************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 tnap1.phase.inp tnap1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tnap1.phase.out_freqs : haplotype frequency estimates tnap1.phase.out_pairs : most likely haplotype pairs for each individual tnap1.phase.out_recom : estimates of recombination parameters tnap1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 20 Positions of loci: 3633 4224 5066 5186 5400 5809 7977 9518 10045 10614 10618 12174 12217 12734 13309 13553 13570 13822 14050 14132 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tnap1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCGCCGCCGCGGGAGIIDCC 2.000000 2 GCGCCGCCGCTGGTGDDDCC 5.000000 3 GCGCCGCCAGGGGAGIIDCC 40.000000 4 GCGCCGCCAGGGGAAIIDCC 5.000000 5 GCGCCGCAGCTGGTGDDDCC 2.000000 6 GCGCCCTCGCGCAAGIIDCC 3.000000 7 GTACCGCCGCGGGAGIIDCC 19.000000 8 GTACCGCCGCGGGAGIIDTC 2.000000 9 GTACCGCCGCGGGAGIIICC 3.000000 10 GTACCGCCGGGGGAGIIDCC 1.000000 11 GTAACGCCGCGGGAGIIDCC 6.000000 12 ACGCTGTCGCTGGTGDDDCT 6.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,7) D002: (5,10) D003: (2,3) D004: (6,7) D005: (2,3) D006: (1,3) D007: (3,7) D008: (4,7) D009: (7,12) D010: (3,4) D011: (3,3) D012: (2,2) D013: (4,6) D014: (7,7) D015: (3,12) D016: (3,5) D033: (7,12) D034: (3,6) D035: (2,3) D036: (3,3) D037: (3,3) D038: (3,12) D039: (3,4) D040: (3,4) E001: (9,11) E002: (3,3) E003: (3,7) E004: (3,7) E005: (3,7) E006: (3,7) E007: (3,11) E008: (3,3) E009: (3,11) E010: (3,9) E011: (7,7) E012: (3,3) E013: (11,11) E014: (3,7) E015: (3,8) E016: (3,7) E017: (7,7) E018: (3,3) E019: (7,12) E020: (3,9) E021: (3,8) E022: (3,12) E023: (3,11) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G C G C C G C C G C G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 D002 G C G C C G C A G (C) T G G T G D D D C C G T A C C G C C G (G) G G G A G I I D C C 0 D003 G C G C C G C C G C T G G T G D D D C C G C G C C G C C A G G G G A G I I D C C 0 D004 G C G C C C T C G C G C A A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 D005 G C G C C G C C G C T G G T G D D D C C G C G C C G C C A G G G G A G I I D C C 0 D006 G C G C C G C C G C G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 D007 G C G C C G C C A G G G G A G I I D C C G T A [C] C G C C G C G G G A G I I D C C 0 D008 G C G C C G C C A G G G G A A I I D C C G T A C C G C C G C G G G A G I I D C C 0 D009 G T A C C G C C G C G G G A G I I D C C A C G C T G T C G C T G G T G D D D C T 0 D010 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A A I I D C C 0 D011 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 D012 G C G C C G C C G C T G G T G D D D C C G C G C C G C C G C T G G T G D D D C C 0 D013 G C G C C G C C A G G G G A A I I D C C G C G C C C T C G C G C A A G I I D C C 0 D014 G T A C C G C C G C G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 D015 G C G C C G C C A G G G G A G I I D C C A C G C T G T C G C T G G T G D D D C T 0 D016 G C G C C G C (C) A G G G G A G I I D C C G C G C C G C (A) G C T G G T G D D D C C 0 D033 G T A C C G C C G C G G G A G I I D C C A C G C T G T C G C T G G T G D D D C T 0 D034 G C G C C G C C A G G G G A G I I D C C G C G C C C T C G C G C A A G I I D C C 0 D035 G C G C C G C C G C T G G T G D D D C C G C G C C G C C A G G G G A G I I D C C 0 D036 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 D037 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 D038 G C G