************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 c1qrf.phase.inp c1qrf.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST c1qrf.phase.out_freqs : haplotype frequency estimates c1qrf.phase.out_pairs : most likely haplotype pairs for each individual c1qrf.phase.out_recom : estimates of recombination parameters c1qrf.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 23 Positions of loci: 131 2431 3758 4495 4924 5097 5162 5310 5347 6158 6544 6558 6735 7022 7398 7471 7518 8251 8907 9199 9280 9925 10059 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file c1qrf.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCCCACAGATGCAAACGGGTIGG 3.000000 2 CCCCACAGATGCGAACAGGTIGG 4.000000 3 CCCCACAGATGTATACGGGGDGG 2.000000 4 CCCCACAGATGTATAGAGGGDGG 1.000000 5 CCCCACAGATGTATTCGGGGIGG 1.000000 6 CCCCACAGATGTATTCGGGTIGA 9.000000 7 CCCCACAGATGTATTCGGGTIGG 3.000000 8 CCCCACAGATACAAACATGTIGG 2.000000 9 CCCCACAGATACAAACGTGTDCG 1.000000 10 CCCCATAGATGCAAACAGGTIGG 3.000000 11 CCCCGCAGATGCAAACAGGTICG 1.000000 12 CCGCACAGATGCGATCATATIGG 8.000000 13 CCGCACAGATGTATTCGGGTIGA 1.000000 14 CCGCACAGGTGCGAACAGGGDGG 2.000000 15 CCGCACAGGTGCGATCAGATIGG 1.000000 16 CCGCACAGGTGCGATCATATIGG 1.000000 17 CTCCACAGATGTAATCATATIGG 1.000000 18 CTCCACAGATGTATACAGGGDGG 2.000000 19 CTCCACAGATGTATACATGTDCG 1.000000 20 CTCCACAGATGTATAGAGGTIGG 10.000000 21 CTCCACAGATGTATTCGGGTIGA 1.000000 22 CTCCACAGATACAAACATGTIGG 1.000000 23 GCCCACAGATGCGAACAGGTIGG 1.000000 24 GCCCACAGATGTATTCGGGTIGG 2.000000 25 GCCCGCGGACGCAAACAGGTICG 1.000000 26 GCCCGCGAACGCAAACAGGTICG 1.000000 27 GCCTGCGAACGCAAACAGGTICG 28.000000 28 GCGCACAGGTGCGATCATATIGG 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (6,10) D002: (6,14) D003: (25,28) D004: (19,22) D005: (11,18) D006: (6,18) D007: (5,7) D008: (10,24) D009: (4,12) D010: (9,20) D011: (15,28) D012: (6,27) D013: (1,13) D014: (24,27) D015: (8,10) D016: (1,12) D033: (6,7) D034: (2,17) D035: (3,16) D036: (2,12) D037: (1,27) D038: (6,26) D039: (6,14) D040: (3,21) E001: (2,27) E002: (6,27) E003: (20,27) E004: (20,20) E005: (12,27) E006: (12,27) E007: (6,27) E008: (20,27) E009: (8,27) E010: (20,27) E011: (23,27) E012: (12,27) E013: (27,27) E014: (20,27) E015: (27,27) E016: (20,27) E017: (2,12) E018: (20,27) E019: (27,27) E020: (12,27) E021: (27,27) E022: (27,27) E023: (7,20) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C C C C A C A G A T G T A T T C G G G T I G A C C C C A T A G A T G C A A A C A G G T I G G 0 D002 C C C C A C A G A T G T A T T C G G G T I G A C C G C A C A G G T G C G A A C A G G G D G G 0 D003 G C C C G C G G A C G C A A A C A G G T I C G G C G C A C A G G T G C G A T C A T A T I G G 0 D004 C T C C A C A G A T (G) (T) A [T] A C A T G T (D) (C) G C T C C A C A G A T (A) (C) A A A C A T G T (I) (G) G 0 D005 C (C) C C (G) C A G A T G C A A A C A G G T I [C] G C (T) C C (A) C A G A T G T A T A C A G G G D G G 0 D006 C (C) C C A C A G A T G T A T T C G G G T I G A C (T) C C A C A G A T G T A T A C A G G G D G G 0 D007 C C C C A C A G A T G T A T T C G G G G I G G C C C C A C A G A T G T A T T C G G G T I G G 0 D008 C C C C A T A G A T G C A A A C A G G T I G G G C C C A C A G A T G T A T T C G G G T I G G 0 D009 [C] C C C A C A G A T G T A T A (G) A G G