************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 ilkn9.phase.inp ilkn9.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ilkn9.phase.out_freqs : haplotype frequency estimates ilkn9.phase.out_pairs : most likely haplotype pairs for each individual ilkn9.phase.out_recom : estimates of recombination parameters ilkn9.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 12 Positions of loci: 79 164 448 1245 2049 2710 3392 3652 3819 4272 5515 5738 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ilkn9.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ADTCGATACGAT 6.000000 2 AICCAACAGACC 1.000000 3 AICCAATACGAT 1.000000 4 AICCAATACGCC 2.000000 5 AICTAACAGACC 38.000000 6 AICTAACAGGCC 1.000000 7 AICTAACCGACC 30.000000 8 AICTAGCAGGCC 4.000000 9 AITCAACAGACC 3.000000 10 AITCAATACGAT 5.000000 11 CICCAATACGCC 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,5) D002: (5,7) D003: (7,7) D004: (5,5) D005: (5,10) D006: (5,8) D007: (5,6) D008: (9,10) D009: (7,8) D010: (7,11) D011: (5,9) D012: (5,7) D013: (5,5) D014: (5,9) D015: (2,5) D016: (5,5) D033: (1,7) D034: (4,4) D035: (1,10) D036: (5,11) D037: (5,7) D038: (7,8) D039: (8,11) D040: (5,5) E001: (7,7) E002: (3,5) E003: (1,5) E004: (7,10) E005: (5,7) E006: (5,7) E007: (5,7) E008: (5,7) E009: (5,10) E010: (5,7) E011: (5,7) E012: (1,5) E013: (7,7) E014: (7,7) E015: (5,5) E016: (5,7) E017: (5,7) E018: (5,7) E019: (5,7) E020: (5,7) E021: (7,7) E022: (5,5) E023: (1,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A D T C G A T A C G A T A I C T A A C A G A C C 0 D002 A I C T A A C A G A C C A I C T A A C C G A C C 0 D003 A I C T A A C C G A C C A I C T A A C C G A C C 0 D004 A I C T A A C A G A C C A I C T A A C A G A C C 0 D005 A I C T A A C A G A C C A I T C A A T A C G A T 0 D006 A I C T A A C A G A C C A I C T A G C A G G C C 0 D007 A I C T A A C A G A C C A I C T A A C A G G C C 0 D008 A I T C A A C A G A C C A I T C A A T A C G A T 0 D009 A I C T A A C C G A C C A I C T A G C A G G C C 0 D010 A I C T A A C C G A C C C I C C A A T A C G C C 0 D011 A I C T A A C A G A C C A I T C A A C A G A C C 0 D012 A I C T A A C A G A C C A I C T A A C C G A C C 0 D013 A I C T A A C A G A C C A I C T A A C A G A C C 0 D014 A I C T A A C A G A C C A I T C A A C A G A C C 0 D015 A I C C A A C A G A C C A I C T A A C A G A C C 0 D016 A I C T A A C A G A C C A I C T A A C A G A C C 0 D033 A D T C G A T A C G A T A I C T A A C C G A C C 0 D034 A I C C A A T A C G C C A I C C A A T A C G C C 0 D035 A D T C G A T A C G A T A I [T] C A A T A C G A T 0 D036 A I C T A A C A G A C C C I C C A A T A C G C C 0 D037 A I C T A A C A G A C C A I C T A A C C G A C C 0 D038 A I C T A A C C G A C C A I C T A G C A G G C C 0 D039 A I C T A G C A G G C C C I C C A A T A C G C C 0 D040 A I C T A A C A G A C C A I C T A A C A G A C C 0 E001 A I C T A A C C G A C C A I C T A A C C G A C C 0 E002 A I C C A A T A C G A T A I C T A A C A G A C C 0 E003 A D T C G A T A C G A T A I C T A A C A G A C C 0 E004 A I C T A A C C G A C C A I [T] C A A T A C G A T 0 E005 A I C T A A C A G A C C A I C T A A C C G A C C 0 E006 A I C T A A C A G A C C A I C T A A C C G A C C 0 E007 A I C T A A C A G A C C A I C T A A C C G A C C 0 E008 A I C T A A C A G A C C A I C T A A C C G A C C 0 E009 A I C T A A C A G A C C A I T C A A T A C G A T 0 E010 A I C T A A C A G A C C A I C T A A C C G A C C 0 E011 A I C T A A C A G A C C A I C T A A C C G A C C 0 E012 A D T C G A T A C G A T A I C T A A C A G A C C 0 E013 A I C T A