************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 fct12.phase.inp fct12.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fct12.phase.out_freqs : haplotype frequency estimates fct12.phase.out_pairs : most likely haplotype pairs for each individual fct12.phase.out_recom : estimates of recombination parameters fct12.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 27 Positions of loci: 101 366 580 640 654 658 668 754 918 1627 1857 3001 3458 4707 4714 4744 4842 4853 4856 4873 4903 6570 7040 7532 7589 10344 10513 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fct12.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 IGCACCAGCCTCCACCGTATCCCCCGG 1.000000 2 IGCACCAGTCCCCACCGTATTCCCCGG 3.000000 3 IGCACCAACCTCCACCGTATTCTCCGG 1.000000 4 IGCACGAGCCTCCACCGTATCCCTCGG 1.000000 5 ITCACCAACCTTTACCGTATTCTCCGG 3.000000 6 ITCACGAGCCTCCACCGCGTTCTCCGG 2.000000 7 ITCACGAGCCTCCACCGCGTTCTCTGG 1.000000 8 ITCACGAGCCTCCACCGCGTTTCTCCG 3.000000 9 ITCACGAGCCTCCACCGTATCCCTCGG 1.000000 10 ITCACGAGCCTCCACTGTATTCCTCCG 16.000000 11 ITCACGAGCCTCCACTGTACTCCTCCG 1.000000 12 ITCACGAGCTTCCACCGCGTTCTCCGG 9.000000 13 ITCACGAGCTTCCACCGTATTCTCCGG 8.000000 14 ITCACGAGCTTCCACCGTATTCTCCGA 1.000000 15 ITCACGAGCTTCCACCGTACTCTCCGG 2.000000 16 ITCACGAGCTTCCACCTCGTTCTCCGG 8.000000 17 ITCACGAGCTTCCACTGTATTCCTCCG 1.000000 18 ITCACGAGCTTCCCTCGCGTTCCCCGA 1.000000 19 ITCACGAGCTTCCCTCGTATTCTCCGA 2.000000 20 ITCATGCGCCTCCACCGTATTCTCCGG 1.000000 21 ITCATGCGCCTCCACCGTATTTCTCCG 4.000000 22 ITCATGCGCCTCCACTGCGTTCCTCCG 1.000000 23 ITCATGCGCCTCCACTGTATTCCTCCG 2.000000 24 ITCATGCGCCTCCACTGTGTTCTTCCG 1.000000 25 ITCGCGAGCCTCCACTGTATTCCTCCG 9.000000 26 ITCGCGAGCTTCCACCGCGTTCTCCGG 1.000000 27 ITCGCGAGCTTCCACCGTATTCTCCGG 1.000000 28 ITTACGAGCCTCCACTGTATTCCTCCG 3.000000 29 DTCACGAGCCTCCACTGTATTCCTCCG 6.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,6) D002: (8,16) D003: (14,16) D004: (10,29) D005: (5,13) D006: (13,13) D007: (6,21) D008: (9,13) D009: (13,16) D010: (5,15) D011: (13,23) D012: (2,12) D013: (2,13) D014: (7,13) D015: (16,18) D016: (2,4) D033: (15,16) D034: (10,16) D035: (10,11) D036: (10,25) D037: (16,16) D038: (3,19) D039: (12,19) D040: (5,12) E001: (10,28) E002: (12,24) E003: (10,10) E004: (12,29) E005: (10,25) E006: (10,29) E007: (25,29) E008: (10,10) E009: (12,12) E010: (12,25) E011: (21,27) E012: (10,10) E013: (25,25) E014: (12,26) E015: (10,17) E016: (10,10) E017: (20,25) E018: (21,25) E019: (21,28) E020: (8,23) E021: (8,29) E022: (28,29) E023: (22,25) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 I G C A C C A G C C T C C A C C G T A T C C C [C] [C] G G I T C A C G A G C C T C C A C C G C G T T C T C [C] G G 0 D002 I T C A C G A G C C T C C A C C G C G T T T C T C C G I T C A C G A G C T T C C A C C T C G T T C T C C G G 0 D003 I T C A C G A G C T T C C A C C G T A T T C T C C G (A) I T C A C G A G C T T C C A C C T C G T T C T C C G (G) 0 D004 I T C A C G A G C C T C C A C T G T A T T C C T C C G D T C A C G A G C C T C C A C T G T A T T C C T C C G 0 D005 I T C A C C A A C C T T T A C C G T A T T C T C C G G I T C A C G A G C T T C C A C C G T A T T C T C C G G 0 D006 I T C A C G A G C T T C C A C C G T A T T C T C C G G I T C A C G A G C T T C C A C C G T A T T C T C C G G 0 D007 I T C A (C) G (A) G C C T C C A C C G (C) (G) T T C T C [C] G G I T C A (T) G (C) G C C T C C A C C G (T) (A) T T T C T C C G 0 D008 I T C A C G A G C C T C C A C C G T A T C C C [T] [C] G G I T C A C G A G C T T C C A C C G T A T T C T C C G G 0 D009 I T C A C G A G C T T C C A C C G T A T T C T C C G G I T C A C G A G C T T C C A C C T C G T