************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 fbgng.phase.inp fbgng.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fbgng.phase.out_freqs : haplotype frequency estimates fbgng.phase.out_pairs : most likely haplotype pairs for each individual fbgng.phase.out_recom : estimates of recombination parameters fbgng.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 10 Positions of loci: 129 902 5729 5836 7874 9340 9595 9615 9765 10034 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fbgng.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AAAGGCCCTC 20.000000 2 AAAGGCTCTC 2.000000 3 AAAGGTCCTC 9.000000 4 AAAGGTCCAC 5.000000 5 AGAGGCCCTC 1.000000 6 AGAGGTCCTC 29.000000 7 AGAGGTCTTT 1.000000 8 AGAAGTCCTC 5.000000 9 TAAGGTCCTC 1.000000 10 TAAGGTCTTT 1.000000 11 TAAGATCTTT 17.000000 12 TAGGATCTTT 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,7) D002: (6,3) D003: (3,6) D004: (1,12) D005: (3,11) D006: (1,6) D007: (11,12) D008: (1,4) D009: (3,4) D010: (1,6) D011: (1,10) D012: (3,11) D013: (4,11) D014: (6,11) D015: (3,3) D016: (1,2) D033: (2,11) D034: (3,11) D035: (3,6) D036: (4,11) D037: (1,1) D038: (1,4) D039: (11,12) D040: (5,11) E001: (6,6) E002: (1,11) E003: (1,11) E004: (6,8) E005: (6,6) E006: (6,6) E007: (6,6) E008: (6,11) E009: (6,8) E010: (6,8) E011: (6,11) E012: (1,6) E013: (1,1) E014: (1,6) E015: (6,8) E016: (1,6) E017: (1,11) E018: (1,6) E019: (6,11) E020: (8,11) E021: (1,6) E022: (6,6) E023: (6,9) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A (A) A G G (C) C C T C A (G) A G G (T) C T T T 0 D002 A [G] A G G T C C T C A [A] A G G T C C T C 0 D003 A A A G G T C C T C A G A G G T C C T C 0 D004 A A A G G C C C T C T A G G A T C T T T 0 D005 A A A G G T C C T C T A A G A T C T T T 0 D006 A A A G G C C C T C A G A G G T C C T C 0 D007 T A A G A T C T T T T A G G A T C T T T 0 D008 A A A G G C C C T C A A A G G T C C A C 0 D009 A A A G G T C C T C A A A G G T C C A C 0 D010 A A A G G C C C T C A [G] A G G T C C T C 0 D011 (A) A A G G (C) C C T C (T) A A G G (T) C T T T 0 D012 A A A G G T C C T C T A A G A T C T T T 0 D013 A A A G G T C C A C T A A G A T C T T T 0 D014 A G A G G T C C T C T A A G A T C T T T 0 D015 A A A G G T C C T C A A A G G T C C T C 0 D016 A A A G G C C C T C A A A G G C T C T C 0 D033 A A A G G C T C T C T A A G A T C T T T 0 D034 A A A G G T C C [T] C T A A G A T C T T T 0 D035 A A A G G T C C T C A G A G G T C C T C 0 D036 A A A G G T C C A C T A A G A T C T T T 0 D037 A A A G G C C C T C A A A G G C C C T C 0 D038 A A A G G C C C T C A A A G G T C C A C 0 D039 T A A G A T C T T T T A G G A T C T T T 0 D040 A (G) A G G (C) C C T C T (A) A G A (T) C T T T 0 E001 A G A G G T C C T C A G A G G T C C T C 0 E002 A A A G G C C C T C T A A G A T C T T T 0 E003 A A A G G C C C T C T A A G A T C T T T 0 E004 A G A G G T C C T C A G A A G T C C T C 0 E005 A G A [G] G T C C T C A G A G G T C C T C 0 E006 A G A G G T C C T C A G A G G T C C T C 0 E007 A G A G G T C C T C A G A G G T C C T C 0 E008 A G A G G T C C T C T A A G A T C T T T 0 E009 A [G] A G G T C C T C A G A A G T C C T C 0 E010 A G A G G T C C T C A G A A G T C C T C 0 E011 A G A G G T C C T C T A A G A T C T T T 0 E012 A A A G G C C C T C A G A G G T C C T C 0 E013 A A A G G C C C T C A A A G G C C C T C 0 E014 A A A G G C C C T C A G A G G T C C T C 0 E015 A G A G G T C C T C A G A A G T C C T C 0 E016 A A A G G C C C T C A G A G G T C C T C 0 E017 A A A G G C C C T C T A A G A T C T T T 0 E018 A A A G G C C C T C A G A G G T C C T C 0 E019 A G A G G T C C T C