C C G C C A G G G G A G I I D C C A C G C T G T C G C T G G T G D D D C T 0 D039 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A A I I D C C 0 D040 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A A I I D C C 0 E001 G T A C C G C C G C G G G A G I I I C C G T A A C G C C G C G G G A G I I D C C 0 E002 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 E003 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E004 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E005 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E006 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E007 G C G C C G C C A G G G G A G I I D C C G T A A C G C C G C G G G A G I I D C C 0 E008 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 E009 G C G C C G C C A G G G G A G I I D C C G T A A C G C C G C G G G A G I I D C C 0 E010 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I I C C 0 E011 G T A [C] C G C C G C G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E012 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 E013 G T A A C G C C G C G G G A G I I D C C G T A A C G C C G C G G G A G I I D C C 0 E014 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E015 G C G C C G C C A G G G G A G I I D (C) C G T A C C G C C G C G G G A G I I D (T) C 0 E016 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E017 G T A C C G C C G C G G G A G I I D C C G T A C C G C C G C G G G A G I I D C C 0 E018 G C G C C G C C A G G G G A G I I D C C G C G C C G C C A G G G G A G I I D C C 0 E019 G T A C C G C C G C G G G A G I I D C C A C G C T G T C G C T G G T G D D D C T 0 E020 G C G C C G C C A G G G G A G I I D C C G T A C C G C C G C G G G A G I I I C C 0 E021 G C G C C G C C A G G G G A G I I D (C) C G T A C C G C C G C G G G A G I I D (T) C 0 E022 G C G C C G C C A G G G G A G I I D C C A C G C T G T C G C T G G T G D D D C T 0 E023 G C G C C G C C A G G G G A G I I D C C G T A A C G C C G C G G G A G I I D 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 = C G = = = = = = = = = = = = = = = = = = T A = = = = = = = = = = = = = = = = = 0 D002 = C G = = = = A = (C) T = = T = D D ? = = = T A = = = = C = (G) G = = A = I I ? = = 0 D003 = = ? ? = = = = G C T ? ? T = D D ? ? ? = = ? ? = = = = A G G ? ? A = I I ? ? ? 0 D004 = C G = = C T = = = = C A = = = = = = = = T A = = G C = = = = G G = = = = = = = 0 D005 = = ? ? = = = = G C T = = T = D D = = = = = ? ? = = = = A G G = = A = I I = = = 0 D006 = = ? = = = = = G C = ? ? = = = = = = = = = ? = = = = = A G = ? ? = = = = = = = 0 D007 = C ? ? = ? = = A G = = = = = = = = = = = T ? ? = ? = = G C = = = = = = = = = = 0 D008 = C G = = = = = A G = = = = A = = = = = = T A = = = = = G C = = = = G = = = = = 0 D009 G T A = C ? ? = = = G = = A = I I = = C A C G = T ? ? = = = T = = T = D D = = T 0 D010 = = = = = = = = = = = = = = G ? ? = = = = = = = = = = = = = = = = = A ? ? = = = 0 D011 = = ? ? = = = ? = = = = = = = = = ? ? ? = = ? ? = = = ? = = = = = = = = = ? ? ? 0 D012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D013 = = = = = G ? ? A G = ? ? = A = = = = = = = = = = C ? ? G C = ? ? = G = = = = = 0 D014 = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 D015 G = = = C = C = A G G = = A ? I I = = C A = = = T = T = G C T = = T ? D D = = T 0 D016 = = = = = = = (C) A G G = = A = ? ? = = = = = = = = = = (A) G C T = = T = ? ? = = = 0 D033 G T A = C ? C = = = G = = A = I I = = C A C G = T ? T = = = T = = T = D D = = T 0 D034 = = = = = G C ? A G = G G = = = = = = = = = = = = C T ? G C = C A = = = = = = = 0 D035 = = ? ? = = ? ? G C T = = T ? ? D ? ? ? = = ? ? = = ? ? A G G = = A ? ? I ? ? ? 