C C G C G G C G C G C G A D G T A G A C C C G T G G A C C G T G 0 D016 A I A C A A C G C C G C G G C G C G C G A I A C A A C G T C G T G G A G [T] G C G 0 D033 A I (A) C A A A G C C G C G G C G C G C (A) A I (G) C A A A C C C G C G G C G C G C (G) 0 D034 A I A C A A C G C C G C G G C G C G C G C I G C A A C G C C G C G G C G C G C G 0 D035 A I (A) C A A C G T C G T G G A [G] [C] G (T) G A I (G) C A A C G C C G T A [A] [A] G [T] G (C) G 0 D036 A I A C A A C G (T) C G T G G [A] G (T) G C G A D G T A A C G (C) C G T G G [A] G (C) G C G 0 D037 A (I) (A) C [A] A C G T C G T G G A G C G C G A (D) (G) [T] A [G] C C C C G T G G A C C G T G 0 D038 A I A C A A C G (C) C G C G G C G C G C G A I A C A A C G (T) C G T G G A C C G C G 0 D039 (A) I A C A A C G C C G C G G C G C G C G (C) I A C A A C G T T G [C] G G [C] G C G C G 0 D040 A I A C A A A G C C G C G G C G C G C [G] A D G T A G A C C C G T G G A C C G T G 0 E001 A I A C A A C G C C G T A A A G T (G) C G C I A T A A C G C C G T A A [A] G T (A) C G 0 E002 (A) I A (C) A A C G C C G C G G C G C G C G (C) I A (T) A A C G C C G T A A [A] G [T] [G] C G 0 E003 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E004 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E005 C I A T A A C G C C G T A A A G T A C G C I A T A A C G C C G T A A A G T A C G 0 E006 A I A C A A C G C C G C G G C G C G C G C I A T A A C G C C G T A A A G T G C A 0 E007 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E008 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G T A A A G T G C A 0 E009 A I A C A A C G C C G C G G C G C (G) C G C I A T A A C G C C G T A A C G T (A) C G 0 E010 A I A C A A A G C C G C G G C G C G C (A) C I A T A A C G C C G T A A [C] G C G C (G) 0 E011 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E012 A I A C A A C G C C (A) C G G C G C G C G A I A C A A C G C C (G) T A A A G T A C G 0 E013 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E014 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E015 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E016 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E017 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E018 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E019 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G C G G C G C G C G 0 E020 A I A C A A (C) (G) C C G [T] A G [C] G C G C G A I A C A A (A) (C) C C G C G G C G C G C G 0 E021 A I A C A A C G C C G C G G C G C G C G C I A T A A C G C C G C G G C G C G C G 0 E022 A I A C A A C G C C G C G G C G C G C G C I A T A A C G C C G C G G C G C G C G 0 E023 A I A C A A C G C C G C G G C G C G C G A I A C A A C G C C G T A A A G T G C 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 ? ? = (C) G = = = T T A = = = = = = = = = ? ? = (T) A = = = C C G = = = = = = = = = 0 D002 ? ? = (T) = = = = C = (A) = = = C = C = = = ? ? = (C) = = = = T = (G) = = = A = T = = = 0 D003 = = = (C) = = = = C = = = A A = = = = = A = = = (T) = = = = T = = = G G = = = = = G 0 D004 = = = = A = = = = C G T = = A = T = = = = = = = G = = = = T A C = = C = C = = = 0 D005 (A) = (A) = = = = G (T) (T) = (C) = = (C) = = = = (A) (C) = (G) = = = = C (C) (C) = (T) = = (A) = = = = (G) 0 D006 = ? A C = A C G T = = = = = = G T = C = = ? G T = G A C C = = = = = = C C = T = 0 D007 A = A = G = ? ? T = = = = = = = = = = = C = G = A = ? ? C = = = = = = = = = = = 0 D008 = I ? ? = A = = = = = = = = (A) (C) = = (T) ? = D ? ? = G = = = = = = = = (C) (G) = = (C) ? 0 D009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D010 = = = = A = = = C = ? C = = C = = = = = = = = = G = = = T = ? T = = A = = = = = 0 D011 = (I) (A) (C) = (A) = (G) = = = C G G C = C = = ? = (D) (G) (T) = (G) = (C) = = = T A A A = T = = ? 0 D012 = I A C = = = = = = = = = = (C) (G) = = = = = D G T = = = = = = = = = = (A) (C) = = = = 0 D013 = (I) (A) (C) = = = = = = (A) (C) = = (C) (G) = = = = = (D) (G) (T) = = = = = = (G) (T) = = (A) (C) = = = = 0 D014 = I A C = A C G = = ? C = = C G = = C = = D G T = G A C = = ? T = = A C = = T = 0 D015 = I A C = A C G = = = C = = C ? = = C = = D G T = G A C = = = T = = A ? = = T = 0 D016 = = = = = = = = C = = C = ? ? ? ? = = = = = = = = = = = T = = T = ? ? ? ? = = = 0 D033 = = (A) = ? ? = G = = ? ? ? = = = = ? = (A) = = (G) = ? ? = C = = ? ? ? = = = = ? = (G) 0 D034 A = A = ? ? = = = = ? ? ? = = = = = = = C = G = ? ? = = = = ? ? ? = = = = = = = 0 D035 = = (A) = ? = = = T = = = G ? ? ? ? ? (T) = = = (G) = ? = = = C = = = A ? ? ? ? ? (C) = 0 D036 = I A C = = = = (T) = = = = = ? = (T) = = ? = D G T = = = = (C) = = = = = ? = (C) = = ? 