************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 il17b.phase.inp il17b.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il17b.phase.out_freqs : haplotype frequency estimates il17b.phase.out_pairs : most likely haplotype pairs for each individual il17b.phase.out_recom : estimates of recombination parameters il17b.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 20 Positions of loci: 238 670 755 1748 1845 2101 2164 2832 3275 3281 3425 3426 3656 4131 5020 7348 7685 8254 8258 8839 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il17b.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ATAATGTCCCACGGGTGACG 3.000000 2 ATAGTGTCCCACGGGTGACG 37.000000 3 ATAGTGTCCCACGGGTGGTA 3.000000 4 ATAGTGTACCACGGGTGGTA 3.000000 5 ATAGTGTACCGTGGGTGGTA 27.000000 6 ATAGTATCCCACGGGTGGTA 2.000000 7 ATGGTGTACCGTGGGTGGTA 3.000000 8 ACAGTGTCCCACGGGTGGTA 1.000000 9 ACAGTGGCCCACGGGTGGTA 1.000000 10 ACAGCGGCTTACAGACAGTA 6.000000 11 ACAGCGGCTTACAAACAGTA 4.000000 12 TTAGTGTACCACGGGTGGTA 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,2) D002: (5,12) D003: (2,5) D004: (5,5) D005: (3,6) D006: (2,2) D007: (2,5) D008: (1,5) D009: (5,5) D010: (2,2) D011: (2,5) D012: (2,9) D013: (5,5) D014: (2,5) D015: (2,2) D016: (5,12) D033: (3,4) D034: (4,6) D035: (3,12) D036: (2,12) D037: (2,5) D038: (2,5) D039: (2,4) D040: (1,2) E001: (2,7) E002: (2,2) E003: (2,5) E004: (2,7) E005: (2,5) E006: (2,11) E007: (2,5) E008: (5,10) E009: (2,7) E010: (2,10) E011: (2,2) E012: (10,11) E013: (5,5) E014: (2,5) E015: (2,2) E016: (5,5) E017: (2,5) E018: (2,2) E019: (5,8) E020: (2,10) E021: (10,10) E022: (11,11) 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 T A A T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 D002 A T A G T G T A C C G T G G G T G G T A T T A G T G T A C C A C G G G T G G T A 0 D003 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D004 A T A G T G T A C C G T G G G T G G T A A T A G T G T A C C G T G G G T G G T A 0 D005 A [T] A G T G T C C C A C G G G T G G T A A T A G T A T C C C A C G G G T G G T A 0 D006 A T A G T G T C C C A C G G G T G A C G A T A [G] T G T C C C A C G G G T G A C G 0 D007 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D008 A T A A T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D009 A T A G T G T A C C G T G G G T G G T A A T A G T G T A C C [G] [T] G G G T G G T A 0 D010 A T A G T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 D011 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D012 A T A G T G (T) C C C A C G G G T G A C G A C A G T G (G) C C C A C G G G T G G T A 0 D013 A T A G T G T A C C G T G G G T G G T A A T A G T G T A C C G T G G G T G G T A 0 D014 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D015 A T A G T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 D016 A T A G T G T A C C G T G G G T G G T A T T A G T G T A C C A C G G G T G G T A 0 D033 A T A G T G T C C C A C G G G T G G T A A T A G T G T A C C A C G G G T G G T A 0 D034 A T A G T G T A C C A C G G G T G G T A A T A G T A T C C C A C G G G T G G T A 0 D035 A T A G T G T C C C A C G G G T G G T A T T A G T G T A C C A C G G G T G G T A 0 D036 A T A G T G T C C C A C G G G T G A C G T T A G T G T A C C A C G G G T G G T A 0 D037 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D038 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 D039 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C A C G G G T G G T A 0 D040 A T A A T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 E001 A T (A) G T G T C C C A C G G G T G A C G A T (G) G T G T A C C G T G G G T G G T A 0 E002 A T A G T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 E003 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 E004 A T (A) G T G T C C C A C G G G T G A C G A T (G) G T G T A C C G T G G G T G G T A 0 E005 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 E006 A T A G T G T C C C A C G G G T G A C G A C A G C G G C T T A C A A A C A G T A 0 E007 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 E008 A T A G T G T A C C G T G G G T G G T A A C A G C G G C T T A C A G A C A G T A 0 E009 A T (A) G T G T C C C A C G G G T G A C G A T (G) G T G T A C C G T G G G T G G T A 0 E010 A T A G T G T C C C A C G G G T G A C G A C A G C G G C T T A C A [G] A C A G T A 0 E011 A T A G T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 E012 A C A G C G G C T T A C A G A C A G T A A C A G C G G C T T A C A A A C A G T A 0 E013 A T A G T G T A C C G T G G G T G G T A A T A G T G T A C C G T G G G T G G T A 0 E014 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 E015 A T A G T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 E016 A T A G T G T A C C G T G G G T G G T A A T A G T G T A C C G T G G G T G G T A 0 E017 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T