T C T C C G G 0 D010 I T C A C C A A C C T T T A C C G T A T T C T C C G G I T C A C G A G C T T C C A C C G T A C T C T C C G G 0 D011 I T C A (C) G (A) G C (T) T C C A C C G T A T T C T C C G G I T C A (T) G (C) G C (C) T C C A C T G T A T T C C T C C G 0 D012 I G C A C C A G T C C C C A C C G T A T T C C C C G G I T C A C G A G C T T C C A C C G C G T T C T C C G G 0 D013 I G C A C C A G T C C C C A C C G T A T T C C C C G G I T C A C G A G C T T C C A C C G T A T T C T C C G G 0 D014 I T C A C G A G C C T C C A C C G C G T T C T C (T) G G I T C A C G A G C T T C C A C C G T A T T C T C (C) G G 0 D015 I T C A C G A G C T T C C A C C (T) C G T T C T C C G G I T C A C G A G C T T C C C T C (G) C G T T C C C C G A 0 D016 I G C A C C A G T C C C C A C C G T A T T C C C C G G I G C A C G A G C C T C C A C C G T A T C C C [T] [C] G G 0 D033 I T C A C G A G C T T C C A C C G T A C T C T C C G G I T C A C G A G C T T C C A C C T C G T T C T C C G G 0 D034 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C T T C C A C C T C G T T C T C C G G 0 D035 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C C T C C A C T G T A C T C C T C C G 0 D036 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C G C G A G C C T C C A C T G T A T T C C T C C G 0 D037 I T C A C G A G C T T C C A C C T C G T T C T C C G G I T C A C G A G C T T C C A C C T C G T T C T C C G G 0 D038 I (G) C A C (C) A (A) C C T C C A C C G T A T T C T C C G G I (T) C A C (G) A (G) C T T C C C T C G T A T T C T C C G A 0 D039 I T C A C G A G C T T C C A C C G C G T T C T C C G G I T C A C G A G C T T C C C T C G T A T T C T C C G A 0 D040 I T C A C C A A C C T T T A C C G T A T T C T C C G G I T C A C G A G C [T] T C C A C C G C G T T C T C C G G 0 E001 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T T A C G A G C C T C C A C T G T A T T C C T C C G 0 E002 I T C A C G A G C T T C C A C C G (C) G T T C T C C G G I T C A T G C G C C T C C A C T G (T) G T T C T T C C G 0 E003 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E004 I T C A C G A G C T T C C A C C G C G T T C T C C G G D T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E005 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C G C G A G C C T C C A C T G T A T T C C T C C G 0 E006 I T C A C G A G C C T C C A C T G T A T T C C T C C G D T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E007 I T C G C G A G C C T C C A C T G T A T T C C T C C G D T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E008 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E009 I T C A C G A G C T T C C A C C G C G T T C T C C G G I T C A C G A G C T T C C A C C G C G T T C T C C G G 0 E010 I T C (A) C G A G C T T C C A C C G C G T T C T C C G G I T C (G) C G A G C C T C C A C T G T A T T C C T C C G 0 E011 I T C (A) T G C G C C T C C A C C G T A T T T C T C C G I T C (G) C G A G C T T C C A C C G T A T T C T C C G G 0 E012 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E013 I T C G C G A G C C T C C A C T G T A T T C C T C C G I T C G C G A G C C T C C A C T G T A T T C C T C C G 0 E014 I T C A C G A G C T T C C A C C G C G T T C T C C G G I T C G C G A G C T T C C A C C G C G T T C T C C G G 0 E015 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C T T C C A C T G T A T T C C T C C G 0 E016 I T C A C G A G C C T C C A C T G T A T T C C T C C G I T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E017 I T C (A) (T) G (C) G C C T C C A C C G T A T T C T C C G G I T C (G) (C) G (A) G C C T C C A C T G T A T T C C T C C G 0 E018 I T C (A) T G C G C C T C C A C C G T A T T T C T C