T A A G A T C T T T 0 E020 A G A A G T C C T C T A A G A T C T T T 0 E021 A A A G G C C C T C A G A G G T C C T C 0 E022 A G A G G T C C T C A G A G G T C C T C 0 E023 (A) G A G G T C C T C (T) A A G G T C C T 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 = (A) = = = (C) = C = C = (G) = = = (T) = T = T 0 D002 ? ? ? = = = = = ? = ? ? ? = = = = = ? = 0 D003 ? A = = = = = = = = ? G = = = = = = = = 0 D004 A = A = G C = C = C T = G = A T = T = T 0 D005 A = ? = G = = C = C T = ? = A = = T = T 0 D006 = A = = = C = = = = = G = = = T = = = = 0 D007 = = A = = = = = = = = = G = = = = = = = 0 D008 = = = = = C = = T = = = = = = T = = A = 0 D009 = = = = = = ? = T = = = = = = = ? = A = 0 D010 ? ? ? = = C = ? ? ? ? ? ? = = T = ? ? ? 0 D011 (A) = = = = (C) = C = C (T) = = = = (T) = T = T 0 D012 A = = = G = = C = C T = = = A = = T = T 0 D013 A = = = G = = C A C T = = = A = = T T T 0 D014 A G = = G = ? ? ? C T A = = A = ? ? ? T 0 D015 = = = = = = = = = = = = = = = = = = = = 0 D016 = = = = = = C = = = = = = = = = T = = = 0 D033 A = = = G C T C = C T = = = A T C T = T 0 D034 A = = = G = ? ? ? ? T = = = A = ? ? ? ? 0 D035 = A = = = = = = = = = G = = = = = = = = 0 D036 A = = = G = = C A C T = = = A = = T T T 0 D037 = = ? ? = = ? ? ? ? = = ? ? = = ? ? ? ? 0 D038 = = = = = C = = T = = = = = = T = = A = 0 D039 = = A = = = = = = = = = G = = = = = = = 0 D040 A (G) = = G (C) = C = C T (A) = = A (T) = T = T 0 E001 = = = = ? = = = = = = = = = ? = = = = = 0 E002 A = = = G C ? ? ? ? T = = = A T ? ? ? ? 0 E003 A = = = G C = C = C T = = = A T = T = T 0 E004 = = = G = = = = = = = = = A = = = = = = 0 E005 = = ? ? = = = = = = = = ? ? = = = = = = 0 E006 = = = = = = ? ? ? ? = = = = = = ? ? ? ? 0 E007 = = = = = = = = = = = = = = = = = = = = 0 E008 A G = = G = = C = C T A = = A = = T = T 0 E009 = ? = G ? = = = = = = ? = A ? = = = = = 0 E010 = = = G = = = = = = = = = A = = = = = = 0 E011 A G = = ? = = C = C T A = = ? = = T = T 0 E012 = A = = = C = = ? ? = G = = = T = = ? ? 0 E013 = = = = = = = = = = = = = = = = = = = = 0 E014 = A = = = C = = = ? = G = = = T = = = ? 0 E015 = = = G = = = = = = = = = A = = = = = = 0 E016 = A = = = C = = = = = G = = = T = = = = 0 E017 A = = = G C ? ? ? ? T = = = A T ? ? ? ? 0 E018 = A = = = C = = = = = G = = = T = = = = 0 E019 A G = = G = = C = C T A = = A = = T = T 0 E020 ? ? = A ? = = C = C ? ? = G ? = = T = T 0 E021 = A = = = C = = = = = G = = = T = = = = 0 E022 = = ? = ? = = = ? = = = ? = ? = = = ? = 0 E023 (A) G = = = = = = ? = (T) A = = = = = = ? = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.59 = = = 0.64 = 1.00 = 1.00 ? ? ? = = = = = ? = ? 1.00 = = = = = = = = 1.00 = 0.98 = 1.00 1.00 = 1.00 = 1.00 1.00 = ? = 1.00 = = 1.00 = 1.00 = 0.98 = = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = 0.99 = = 1.00 = = = = = = = ? = 1.00 = ? ? ? = = 1.00 = ? ? ? 0.78 = = = = 0.77 = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 0.98 1.00 1.00 0.99 = = 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 0.99 1.00 = = ? ? = = ? ? ? ? = = = = = 0.99 = = 1.00 = = = 1.00 = = = = = = = 1.00 0.85 = = 1.00 0.78 = 1.00 = 1.00 = = = = ? = = = = = 1.00 = = = 1.00 0.98 ? ? ? ? 1.00 = = = 1.00 0.99 = 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 = 1.00 = 0.97 = = = 1.00 = = ? ? = = = = = = = = = = = 0.98 = = = 1.00 = = = ? = = = 1.00 = = = = = = = 0.98 = = = 1.00 = = = = 1.00 = = = 1.00 0.98 ? ? ? ? = 0.98 = = = 1.00 = = = = 1.00 0.99 = = 1.00 = = 1.00 = 1.00 ? ? = 1.00 ? = = 1.00 = 1.00 = 0.98 = = = 1.00 = = = = = = ? = ? = = = ? = 0.80 1.00 = = = = = = ? = END PHASEPROBS