A 0 E018 A T A G T G T C C C A C G G G T G A C G A T A G T G T C C C A C G G G T G A C G 0 E019 A (T) A G T G T A C C G T G G G T G G T A A (C) A G T G T C C C A C G G G T G G T A 0 E020 A T A G T G T C C C A C G G G T G A C G A C A G C G G C T T A C A G A C A G T A 0 E021 A C A G C G G C T T A C A G A C A G T A A C A G C G G C T T A C A G A C A G T A 0 E022 A C A G C G G C T T A C A A A C A G T A A C A G C G G C T T A C A A A C A G T A 0 E023 A T A G T G T C C C A C G G G T G A C G A T A G T G T A C C G T G G G T G G T 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 = = = A ? = = = = = = = ? = ? = = = = = = = = G ? = = = = = = = ? = ? = = = = = 0 D002 A = = = = = = = = = G T = = = = = = = = T = = = = = = = = = A C = = = = = = = = 0 D003 = ? ? = = ? ? C = = A C = = = = = A C G = ? ? = = ? ? A = = G T = = = = = G T A 0 D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D005 = ? ? ? ? G = = ? ? ? ? = = = = = = = = = ? ? ? ? A = = ? ? ? ? = = = = = = = = 0 D006 = = = ? ? ? ? = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = 0 D007 = = = = = = = C = = A C = = = = = A C G = = = = = = = A = = G T = = = = = G T A 0 D008 = = = A = ? ? C = = A C = = = = = A C G = = = G = ? ? A = = G T = = = = = G T A 0 D009 = ? ? ? ? = = = ? ? ? ? = = = = = = = = = ? ? ? ? = = = ? ? ? ? = = = = = = = = 0 D010 = ? ? = = ? ? = = = = = = = = = ? = = = = ? ? = = ? ? = = = = = = = = = ? = = = 0 D011 = = = = = = = C = = A C = = = = = A C G = = = = = = = A = = G T = = = = = G T A 0 D012 = T = ? ? = (T) ? = = = = = = = = ? A C G = C = ? ? = (G) ? = = = = = = = = ? G T A 0 D013 = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = 0 D014 = = = ? ? = = C = = A C = = = = = A C G = = = ? ? = = A = = G T = = = = = G T A 0 D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D016 A = = ? ? = = = = = G T = = = = = = = = T = = ? ? = = = = = A C = = = = = = = = 0 D033 = = = = = = = C = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = 0 D034 = = = = = G = A = = = = = = = = = = = = = = = = = A = C = = = = = = = = = = = = 0 D035 A = = ? ? = = C = = = = = = = = ? = = = T = = ? ? = = A = = = = = = = = ? = = = 0 D036 A = = = = = = C = = = = = = = = = A C G T = = = = = = A = = = = = = = = = G T A 0 D037 ? ? ? = = = = C = = A C = = ? = ? A C G ? ? ? = = = = A = = G T = = ? = ? G T A 0 D038 = = = = = = = C = = A C = = = = ? A C G = = = = = = = A = = G T = = = = ? G T A 0 D039 = = = ? ? = = C = = = = = = = ? ? A C G = = = ? ? = = A = = = = = = = ? ? G T A 0 D040 = = = A = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = 0 E001 = = (A) = = = = C = = A C ? = = = ? A C G = = (G) = = = = A = = G T ? = = = ? G T A 0 E002 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = 0 E003 = = = = = = = C = = A C = = = = = A C G = = = = = = = A = = G T = = = = = G T A 0 E004 = = (A) = = = = C = = A C = = = = = A C G = = (G) = = = = A = = G T = = = = = G T A 0 E005 = = = = = = = C = = A C = = = = = A C G = = = = = = = A = = G T = = = = = G T A 0 E006 = T = = T = T = C C = = G G G T G A C G = C = = C = G = T T = = A A A C A G T A 0 E007 = ? ? = = = = C = = A C = = = = = A C G = ? ? = = = = A = = G T = = = = = G T A 0 E008 = T = = T = T A C C G T ? = G T G = = = = C = = C = G C T T A C ? = A C A = = = 0 E009 = = (A) = = = = C ? ? A C = = = = = A C G = = (G) = = = = A ? ? G T = = = = = G T A 0 E010 = T = = T ? T = C C = = G ? G T G A C G = C = = C ? G = T T = = A ? A C A G T A 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 ? = = = = = = = = = = = = G = = = = = = ? = = = = = = = = = = = = A = = = = = = 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = = = = = C = = A C = = = = = A C G = = = = = = = A = = G T = = = = = G T A 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E017 ? = = = = = = C = = A C = = = = = A C G ? = = = = = = A = = G T = = = = = G T A 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 = (T) = = = = = A = = G T = = = = = = = = = (C) = = = = = C = = A C = = = = = = = = 0 E020 = T = = T = T = C C = = G = ? T G A C G = C = = C = G = T T = = A = ? C A G T A 0 E021 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E023 ? = = = = = = C = = A C = = = = = A C G ? = = = = = = A = = G T = = = = = G T A 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 = = 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 = 0.93 = ? ? = 0.54 ? = = = = = = = = ? 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 = = = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = 0.78 = = = = 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 = = 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 = = = = = 0.77 = = = = 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 = = = = = = = = = = = = = = = = = = = = = 0.79 = = = = = 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