************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 igft2.phase.inp igft2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST igft2.phase.out_freqs : haplotype frequency estimates igft2.phase.out_pairs : most likely haplotype pairs for each individual igft2.phase.out_recom : estimates of recombination parameters igft2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 15 Positions of loci: 4521 4907 5179 5550 5571 5656 5770 6164 6487 6545 6716 6824 7737 7780 8513 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file igft2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ATAGTCCTTAGGCCC 22.000000 2 ATAGTGCCCAGGCCC 5.000000 3 ATTGCGCCTGGGCGC 3.000000 4 GTAGCGCCTAGGCCC 1.000000 5 GTAGCGCCTGGGCGC 1.000000 6 GTAGTCCTTAGGCCC 2.000000 7 GTAGTCCTTAGGTCC 9.000000 8 GTAGTCCTTAGGTCT 7.000000 9 GTAGTGCCTACGCCC 5.000000 10 GTAGTGCCCAGGCCC 12.000000 11 GTAGTGCCCAGACCC 6.000000 12 GTAGTGCTTAGGCCC 1.000000 13 GTAGTGCTTAGGTCC 1.000000 14 GTAATGCCTAGGCCC 2.000000 15 GTAATGCCCAGACCC 2.000000 16 GTTGCCCCTAGGCGC 3.000000 17 GTTGCGCCCAGACCC 2.000000 18 GAAGTCTTTAGGCCC 10.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,7) D002: (6,16) D003: (1,10) D004: (5,14) D005: (7,7) D006: (7,9) D007: (7,9) D008: (1,3) D009: (13,16) D010: (7,18) D011: (9,11) D012: (3,10) D013: (11,17) D014: (10,10) D015: (7,15) D016: (7,7) D033: (1,14) D034: (2,15) D035: (1,9) D036: (16,18) D037: (6,18) D038: (1,9) D039: (4,12) D040: (8,17) E001: (2,11) E002: (2,11) E003: (1,10) E004: (2,8) E005: (1,1) E006: (1,18) E007: (2,8) E008: (1,8) E009: (1,8) E010: (10,18) E011: (1,8) E012: (1,10) E013: (10,18) E014: (1,18) E015: (10,11) E016: (1,10) E017: (10,11) E018: (1,18) E019: (1,1) E020: (1,1) E021: (10,18) E022: (1,18) E023: (1,8) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A T T G C G C C T G G G C G C G T A G T C C T T A G G T C C 0 D002 G T A G T C C T T A G G C C C G T T G C C C C T A G G C G C 0 D003 (A) T A G T C C T T A G G C C C (G) T A G T G C C C A G G C C C 0 D004 G T A (G) C G C C T [G] G G C (G) C G T A (A) T G C C T A G G C (C) C 0 D005 G T A G T C C T T A G G T C C G T A G T C C T T A G G T C C 0 D006 G T A G T C C T T A G G T C [C] G T A G T G C C T A C G C C C 0 D007 G T A G T C C T T A G G T C C G T A G T G C C T A C G C C C 0 D008 A T A G T C C T T A G G C C C A T T G C G C C T G G G C G C 0 D009 G T A G T (G) C T T A G G T C C [G] T T G C (C) C C T A G G C G C 0 D010 G T A G T C C T T A G G T C C G A A G T C T T T A G G C C C 0 D011 G T A G T G C C T A C G C C C G T A G T G C C C A G A C C C 0 D012 A T T G C G C C T G G G C G C G T A G T G C C C A G G C C C 0 D013 G T A G T G C C C A G A C C C G T T G C G C C C A G A C C C 0 D014 G T A G T G C C C A G G C C C G T A G T G C C C A G G C C C 0 D015 G T A G T C C T T A G G [T] C C G T A A T G C C C A G A C C C 0 D016 G T A G T C C T T A G G T C C G T A G T C C T T A G G T C C 0 D033 A T A G T C C T T A G G C C C G T A A T G C C T A G G C C C 0 D034 (A) T A G T G C C C A G (G) C C C (G) T A A T G C C C A G (A) C C C 0 D035 A T A G T C C T T A G G C C C G T A G T G C C T A C G C C C 0 D036 G T T G C C C C T A G G C G C G A A G T C T T T A G G C C C 0 D037 G T A G T C C T T A G G C C C G A A G T C T T T A G G C C C 0 D038 A T A G T C C T T A G G C C C G T A G T G C C T A C G C C C 0 D039 G T A G (C) G C C T A G G