0 D037 = (I) (A) ? ? ? = G T = = = = = = G = ? C ? = (D) (G) ? ? ? = C C = = = = = = C = ? T ? 0 D038 = = = = = = = = (C) = = C = = C G = = = = = = = = = = = = (T) = = T = = A C = = = = 0 D039 (A) = = = = = = = C C = ? ? = ? = = = = = (C) = = = = = = = T T = ? ? = ? = = = = = 0 D040 = I A C = A = G = = = C = = C G = ? C ? = D G T = G = C = = = T = = A C = ? T ? 0 E001 A = = C = = = = = = = = = ? ? ? = (G) = = C = = T = = = = = = = = = ? ? ? = (A) = = 0 E002 (A) = = (C) = = = = = = = C G ? ? ? ? ? ? ? (C) = = (T) = = = = = = = T A ? ? ? ? ? ? ? 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 A = = C = = = = = = = C G ? ? ? C = = G C = = T = = = = = = = T A ? ? ? T = = A 0 E007 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E008 = = = = = = = = = = = C G G C = C = = G = = = = = = = = = = = T A A A = T = = A 0 E009 A = = C = = = = = = = C G G = = C (G) = = C = = T = = = = = = = T A A = = T (A) = = 0 E010 A = = C = = A = = = = C G G ? = = = = (A) C = = T = = C = = = = T A A ? = = = = (G) 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 = = = = = = = = = = (A) C G G C = C G = = = = = = = = = = = = (G) T A A A = T A = = 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E017 = = = = = ? = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = ? = = 0 E018 = = = = ? = ? ? = = = = = = = = = = = = = = = = ? = ? ? = = = = = = = = = = = = 0 E019 = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = 0 E020 = = = = ? ? (C) (G) = = ? ? A ? ? ? = = = = = = = = ? ? (A) (C) = = ? ? G ? ? ? = = = = 0 E021 A = = C ? = = = = = ? ? ? = = = = = = = C = = T ? = = = = = ? ? ? = = = = = = = 0 E022 A = = C = = = = = = = = = = = = = = = = C = = T = = = = = = = = = = = = = = = = 0 E023 = = = = = = = = = = = C G G C = C = = G = = = = = = = = = = = T A A A = T = = A END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS ? ? = 0.89 1.00 = = = 0.99 0.99 0.99 = = = = = = = = = ? ? = 0.53 = = = = 0.98 = 0.87 = = = 1.00 = 1.00 = = = = = = 0.53 = = = = 1.00 = = = 1.00 1.00 = = = = = 0.97 = = = = 0.98 = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 = = = 0.65 = 0.80 = = = = 0.95 0.57 0.66 = 0.81 = = 0.81 = = = = 0.69 = ? 0.99 0.99 = 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = 0.99 = 0.93 = 0.94 = 0.98 = ? ? 0.96 = = = = = = = = = = = = 0.96 ? ? = 0.99 = = = = = = = = 0.61 0.61 = = 0.61 ? = = = = = = = = = = = = = = = = = = = = = = = = 0.94 = = = 0.99 = ? 1.00 = = 1.00 = = = = = = 0.56 0.56 0.56 = 0.57 = 0.57 = = = 0.99 0.99 0.99 0.99 = 0.99 = = ? = 0.99 0.99 0.99 = = = = = = = = = = 0.55 0.55 = = = = = 0.83 0.83 0.82 = = = = = = 0.73 0.85 = = 0.82 0.79 = = = = = 0.99 0.99 0.99 = 1.00 0.99 1.00 = = ? 1.00 = = 1.00 1.00 = = 1.00 = = 0.99 0.99 0.99 = 1.00 0.99 1.00 = = = 1.00 = = 1.00 ? = = 1.00 = = = = = = = = = 1.00 = = 1.00 = ? ? ? ? = = = = = 0.75 = ? ? = 0.97 = = ? ? ? = = = = ? = 0.81 0.94 = 1.00 = ? ? = = = = ? ? ? = = = = = = = = = 0.57 = ? = = = 1.00 = = = 1.00 ? ? ? ? ? 0.50 = = 1.00 1.00 0.97 = = = = 0.73 = = = = = ? = 0.71 = = ? = 0.83 0.83 ? ? ? = 0.95 0.95 = = = = = = 0.94 = ? 0.94 ? = = = = = = = = 0.86 = = 0.94 = = 1.00 0.92 = = = = 0.54 = = = = = = = 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 = = = = = = = = = ? ? ? = 0.75 = = 0.90 = = 0.90 = = = = = = = 1.00 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 0.92 = = 0.92 = = = = = = = 0.99 0.99 0.99 = = 0.91 0.89 = = 0.95 = = 0.95 = = 1.00 = = = = 1.00 1.00 1.00 ? = = = = 0.77 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.76 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? = = = = = = ? = ? ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? 0.73 0.73 = = ? ? 0.92 ? ? ? = = = = 0.99 = = 1.00 ? = = = = = ? ? ? = = = = = = = 0.99 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 0.96 END PHASEPROBS