G D G G C C G C A C A G A T G C G A T (C) A T A T I G G 0 D010 C (C) C C A C A G A T (A) C A A A C (G) (T) G T (D) (C) G C (T) C C A C A G A T (G) T A T A G (A) (G) G T (I) (G) G 0 D011 (C) C G C A C A G G T G C G A T C A G A T I G G (G) C G C A C A G G T G C G A T C A T A T I G G 0 D012 C C C C A C A G A T G T A T T C G G G T I G A G C C T G C G A A C G C A A A C A G G T I C G 0 D013 C C (C) C A C A G A T G C A A A C G G G T I G G C C (G) C A C A G A T G T A T T C G G G T I G A 0 D014 G C C C A C A G A T G T A T T C G G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 D015 C C C C A C A G A T A C A A A C A T G T I G G C C C C A T A G A T G C A A A C A G G T I G G 0 D016 C C C C A C A G A T G C A A A C G G G T I G G C C G C A C A G A T G C G A T C A T A T I G G 0 D033 C C C C A C A G A T G T A T T C G G G T I G A [C] C C C A C A G A T G T A T T C G G G T I G G 0 D034 [C] (C) C C A C A G A T G (C) (G) A A C A G G T I G G C (T) C C A C A G A T G (T) (A) A T C A T A T I G G 0 D035 C C C C A C A G A T G T A T A C G G G G D G G C C G C A C A G G T G C G A T C A T A T I G G 0 D036 C C C C A C A G A T G C G A A C A G G T I G G C C G C A C A G A T G C G A T C A T A T I G G 0 D037 C C C C A C A G A T G C A A A C G G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 D038 C C C C A C A G A T G T A T T C G G G T I G A G C C C G C G A A C G C A A A C A G G T I C G 0 D039 C C C C A C A G A T G T A T T C G G G T I G [A] C C G C A C A G G T G C G A A C A G G G D G G 0 D040 C (C) C C A C A G A T G T A T A C G G G G D G G C (T) C C A C A G A T G T A T T C G G G T I G A 0 E001 [C] C C C A C A G A T G C G A A C A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E002 C C C C A C A G A T G T A T T C G G G T I G [A] G C C T G C G A A C G C A A A C A G G T I C G 0 E003 C T C C A C A G A T G T A T A G A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E004 C T C C A C A G A T G T A T A G A G G T I G G C T C C A C A G A T G T A T A G A G G T I G G 0 E005 C C G C A C A G A T G C G A T C A T A T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E006 C C G C A C A G A T G C G A T C A T A T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E007 C C C C A C A G A T G T A T T C G G G T I G A G C C T G C G A A C G C A A A C A G G T I C G 0 E008 C T C C A C A G A T G T A T A G A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E009 C C C C A C A G A T A C A A A C A T G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E010 C T C C A C A G A T G T A T A G A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E011 G C C C A C A G A T G C G A A C A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E012 C C G C A C A G A T G C G A T C A T A T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E013 G C C T G C G A A C G C A A A C A G G T I C G G C C T G C G A A C G C A A A C A G G T I C G 0 E014 C T C C A C A G A T G T A T A G A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E015 G C C T G C G A A C G C A A A C A G G T I C G G C C T G C G A A C G C A A A C A G G T I C G 0 E016 C T C C A C A G A T G T A T A G A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E017 C C C C A C A G A T [G] C [G] A A C A [G] G T I G G C C G C A C A G A T G C G A T C A T A T I G G 0 E018 C T C C A C A