C C C G T A G (T) G C T T A G G C C C 0 D040 G T A G (T) C C T T A G G T C T G T T G (C) G C C C A G A C C C 0 E001 (A) T A G T G C C C A G G C C C (G) T A G T G C C C A G A C C C 0 E002 (A) T A G T G C C C A G G C C C (G) T A G T G C C C A G A C C C 0 E003 A T A G T C C T T A G G C C C G T A G T G C C C A G G C C C 0 E004 (A) T A G T G C C C A G G C C C (G) T A G T C C T T A G G T C T 0 E005 A T A G T C C T T A G G C C C A T A G T C C T T A G G C C C 0 E006 A T A G T C C T T A G G C C C G A A G T C T T T A G G C C C 0 E007 (A) T A G T G C C C A G G C C C (G) T A G T C C T T A G G T C T 0 E008 A T A G T C C T T A G G C C C [G] T A G T C C T T A G G T C T 0 E009 (A) T A G T C C T T A G G C C C (G) T A G T C C T T A G G T C T 0 E010 G T A G T G C C C A G G C C C G A A G T C T T T A G G C C C 0 E011 (A) T A G T C C T T A G G C C C (G) T A G T C C T T A G G T C T 0 E012 A T A G T C C T T A G G C C C G T A G T G C C [C] A G G C C C 0 E013 G T A G T G C C C A G G C C C G A A G T C T T T A G G C C C 0 E014 A T A G T C C T T A G G C C C G A A G T C T T T A G G C C C 0 E015 G T A G T G C C C A G G C C C G T A G T G C C C A G A C C C 0 E016 A T A G T C C T T A G G C C C G T A G T G C C C A G G C C C 0 E017 G T A G T G C C C A G G C C C G T A G T G C C C A G A C C C 0 E018 A T A G T C C T T A G G C C C G A A G T C T T T A G G C C C 0 E019 A T A G T C C T T A G G C C C A T A G T C C T T A G G C C C 0 E020 [A] T A G T C C T T A G G C C C A T A G T C C T T A G G C C C 0 E021 G T A G T G C C C A G G C C C G A A G T C T T T A G G C C C 0 E022 A T A G T C C T T A G G C C C G A A G T C T T T A G G C C C 0 E023 (A) T A G T C C T T A G G C C C (G) T A G T C C T T A G G T C 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 = T = C G = C ? G = = C G = G = A = T C = T ? A = = T C = 0 D002 = = A = T = = T ? = = = = C = = = T = C = = C ? = = = = G = 0 D003 (A) = = = = C = T ? = = = ? = = (G) = = = = G = C ? = = = ? = = 0 D004 = = = (G) C = = = ? ? = = = (G) = = = = (A) T = = = ? ? = = = (C) = 0 D005 = = = = = = = = ? ? ? ? = = = = = = = = = = = ? ? ? ? = = = 0 D006 = = = = = C ? T ? = G = T = ? = = = = = G ? C ? = C = C = ? 0 D007 = = = = = C ? T = = G = T = = = = = = = G ? C = = C = C = = 0 D008 ? = A = T C = T ? A = = = C = ? = T = C G = C ? G = = = G = 0 D009 ? = A = T (G) = T = = = = T C = ? = T = C (C) = C = = = = C G = 0 D010 = T = = = ? ? = ? = = = T = = = A = = = ? ? = ? = = = C = = 0 D011 = = = = = = = = ? = C G = = = = = = = = = = = ? = G A = = = 0 D012 A = T = C ? = = ? G = = = G = G = A = T ? = = ? A = = = C = 0 D013 = = A = ? ? = = = = = = = = = = = T = ? ? = = = = = = = = = 0 D014 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = ? ? = 0 D015 = = = G = C = T ? = = G ? ? = = = = A = G = C ? = = A ? ? = 0 D016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D033 A = = G = C = T = = = = = = = G = = A = G = C = = = = = = = 0 D034 (A) = = G = = = = = = = (G) = = = (G) = = A = = = = = = = (A) = = = 0 D035 A = = = = ? ? T = = G = = = = G = = = = ? ? C = = C = = = = 0 D036 = T T = C = C C = = = = = G = = A A = T = T T = = = = = C = 0 D037 = T = = = = C = = = = = = = = = A = = = = T = = = = = = = = 0 D038 A = = = = C = T = = G = = = = G = = = = G = C = = C = = = = 0 D039 = = = = (C) = = C = = = = = = = = = = = (T) = = T = = = = = = = 0 D040 = = A = (T) C = T T = = G T = T = = T = (C) G = C C = = A C = C 0 E001 (A) = = = = = = ? = = = G = = = (G) = = = = = = ? = = = A = = = 0 E002 (A) = = = = = = = = = = G = = = (G) = = = = = = = = = = A = = = 0 E003 A = = = = C = T T = = = = = = G = = = = G = C C = = = = = = 0 E004 (A) = = = = G = C C = = = C = C (G) = = = = C = T T = = = T = T 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 A T = = = = C = = = = = = = = G A = = = = T = = = = = = = = 0 E007 (A) = = = = G = C C = = = C = C (G) = = = = C = T T = = = T = T 0 E008 ? = = = = = = = = = = = C = C ? = = = = = = = = = = = T = T 0 E009 (A) = = = = = = = ? ? ? ? C = C (G) = = = = = = = ? ? ? ? T = T 0 E010 = T = = = G C C C = = = = = = = A = = = C T T T = = = = = = 0 E011 (A) = = = = = = = = = = = C = C (G) = = = = = = = = = = = T = T 0 E012 A = = = = C = T ? ? ? = = = = G = = = = G = C ? ? ? = = = = 0 E013 = T = = = G C C C = = = = = ? = A = = = C T T T = = = = = ? 0 E014 ? T = = = = C = = = = = = = ? ? A = = = = T = = = = = = = ? 0 E015 = = = = = = = = = = = G = = = = = = = = = = = = = = A = = = 0 E016 A = = = = C = T T = = = = = = G = = = = G = C C = = = = = = 0 E017 = = = = = = = = = = = G = = ? = = = = = = = = = = = A = = ? 0 E018 A T = = = = C = = = = = = = = G A = = = = T = = = = = = = = 0 E019 = = = = = = = = ? ? ? = = = ? = = = = = = = = ? ? ? = = = ? 0 E020 ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 E021 = T = = = G C C C = = = = = = = A = = = C T T T = = = = = = 0 E022 A T = = = = C = = = = = = = = G A = = = = T = = = = = = = = 0 E023 (A) = = = = = = = = = = = C = C (G) = = = = = = = = = = = T = T END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.95 = 1.00 = 1.00 1.00 = 1.00 ? 1.00 = = 0.99 1.00 = = = 1.00 = 1.00 = = 1.00 ? = = = = 1.00 = 0.82 = = = = 1.00 = 1.00 ? = = = ? = = = = = 0.88 0.95 = = = ? ? = = = 0.86 = = = = = = = = = ? ? ? ? = = = = = = = = 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 0.50 = 1.00 = = = = 0.98 1.00 = = 1.00 = = = ? ? = ? = = = 0.99 = = = = = = = = = = ? = 1.00 0.98 = = = 0.92 = 1.00 = 1.00 ? = = ? 1.00 = = = 1.00 = = = 1.00 = ? ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = 0.91 = 0.98 = 0.98 ? = = 0.94 ? ? = = = = = = = = = = = = = = = = 0.99 = = 0.97 = 1.00 = 1.00 = = = = = = = 0.88 = = 0.96 = = = = = = = 0.86 = = = 0.99 = = = = ? ? 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 = = = = = = = = 0.59 = = 1.00 = = = = = = = = = 0.91 = 0.88 0.96 = 1.00 1.00 = = 1.00 1.00 = 1.00 0.69 = = = = = = ? = = = 1.00 = = = 0.67 = = = = = = = = = = 1.00 = = = 0.92 = = = = 1.00 = 1.00 1.00 = = = = = = 0.57 = = = = 1.00 = 1.00 1.00 = = = 0.96 = 0.96 = = = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = = = = = = = = 0.57 = = = = 1.00 = 1.00 1.00 = = = 0.95 = 0.95 ? = = = = = = = = = = = 1.00 = 0.99 0.88 = = = = = = = ? ? ? ? 1.00 = 0.99 = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = = 0.89 = = = = = = = = = = = 1.00 = 0.99 0.94 = = = = 1.00 = 1.00 ? ? ? = = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = ? ? 1.00 = = = = 1.00 = = = = = = = ? = = = = = = = = = = = 1.00 = = = 0.92 = = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 = = ? 1.00 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = ? ? ? = = = ? ? = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = = = 1.00 = = = = = = = = 0.88 = = = = = = = = = = = 1.00 = 0.99 END PHASEPROBS