************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 nfkb3.phase.inp nfkb3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST nfkb3.phase.out_freqs : haplotype frequency estimates nfkb3.phase.out_pairs : most likely haplotype pairs for each individual nfkb3.phase.out_recom : estimates of recombination parameters nfkb3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 14 Positions of loci: 2942 3346 3470 3684 4098 4320 4673 5347 6499 8813 9075 9292 10549 10906 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file nfkb3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACADCCTAGTGGCC 19.000000 2 ACGDCCTAGTGGCG 11.000000 3 ACGDCCTACTGGCG 8.000000 4 ACGDCCTGGTGGCG 2.000000 5 ACGDCCCACGGACG 4.000000 6 ACGDTCTAGTGGCG 5.000000 7 ACGICCTAGTGGCG 6.000000 8 AAGDCTTAGGAGCG 16.000000 9 GCGDCCTACTGGCG 18.000000 10 GCGDCCTACTGGGG 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,6) D002: (1,5) D003: (8,9) D004: (8,9) D005: (2,8) D006: (2,2) D007: (8,9) D008: (3,3) D009: (2,4) D010: (5,8) D011: (3,8) D012: (2,8) D013: (8,8) D014: (8,9) D015: (5,9) D016: (1,9) D033: (1,3) D034: (2,2) D035: (3,3) D036: (3,5) D037: (2,2) D038: (3,9) D039: (2,4) D040: (2,8) E001: (1,7) E002: (7,10) E003: (1,9) E004: (1,10) E005: (1,1) E006: (1,1) E007: (7,9) E008: (8,9) E009: (7,9) E010: (1,7) E011: (9,10) E012: (1,9) E013: (6,8) E014: (1,6) E015: (8,10) E016: (1,6) E017: (1,9) E018: (6,9) E019: (1,1) E020: (1,9) E021: (7,10) E022: (9,9) E023: (8,8) 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 D C C T A G T G G C C A C G D T C T A G T G G C G 0 D002 A C A D C C T A G T G G C C A C G D C C C A C G G A C G 0 D003 A A G D C T T A G G A G C G G C G D C C T A C T G G C G 0 D004 A A G D C T T A G G A G C G G C G D C C T A C T G G C G 0 D005 A C G D C C T A G T G G C G A A G D C T T A G G A G C G 0 D006 A C G D C C T [A] G T G G C G A C G D C C T A G T G G C G 0 D007 A A G D C T T A G G A G C G G C G D C C T A C T G G C G 0 D008 A C G D C C T A C T G G C G A C G D C C T A C T G G C G 0 D009 A C G D C C T A G T G G C G A C G D C C T G G T G G C G 0 D010 A C G D C C C A C G G A C G A A G D C T T A G G A G C G 0 D011 A C G D C C T A C T G G C G A A G D C T T A G G A G C G 0 D012 A C G D C C T A G T G G C G A A G D C T T A G G A G C G 0 D013 A A G D C T T A G G A G C G A A G D C T T A G G A G C G 0 D014 A A G D C T T A G G A G C G G C G D C C T A C T G G C G 0 D015 A C G D C C C A C G G A C G G C G D C C T A C T G G C G 0 D016 A C A D C C T A G T G G C C G C G D C C T A C T G G C G 0 D033 A C A D C C T A G T G G C C A C G D C C T A C T G G C G 0 D034 A C G D C C T A G T G G C G A C G D C C T A G T G G C G 0 D035 A C G D C C T A C T G G C G A C G D C C T A C T G G C G 0 D036 A C G D C C T A C T G G C G A C G D C C C A C G G A C G 0 D037 A C G D C C T A G T G G C G A C G D C C T A G T G G C G 0 D038 A C G D C C T A C T G G C G G C G D C C T A C T G G C G 0 D039 A C G D C C T A G T G G C G A C G D C C T G G T G G C G 0 D040 A C G D C C T A G T G G C G A A G D C T T A G G A G C G 0 E001 A C A D C C T A G T G G C C A C G I C C T A G T G G C G 0 E002 A C G I C C T A G T G G C G G C G D C C T A C T G G G G 0 E003 A C A D C C T A G T G G C C G C G D C C T A C T G G C G 0 E004 A C A D C C T A G T G G C C G C G D C C T A C T G G G G 0 E005 A C A D C C T A G T G G C C A C A D C C T A G T G G C C 0 E006 A C A D C C T A G T G G C C A C A D C C T A G T G G C C 0 E007 A C G I C C T A G T G G C G G C G D C C T A C T G G C G 0 E008 A A G D C T T A G G A G C G G C G D C C T A C T G G C G 0 E009 A C G I C C T A G T G G C G G C G D C C T A C T G G C G 0 E010 A C A D C C T A G T G G C C A C G I C C T A G T G G C G 0 E011 G C G D C C T A C T G G C G G C G D C C T A C T G G G G 0 E012 A C A D C C T A G T G G C C G C G D C C T A C T G G C G 0 E013 A C G D T C T A G T G G C G A A G D C T T A G G A G C G 0 E014 A C A D C C T A G T G G C C A C G D T C T A G T G G C G 0 E015 A A G D C T T A G G A G C G G C G D C C T A C T G G G G 0 E016 A C A D C C T A G T G G C C A C G D T C T A G T G G C G 0 E017 A C A D C C T A G T G G C C G C G D C C T A C T G G C G 0 E018 A C G D T C T A G T G G C G G C G D C C T A C T G G C G 0 E019 A C A D C C T A G T G G C C A C A D C C T A G T G G C C 0 E020 A C A D C C T A G T G G C C G C G D C C T A C T G G C G 0 E021 A C G I C C T A G T G G C G G C G D C C T A C T G G G G 0 E022 G C G D C C T A C T G G C G G C G D C C T A C T G G C G 0 E023 A A G D C T T A G G A G C G A A G D C T T A G G A G C G 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 = = ? = = = = = ? = = G = T = = ? = = = = = ? 