************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 crprt.phase.inp crprt.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST crprt.phase.out_freqs : haplotype frequency estimates crprt.phase.out_pairs : most likely haplotype pairs for each individual crprt.phase.out_recom : estimates of recombination parameters crprt.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 18 Positions of loci: 790 969 1009 1123 1421 1440 1919 3006 3014 3872 4069 4741 4974 5237 6150 6192 6333 6469 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file crprt.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACAAG 1 ACCGAGTAIAIG 5.000000 2 ACAAG 1 AACGACTAIAIG 2.000000 3 ACAAG 1 AACGACGADAIG 12.000000 4 ATAAG 2 ACCAACTAICIT 16.000000 5 ATAAG 2 ACCAGCTAICIT 5.000000 6 ATAAG 2 ACTGAGTAICIT 2.000000 7 ATAAG 4 TCTGACTAICIG 2.000000 8 ATAAG 4 TCTGACTAICIT 20.000000 9 ATGAG 2 ACCGACTGICIT 19.000000 10 TTAGA 4 ACCGAGTAICDT 11.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,10) D002: (5,10) D003: (3,8) D004: (4,9) D005: (4,6) D006: (3,5) D007: (10,10) D008: (8,8) D009: (2,3) D010: (1,5) D011: (3,8) D012: (2,7) D013: (3,10) D014: (3,8) D015: (3,5) D016: (7,8) D033: (6,10) D034: (3,10) D035: (5,9) D036: (3,9) D037: (3,3) D038: (4,10) D039: (10,10) D040: (3,10) E001: (4,8) E002: (8,9) E003: (4,8) E004: (9,9) E005: (4,8) E006: (9,9) E007: (4,8) E008: (4,9) E009: (1,4) E010: (4,9) E011: (8,9) E012: (4,8) E013: (8,9) E014: (9,9) E015: (4,8) E016: (8,8) E017: (9,9) E018: (1,9) E019: (9,9) E020: (4,4) E021: (1,8) E022: (4,8) E023: (4,8) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A C A A G 1 A C C G A G T A I A I G T T A G A 4 A C C G A G T A I C D T 0 D002 A T A A G 2 A C C A G C T A I C I T T T A G A 4 A C C G A G T A I C D T 0 D003 A C A A G 1 A A C G A C G A D A I G A T A A G 4 T C T G A C T A I C I T 0 D004 A T A A G 2 A C C A A C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 D005 A T A A G 2 A C C A A C T A I C I T A T A A G 2 A C T G A G T A I C I T 0 D006 A C A A G 1 A A C G A C G A D A I G A T A A G 2 A C C A G C T A I C I T 0 D007 T T A G A 4 A C C G A G T A I C D T T T A G A 4 A C C G A G T A I C D T 0 D008 A T A A G 4 T C T G A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 D009 A C A A G 1 A A C G A C T A I A I G A C A A G 1 A A C G A C G A D A I G 0 D010 A C A A G 1 A C C G A G T A I A I G A T A A G 2 A C C A G C T A I C I T 0 D011 A C A A G 1 A A C G A C G A D A I G A T A A G 4 T C T G A C T A I C I T 0 D012 A C A A G 1 A A C G A C T A I A I G A T A A G 4 T C T G A C T A I C I G 0 D013 A C A A G 1 A A C G A C G A D A I G T T A G A 4 A C C G A G T A I C D T 0 D014 A C A A G 1 A A C G A C G A D A I G A T A A G 4 T C T G A C T A I C I T 0 D015 A C A A G 1 A A C G A C G A D A I G A T A A G 2 A C C A G C T A I C I T 0 D016 A T A A G 4 T C T G A C T A I C I G A T A A G 4 T C T G A C T A I C I T 0 D033 A T A A G 2 A C T G A G T A I C I T T T A G A 4 A C C G A G T A I C D T 0 D034 A C A A G 1 A A C G A C G A D A I G T T A G A 4 A C C G A G T A I C D T 0 D035 A T A A G 2 A C C A G C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 D036 A C A A G 1 A A C G A C G A D A I G A T G A G 2 A C C G A C T G I C I T 0 D037 A C A A G 1 A A C G A C G A D A I G A C A A G 1 A A C G A C G A D A I G 0 D038 A T A A G 2 A C C A A C T A I C I T T T A G A 4 A C C G A G T A I C D T 0 D039 T T A G A 4 A C C G A G T A I C D T T T A G A 4 A C C G A G T A I C D T 0 D040 A C A A G 1 A A C G A C G A D A I G T T A G A 4 A C C G A G T A I C D T 0 E001 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E002 A T A A G 4 T C T G A C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 E003 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E004 A T G A G 2 A C C G A C T G I C I T A T G A G 2 A C C G A C T G I C I T 0 E005 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E006 A T G A G 2 A C C G A C T G I C I T A T G A G 2 A C C G A C T G I C I T 0 E007 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E008 A T A A G 2 A C C A A C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 E009 A C A A G 1 A C C G A G T A I A I G A T A A G 2 A C C A A C T A I C I T 0 E010 A T A A G 2 A C C A A C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 E011 A T A A G 4 T C T G A C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 E012 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E013 A T A A G 4 T C T G A C T A I C I T A T G A G 2 A C C G A C T G I C I T 0 E014 A T G A G 2 A C C G A C T G I C I T A T G A G 2 A C C G A C T G I C I T 0 E015 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E016 A T A A