A C C G A C C A I C T A A C C G A C C 0 E014 A I C T A A C C G A C C A I C T A A C C G A C C 0 E015 A I C T A A C A G A C C A I C T A A C A G A C C 0 E016 A I C T A A C A G A C C A I C T A A C C G A C C 0 E017 A I C T A A C A G A C C A I C T A A C C G A C C 0 E018 A I C T A A C A G A C C A I C T A A C C G A C C 0 E019 A I C T A A C A G A C C A I C T A A C C G A C C 0 E020 A I C T A A C A G A C C A I C T A A C C G A C C 0 E021 A I C T A A C C G A C C A I C T A A C C G A C C 0 E022 A I C T A A C A G A C C A I C T A A C A G A C C 0 E023 A D T C G A T A C G A T A I C T A A C C G A C C 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 ? D T C G = T = ? G A T ? I C T A = C = ? A C C 0 D002 ? = = = = = = A = = = = ? = = = = = = C = = = = 0 D003 = = = = = = = = = = = = = = = = = = = = = = = = 0 D004 = = = = = = = = = = = = = = = = = = = = = = = = 0 D005 ? = C T = = C = G A C C ? = T C = = T = C G A T 0 D006 = = = = = A = = = A = = = = = = = G = = = G = = 0 D007 ? = = = = = = = = A = = ? = = = = = = = = G = = 0 D008 = = = = = = C = G A C C = = = = = = T = C G A T 0 D009 = = = = = A = C = A ? ? = = = = = G = A = G ? ? 0 D010 A = = T = = C C G A = = C = = C = = T A C G = = 0 D011 = = C T ? = = = = ? = = = = T C ? = = = = ? = = 0 D012 = = = = = = = A = = = = = = = = = = = C = = = = 0 D013 = = = = = = = = = = = = = = = = = = = = = = = = 0 D014 = = C T = = = = = = = = = = T C = = = = = = = = 0 D015 = = = C = = = = ? ? = = = = = T = = = = ? ? = = 0 D016 = = = = = ? ? = = = = = = = = = = ? ? = = = = = 0 D033 ? D T C G = T A C G A T ? I C T A = C C G A C C 0 D034 = = = = = = = = = = = = = = = = = = = = = = = = 0 D035 = D ? = G = = = = = = = = I ? = A = = = = = = = 0 D036 A = = T = = C = G A = = C = = C = = T = C G = = 0 D037 = = = = = = = A = = = = = = = = = = = C = = = = 0 D038 = = = = = A = C = A = = = = = = = G = A = G = = 0 D039 A = = T = G C = G = = = C = = C = A T = C = = = 0 D040 = = = = = = = = = = = = = = = = = = = = = = = = 0 E001 = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 = = = C = = T = C G A T = = = T = = C = G A C C 0 E003 = D ? C G = T = C ? ? ? = I ? T A = C = G ? ? ? 0 E004 ? ? ? T = ? C C G A C C ? ? ? C = ? T A C G A T 0 E005 = = = = = = = A = = = = = = = = = = = C = = = = 0 E006 = = = = = = = A = = = = = = = = = = = C = = = = 0 E007 ? = = = = = = A = = = = ? = = = = = = C = = = = 0 E008 = = = = = = = A = = = = = = = = = = = C = = = = 0 E009 = = C T ? = C = G A C C = = T C ? = T = C G A T 0 E010 = = = = = = = A = = = = = = = = = = = C = = = = 0 E011 = = = = = = = A = = = = = = = = = = = C = = = = 0 E012 ? D T C G = T = C G A T ? I C T A = C = G A C C 0 E013 = = = = = = = = = = ? ? = = = = = = = = = = ? ? 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 = = = = = = = A = = = = = = = = = = = C = = = = 0 E017 = = = = = = = A = = = = = = = = = = = C = = = = 0 E018 = = = = = = = A = = = = = = = = = = = C = = = = 0 E019 = = = = = = = A = ? = = = = = = = = = C = ? = = 0 E020 = = = = = = = A = = = = = = = = = = = C = = = = 0 E021 = = = = = = = = = ? = = = = = = = = = = = ? = = 0 E022 = = = = = = = = = = = = = = = = = = = = = = = = 0 E023 ? D T C G = T A C G A T ? I C T A = C C G A C C 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 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 ? = = = = ? = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = 1.00 = 1.00 1.00 0.96 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 = = = = = = = = = = = 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 END PHASEPROBS