G A T G T A T A G A G G T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E019 G C C T G C G A A C G C A A A C A G G T I C G G C C T G C G A A C G C A A A C A G G T I C G 0 E020 C C G C A C A G A T G C G A T C A T A T I G G G C C T G C G A A C G C A A A C A G G T I C G 0 E021 G C C T G C G A A C G C A A A C A G G T I C G G C C T G C G A A C G C A A A C A G G T I C G 0 E022 G C C T G C G A A C G C A A A C A G G T I C G G C C T G C G A A C G C A A A C A G G T I C G 0 E023 C C C C A C A G A T G T A T T C G G G T I G G C T C C A C A G A T G T A T A G A G G T I G 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 = = = = = C = = = = = T = T T = G = ? ? ? = A = = = = = T = = = = = C = A A = A = ? ? ? = G 0 D002 = = C = = = = = A = = T A T T = G = = T I = A = = G = = = = = G = = C G A A = A = = G D = G 0 D003 = = C = G = G = A C = = A = A = = G G = = C = = = G = A = A = G T = = G = T = = T A = = G = 0 D004 = = = = = = = = = = (G) (T) = ? = = = = = = (D) (C) = = = = = = = = = = = (A) (C) = ? = = = = = = (I) (G) = 0 D005 = (C) = ? (G) = = = = = = C = A = = = = = T I ? ? = (T) = ? (A) = = = = = = T = T = = = = = G D ? ? 0 D006 = (C) = = = = = = = = = = = = T = G = = T I = A = (T) = = = = = = = = = = = = A = A = = G D = G 0 D007 = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = T = = = 0 D008 C = = = = T = = = = = C = A A = A = = = = = = G = = = = C = = = = = T = T T = G = = = = = = 0 D009 ? = C ? = = = = = = = T A T A (G) = G G G D = = ? = G ? = = = = = = = C G A T (C) = T A T I = = 0 D010 ? (C) = = = = = = = ? (A) C = ? = C (G) (T) = = (D) (C) = ? (T) = = = = = = = ? (G) T = ? = G (A) (G) = = (I) (G) = 0 D011 (C) = = = = = = = = = = = = = = = = G = = = = = (G) = = = = = = = = = = = = = = = = T = = = = = 0 D012 ? = = C A = A G = ? = T = T T = G = = = = G A ? = = T G = G A = ? = C = A A = A = = = = C G 0 D013 = = (C) = = = = = = = = C = A A = = = = = = = G = = (G) = = = = = = = = T = T T = = = = = = = A 0 D014 = = = C A = A G = T = T = T T = G = = = = G = = = = T G = G A = C = C = A A = A = = = = C = 0 D015 = = = = = C = = = = A = = ? = = = T = = = = = = = = = = T = = = = G = = ? = = = G = = = = = 0 D016 = = C = = = = = = = = = A = A = G G G = = = = = = G = = = = = = = = = G = T = A T A = = = = 0 D033 ? = = = = = = = = = = = ? = = = = = = = = = A ? = = = = = = = = = = = ? = = = = = = = = = G 0 D034 ? (C) = = = = = = = ? = (C) (G) = A = = G ? ? ? = = ? (T) = = = = = = = ? = (T) (A) = T = = T ? ? ? = = 0 D035 = = C = = = = = A = = T A ? A = G G G ? D ? ? = = G = = = = = G = = C G ? T = A T A ? I ? ? 0 D036 = = C = = = = = = = = = = = A = = G G = = = = = = G = = = = = = = = = = = T = = T A = = = = 0 D037 C = = C A = A G = T = = = = = = G = ? = = G = G = = T G = G A = C = = = = = = A = ? = = C = 0 D038 C = = = A = A G = T = T = T T = G = = = = G A G = = = G = G A = C = C = A A = A = = = = C G 0 D039 = = C = = = = = A = = T A T T = G = = ? I ? ? = = G = = = = = G = = C G A A = A = = ? D ? ? 0 D040 = (C) = = = = = = = = = = = = A = = = ? ? D = G = (T) = = = = = = = = = = = = T = = = ? ? I = A 0 E001 ? ? = C A = A G = T = = G = = = = = = = = ? ? ? ? = T G = G A = C = = A = = = = = = = = ? ? 0 E002 ? = = C A = A G = ? = T = T T = G ? ? ? = ? ? ? = = T G = G A = ? = C = A A = A ? ? ? = ? ? 