0 D002 = = A = = = T = G T = G = ? = = G = = = C = C G = A = ? 0 D003 A A = = = T = = G G A = = = G C = = = C = = C T G = = = 0 D004 A A = = = T = = G G A = = = G C = = = C = = C T G = = = 0 D005 = C = = = C = = = T G = = = = A = = = T = = = G A = = = 0 D006 = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = 0 D007 A A = = = T = ? G G A = = ? G C = = = C = ? C T G = = ? 0 D008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D009 = = = = = = = A = = = = = = = = = = = = = G = = = = = = 0 D010 = C = = = C C = C = G A = = = A = = = T T = G = A G = = 0 D011 = C = = = C = = C T G = = = = A = = = T = = G G A = = = 0 D012 = C = = = C = = = T G = = = = A = = = T = = = G A = = = 0 D013 ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 D014 A A = = = T = ? G G A = = = G C = = = C = ? C T G = = = 0 D015 A = = = = = C = = G = A = = G = = = = = T = = T = G = = 0 D016 A = A = = = = = G = = ? ? ? G = G = = = = = C = = ? ? ? 0 D033 = = A = = = = ? G = = = = C = = G = = = = ? C = = = = G 0 D034 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D036 = = = = = = T = = T = G = = = = = = = = C = = G = A = = 0 D037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D038 A = = = = = = = = = = = = = G = = = = = = = = = = = = = 0 D039 = = = = = = = A = = = = = = = = = = = = = G = = = = = = 0 D040 = C = = = C = = = T G = ? ? = A = = = T = = = G A = ? ? 0 E001 = = A D = = = ? = = = = = C = = G I = = = ? = = = = = G 0 E002 A = = I = = = = G = = = C = G = = D = = = = C = = = G = 0 E003 A = A = = = = = G = = = = C G = G = = = = = C = = = = G 0 E004 A = A = = = = = G = = = C C G = G = = = = = C = = = G G 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 A = = I = = = = G = = = = = G = = D = = = = C = = = = = 0 E008 A A = = = T = = G G A = = = G C = = = C = = C T G = = = 0 E009 A = = I = = = = G = = = = = G = = D = = = = C = = = = = 0 E010 = = A D = = = = = = = = = C = = G I = = = = = = = = = G 0 E011 = = = = = = = = = = = = C = = = = = = = = = = = = = G = 0 E012 A = A = = = = = G = = = = C G = G = = = = = C = = = = G 0 E013 = C = = T C = = = T G = = = = A = = C T = = = G A = = = 0 E014 = = A = C = = = = = = = = C = = G = T = = = = = = = = G 0 E015 A A = = = T = = G G A = C = G C = = = C = = C T G = G = 0 E016 = = A = C = = = = = = = ? ? = = G = T = = = = = = = ? ? 0 E017 A = A = = = = ? G = = = = C G = G = = = = ? C = = = = G 0 E018 A = = = T = = = G = = = = = G = = = C = = = C = = = = = 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E020 A = A = = = = = G = = = = C G = G = = = = = C = = = = G 0 E021 A = = I = = = = G = = = C = G = = D = = = = C = = = G = 0 E022 = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? 0 E023 = = = = = = = = = = = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = 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 1.00 1.00 = = = = 1.00 = = = 1.00 = = = 1.00 1.00 = = = = = = = = = = ? = = = = = = 1.00 1.00 = = = 1.00 = ? 1.00 1.00 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = = 1.00 = = = 1.00 = = = 1.00 1.00 = = = ? = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 = ? 1.00 1.00 1.00 = = = 1.00 = = = = = 1.00 = = 1.00 = 1.00 = = 1.00 = 1.00 = = = = = 1.00 = = ? ? ? = = 1.00 = = = = ? 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 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 = = = 0.98 = 1.00 = 1.00 = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = = 1.00 = = = 0.99 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 0.99 = = = = 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 = 0.97 = = = = = = = = 1.00 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 = 0.99 = = = 1.00 = 0.98 = = = = = = = ? ? 1.00 = 1.00 = = = = ? 1.00 = = = = 1.00 1.00 = = = 0.99 = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 = = = = 1.00 1.00 = = 0.99 = = = = 1.00 = = = 0.97 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = END PHASEPROBS