C G I T C (G) C G A G C C T C C A C T G T A T T C C T C C G 0 E019 I T C A T G C G C C T C C A C C G T A T T T C T C C G I T T A C G A G C C T C C A C T G T A T T C C T C C G 0 E020 I T C A (C) G (A) G C C T C C A C C G C G T T T C T C C G I T C A (T) G (C) G C C T C C A C T G T A T T C C T C C G 0 E021 I T C A C G A G C C T C C A C C G C G T T T C T C C G D T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E022 I T T A C G A G C C T C C A C T G T A T T C C T C C G D T C A C G A G C C T C C A C T G T A T T C C T C C G 0 E023 I T C A T G C G C C T C C A C T G (C) (G) T T C C T C C G I T C G C G A G C C T C C A C T G (T) (A) T T C C T C 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 = G = = = C = = = = ? = = = = = = T A = C ? C ? ? = = = T = = = G = = = = ? = = = = = = C G = T ? T ? ? = = 0 D002 = = = = = = = = = C = = = = = = G = = = = ? C ? ? C = = = = = = = = = = T = = = = = = T = = = = ? T ? ? G = 0 D003 = = = = = = = = = = = = = = = = G T A = = = = ? ? = (A) = = = = = = = = = = = = = = = = T C G = = = = ? ? = (G) 0 D004 I ? = = = = = = = = = = = = = = = = = = = = = ? ? = = D ? = = = = = = = = = = = = = = = = = = = = = ? ? = = 0 D005 = = = = = C = A ? C = T T = = = = = = = = = = ? ? = = = = = = = G = G ? T = C C = = = = = = = = = = ? ? = = 0 D006 = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = 0 D007 = = = = (C) = (A) = = = = = = = = = = (C) (G) = = ? T ? ? G = = = = = (T) = (C) = = = = = = = = = = (T) (A) = = ? C ? ? C = 0 D008 = = = = = = = = = C = = = = = = = = = = C ? C ? ? = = = = = = = = = = = T = = = = = = = = = = T ? T ? ? = = 0 D009 = = = = = = = = = = = = = = = = G T A = = ? = ? ? = = = = = = = = = = = = = = = = = = T C G = = ? = ? ? = = 0 D010 ? ? = = = C = A ? C = T T = = = = = = T = = = ? ? = = ? ? = = = G = G ? T = C C = = = = = = C = = = ? ? = = 0 D011 = = = = (C) = (A) = = (T) = = ? = = C = = = = = = T C = G = = = = = (T) = (C) = = (C) = = ? = = T = = = = = = C T = C = 0 D012 = G = ? ? ? ? ? T C C = = = = = = T A = = = C = = = = = T = ? ? ? ? ? C T T = = = = = = C G = = = T = = = = 0 D013 = G = = = C = = T C C = = = = = = = = = = = C = = = = = T = = = G = = C T T = = = = = = = = = = = T = = = = 0 D014 = = = = = = = = = C = = = = = = = C G = = = = = (T) = = = = = = = = = = = T = = = = = = = T A = = = = = (C) = = 0 D015 = = = ? ? ? ? ? = = = = = A C = (T) = = = = = T ? ? = G = = = ? ? ? ? ? = = = = = C T = (G) = = = = = C ? ? = A 0 D016 = = = = = C = = T = C = = = = = = = = = T ? = ? ? = = = = = = = G = = C = T = = = = = = = = = C ? = ? ? = = 0 D033 = = = = = = = = = = = = = = = = G T A C = = = ? ? = = = = = = = = = = = = = = = = = = T C G T = = = ? ? = = 0 D034 = = = = = = = = = C = = = = = T G T A = = = C T = C = = = = = = = = = = T = = = = = C T C G = = = T C = G = 0 D035 = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = 0 D036 = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D038 = (G) = = = (C) = (A) = C = = = A C = = = = = = = = = = = G = (T) = = = (G) = (G) = T = = = C T = = = = = = = = = = = A 0 D039 = = = = = = = = = = = = = A C = = C G = = = = = = = G = = = = = = = = = = = = = C T = = T A = = = = = = = A 0 D040 = = = = = C = A = ? = T T = = = = T A = = ? = ? ? = = = = = = = G = G = ? = C C = = = = C G = = ? = ? ? = = 0 E001 = = C = = = = = = ? = = = = = = = = = = = = = = = = = = = T = = = = = = ? = = = = = = = = = = = = = = = = = 0 E002 = = = = C = A = = T = = = = = C = (C) = = = = = C = G = = = = = T = C = = C = = = = = T = (T) = = = = = T = C = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 I ? = = = = = = = T = = = = = C = C G = = = T C = G = D ? = = = = = = = C = = = = = T = T A = = = C T = C = 0 E005 = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = 0 E006 I ? = = = = = = = = = = = = = = = = = = = = = = = = = D ? = = = = = = = = = = = = = = = = = = = = = = = = = 0 E007 I ? = G = = = = = = = = = = = = = = = = = = = = = ? = D ? = A = = = = = = = = = = = = = = = = = = = = = ? = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 = = = (A) = = = = = T = = = = = C = C G = = = T C = G = = = = (G) = = = = = C = = = = = T = T A = = = C T = C = 0 E011 = = = (A) T = C = = C = = = = = = = = = = = T C T = C = = = = (G) C = A = = T = = = = = = = = = = = C T C = G = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = A = = = = = = = = = = = = = = = = = ? = = = = = = = = G = = = = = = = = = = = = = = = = = ? = = = = = 0 E015 = = = = = = = = = C = = = = = = = = = = = ? = = = = = = = = = = = = = = T = = = = = = = = = = = ? = = = = = 0 E016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E017 = ? = (A) (T) = (C) = = = = = = = = C = = = = = = T C = G = = ? = (G) (C) = (A) = = = = = = = = T = = = = = = C T = C = 0 E018 = = = (A) T = C = = = = = = = = C = = = = = T = = = = = = = = (G) C = A = = = = = = = = T = = = = = C = = = = = 0 E019 = = C = T = C = = = = = = = = C = = = = = T = = = = = = = T = C = A = = = = = = = = T = = = = = C = = = = = 0 E020 = = = = (C) = (A) = = = = = = = = C = C G = = T = = = = = = = = = (T) = (C) = = = = = = = = T = T A = = C = = = = = 0 E021 I ? = = = = = = = = = = = = = C = C G = = T = = = ? ? D ? = = = = = = = = = = = = = T = T A = = C = = = ? ? 0 E022 I ? T = = = = = = = = = = = = = = = = = = = = = = = = D ? C = = = = = = = = = = = = = = = = = = = = = = = = 0 E023 = = = A T = C = = = = = = = = = = (C) (G) = = = = = = = = = = = G C = A = = = = = = = = = = (T) (A) = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.96 = = = 0.95 = = = = ? = = = = = = 1.00 1.00 = 1.00 ? 1.00 ? ? = = = = = = = = = = = 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 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = 0.69 = 0.69 = = = = = = = = = = 0.68 0.68 = = ? 1.00 ? ? 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 = = = ? ? = = = = = = 0.75 = 0.75 = = 0.81 = = ? = = 1.00 = = = = = = 1.00 1.00 = 1.00 = = 1.00 = ? ? ? ? ? 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 0.94 = = = = = = = 1.00 1.00 = = = = = 0.70 = = = = = ? ? ? ? ? = = = = = 1.00 1.00 = 0.64 = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.71 = = = 0.87 = 0.70 = 1.00 = = = 1.00 1.00 = = = = = = = = = = = 0.99 = = = = = = = = = = = = = 0.99 0.99 = = 0.98 0.98 = = = = = = = 1.00 = = = = = 1.00 = 1.00 = ? = 1.00 1.00 = = = = 1.00 1.00 = = ? = ? ? = = = = 1.00 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 0.98 = 0.98 = = 1.00 = = = = = 1.00 = 0.84 = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 ? = = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 ? = 1.00 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.73 = = = = = 1.00 = = = = = 1.00 = 0.98 0.98 = = = 1.00 1.00 = 1.00 = = = = 0.54 0.95 = 0.95 = = 0.96 = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0.75 0.90 = 0.90 = = = = = = = = 1.00 = = = = = = 1.00 1.00 = 1.00 = = = = 0.70 1.00 = 1.00 = = = = = = = = 1.00 = = = = = 1.00 = = = = = = = 0.98 = 1.00 = 1.00 = = = = = = = = 0.97 = = = = = 0.97 = = = = = = = = = 0.84 = 0.84 = = = = = = = = 0.94 = 0.95 0.95 = = 0.94 = = = = = 0.96 ? = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = 1.00 = = = ? ? 0.97 ? 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 0.97 = 0.97 = = = = = = = = = = 0.66 0.76 = = = = = = = = END PHASEPROBS