0 D036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = ? = = = = = ? = = = ? ? = = = = = = = = ? = = = = = ? = = = ? ? = = = = = = = 0 D038 G = = = C = C = A G G = = A ? I I = = C A = = = T = T = G C T = = T ? D D = = T 0 D039 = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = A = = = = = 0 D040 ? = = = = = = = = = = = = = G = = = = = ? = = = = = = = = = = = = = A = = = = = 0 E001 = = = C = = = = = = = = = = = = = I = = = = = A = = = = = = = = = = = = = D = = 0 E002 = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = 0 E003 = C ? ? = = = ? A G = = = = = = = ? ? ? = T ? ? = = = ? G C = = = = = = = ? ? ? 0 E004 = C G = = = = = A G = = = = = = = = = = = T A = = = = = G C = = = = = = = = = = 0 E005 ? ? G = = = = = A G = = = = = = = = = = ? ? A = = = = = G C = = = = = = = = = = 0 E006 = C G = = = = = A G = = = = = = = = = = = T A = = = = = G C = = = = = = = = = = 0 E007 = C G C = = = = A G = = = = = = = = = = = T A A = = = = G C = = = = = = = = = = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = C G C = = = = A G = = = = = = = = ? ? = T A A = = = = G C = = = = = = = = ? ? 0 E010 = C ? = = = = = A G = = = = = = = D = = = T ? = = = = = G C = = = = = = = I = = 0 E011 = = ? ? = ? = ? = = = = = = = = = ? ? ? = = ? ? = ? = ? = = = = = = = = = ? ? ? 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 0 E014 = C G = = = = = A ? = = = = = = = ? ? ? = T A = = = = = G ? = = = = = = = ? ? ? 0 E015 = C G = = = = = A G = = = = = = = = (C) = = T A = = = = = G C = = = = = = = = (T) = 0 E016 ? C G = = = = = A G = = = = = = = = = = ? T A = = = = = G C = = = = = = = = = = 0 E017 = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 G ? ? ? C = C = = = G ? ? A ? I I ? ? ? A ? ? ? T = T = = = T ? ? T ? D D ? ? ? 0 E020 = C G = = ? = ? A G = = = = = = = D = = = T A = = ? = ? G C = = = = = = = I = = 0 E021 = C G = = ? = = A G = = = = = = = = (C) = = T A = = ? = = G C = = = = = = = = (T) = 0 E022 G = = = C ? C ? A G G = = A = ? ? = = C A = = = T ? T ? G C T = = T = ? ? = = T 0 E023 = C ? C = ? = ? A G = = = = = = = = = = = T ? A = ? = ? G 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 = = = = 0.91 = 0.56 1.00 = = 1.00 = 1.00 1.00 ? = = = = ? ? = = = = 1.00 1.00 1.00 ? ? 1.00 = 1.00 1.00 ? ? ? = 1.00 1.00 = = 1.00 1.00 = = = = 1.00 1.00 = = = = = = = = = ? ? = = = = 1.00 1.00 1.00 = = 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 = 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 = 1.00 1.00 1.00 = = 1.00 ? 1.00 1.00 = = 1.00 = = = = = = = 0.79 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 = = = = = 1.00 1.00 ? 1.00 1.00 = 1.00 1.00 = = = = = = = = = ? ? = = ? ? 1.00 1.00 1.00 = = 1.00 ? ? 1.00 ? ? ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = ? ? = = = = = = = 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 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 0.99 = = = = 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 = = = = = = = = 0.54 = ? 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 = = ? = ? 1.00 1.00 = = = = = = = 0.97 = = = 1.00 1.00 = = ? = = 1.00 1.00 = = = = = = = = 0.56 = 1.00 = = = 1.00 ? 1.00 ? 1.00 1.00 1.00 = = 1.00 = ? ? = = 1.00 = 1.00 ? 0.99 = ? = ? 1.00 1.00 = = = = = = = = = = END PHASEPROBS