G 4 T C T G A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E017 A T G A G 2 A C C G A C T G I C I T A T G A G 2 A C C G A C T G I C I T 0 E018 A C A A G 1 A C C G A G T A I A I G A T G A G 2 A C C G A C T G I C I T 0 E019 A T G A G 2 A C C G A C T G I C I T A T G A G 2 A C C G A C T G I C I T 0 E020 A T A A G 2 A C C A A C T A I C I T A T A A G 2 A C C A A C T A I C I T 0 E021 A C A A G 1 A C C G A G T A I A I G A T A A G 4 T C T G A C T A I C I T 0 E022 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I T 0 E023 A T A A G 2 A C C A A C T A I C I T A T A A G 4 T C T G A C T A I C I 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 A C = A G 1 = = = = = = = = = A I G T T = G A 4 = = = = = = = = = C D T 0 D002 A = = A G 2 = = = ? G C = = = = I = T = = G A 4 = = = ? A G = = = = D = 0 D003 = C = = = 1 A A C = = = G = ? ? ? ? = T = = = 4 T C T = = = T = ? ? ? ? 0 D004 = = A = = = = = = A = = = A ? ? ? ? = = G = = = = = = G = = = G ? ? ? ? 0 D005 = = = = = = = = C A = C = = = = = = = = = = = = = = T G = G = = = = = = 0 D006 = C = ? = 1 = A = G A = G = D A = G = T = ? = 2 = C = A G = T = I C = T 0 D007 = = = ? = = = ? ? = = = = = = = = = = = = ? = = = ? ? = = = = = = = = = 0 D008 ? ? ? ? = = = ? ? = = = = = = = = = ? ? ? ? = = = ? ? = = = = = = = = = 0 D009 = = = = = = = = = = = = T = I = = = = = = = = = = = = = = = G = D = = = 0 D010 = C = = ? ? = = = G A G = = = A = G = T = = ? ? = = = A G C = = = C = T 0 D011 ? C = = = 1 A A C = = = G = D A = G ? T = = = 4 T C T = = = T = I C = T 0 D012 = C = = = 1 A A C = = = = = = A = = = T = = = 4 T C T = = = = = = C = = 0 D013 A C = A G 1 = A = = = C G = ? A I G T T = G A 4 = C = = = G T = ? C D T 0 D014 = C = = = 1 A A C = = = G = D A = G = T = = = 4 T C T = = = T = I C = T 0 D015 = C = = = 1 = A = G A = G = D A = G = T = = = 2 = C = A G = T = I C = T 0 D016 = = = ? = = = = ? = = = = = = = = G = = = ? = = = = ? = = = = = = = = T 0 D033 ? = = A G 2 = = T = = = = = = = I = ? = = G A 4 = = C = = = = = = = D = 0 D034 A C = A G 1 = A = = = C G = D A I G T T = G A 4 = C = = = G T = I C D T 0 D035 = = A = = = ? = = A G = = A = = = = = = G = = = ? = = G A = = G = = = = 0 D036 = C A = = 1 = A = = = = G A D A = G = T G = = 2 = C = = = = T G I C = T 0 D037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D038 A = = A G 2 = = = ? ? C = = = = I = T = = G A 4 = = = ? ? G = = = = D = 0 D039 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D040 A C = A G 1 = A = = = C ? = D A I G T T = G A 4 = C = = = G ? = I C D T 0 E001 = = = = = 2 A = C A = = ? = = = = = = = = = = 4 T = T G = = ? = = = = = 0 E002 = = A = = 4 T = T = = = = A = = = = = = G = = 2 A = C = = = = G = = = = 0 E003 = = = = = 2 A = C A = = = = = = = = = = = = = 4 T = T G = = = = = = = = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 = = = = = 2 ? = C A = = = = = = = = = = = = = 4 ? = T G = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 = = = = = 2 A = C A = = = = = = = = = = = = = 4 T = T G = = = = = = = = 0 E008 = = A = = = = = = A = = = A = = = = = = G = = = = = = G = = = G = = = = 0 E009 = C = = = ? = = = G = G = = = A = G = T = = = ? = = = A = C = = = C = T 0 E010 = = A = = = = = = A = = = A = = = = = = G = = = = = = G = = = G = = = = 0 E011 = = A = = 4 ? = T = = = = A = = = = = = G = = 2 ? = C = = = = G = = = = 0 E012 = = = ? = 2 A = C A = = = = = = = = = = = ? = 4 T = T G = = = = = = = = 0 E013 = = A = = 4 T = T = = = = A = = = = = = G = = 2 A = C = = = = G = = = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 = = = = = 2 A = C A = = = = = = = = = = = = = 4 T = T G = = = = = = = = 0 E016 = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 0 E017 = = = = ? ? ? = = = = ? ? = = = = = = = = = ? ? ? = = = = ? ? = = = = = 0 E018 = C A = = 1 = = = = = G = A = A = G = T G = = 2 = = = = = C = G = C = T 0 E019 ? = = = = = ? = = = = = = = = = = = ? = = = = = ? = = = = = = = = = = = 0 E020 = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E021 = C = = = 1 ? = C = = G = = = A = G = T = = = 4 ? = T = = C = = = C = T 0 E022 = = = = = 2 A = C A = = ? ? = = = = = = = = = 4 T = T G = = ? ? = = = = 0 E023 = = = = = 2 A = C A = = = = = = = = = = = = = 4 T = T G = = = = = = = = 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 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 0.99 = 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 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 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 = = 1.00 = = = 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 = = ? ? = = = = = = = = = 1.00 1.00 = 1.00 1.00 = = = = = = = = END PHASEPROBS