0 E003 C T = C A = A G = T = T = T = G = = = = = G = G C = T G = G A = C = C = A = C = = = = = C = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 C = G C A = A G = T = = G = T = = T A = = G = G = C T G = G A = C = = A = A = = G G = = C = 0 E006 C = G C A = A G = T = = G = T = = T A = = G = G = C T G = G A = C = = A = A = = G G = = C = 0 E007 C = = C A = A G = T = T = T T = G = = = = G A G = = T G = G A = C = C = A A = A = = = = C G 0 E008 C T = C A = A G = T = T = T = G = = = = = G = G C = T G = G A = C = C = A = C = = = = = C = 0 E009 ? = = C A = A G = T ? = = ? = = = T = = = G = ? = = T G = G A = C ? = = ? = = = G = = = C = 0 E010 C T = C ? = A G = T = T = T = G = = = = = G = G C = T ? = G A = C = C = A = C = = = = = C = 0 E011 = = = C A = A G = T = = G = = = = = = = = G = = = = T G = G A = C = = A = = = = = = = = C = 0 E012 C = G C A = A G = T = = G = T = = T A = = G = G = C T G = G A = C = = A = A = = G G = = C = 0 E013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E014 ? T = C A = A G = T = T = T = G = = = = = G = ? C = T G = G A = C = C = A = C = = = = = C = 0 E015 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 E016 C T = C A = A G = T = T = T = G = = = = = G = G C = T G = G A = C = C = A = C = = = = = C = 0 E017 = = C ? ? = = = = ? ? ? ? ? ? = = ? ? = = = = = = G ? ? = = = = ? ? ? ? ? ? = = ? ? = = = = 0 E018 C T = C A = A G = T = T = ? = G = ? = = = G = G C = T G = G A = C = C = ? = C = ? = = = C = 0 E019 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 E020 C = G C ? = A G = T = = G = T = = ? A = = G = G = C T ? = G A = C = = A = A = = ? G = = C = 0 E021 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E022 = = = ? ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = 0 E023 = C = = = = = = = ? = = = = T C G = = = = = = = T = = = = = = = ? = = = = A G A = = = = = = 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 = 1.00 = ? ? ? = 1.00 = = 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = 0.95 = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = = = = 0.75 0.77 = ? = = = = = = 0.85 0.85 = = 0.84 = ? 0.57 = = = = = = 1.00 = 1.00 = = = = = 1.00 1.00 ? ? = 0.88 = = = = = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = 0.99 = = = = = = = = = = = = = = = = = = = 1.00 = = = 0.94 = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 = = = = = = ? = 1.00 ? = = = = = = = 1.00 1.00 1.00 1.00 0.81 = 1.00 1.00 0.91 0.91 = = ? 0.88 = = = = = = = ? 0.87 1.00 = ? = 0.99 0.68 0.76 = = 0.67 0.67 = 0.51 = = = = = = = = = = = = = = = = 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 = 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 = = = = = = = 0.97 = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = ? = = = = = = = = = = = ? = = = = = = = = = 1.00 ? 0.87 = = = = = = = ? = 0.87 0.87 = 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 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = 1.00 = ? = = 1.00 = 0.93 = = = 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 = 1.00 = = ? 1.00 ? ? = 0.52 = = = = = = = = = = = = 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 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 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 = = = = = = END PHASEPROBS