************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 vkrc1.phase.inp vkrc1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST vkrc1.phase.out_freqs : haplotype frequency estimates vkrc1.phase.out_pairs : most likely haplotype pairs for each individual vkrc1.phase.out_recom : estimates of recombination parameters vkrc1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 17 Positions of loci: 381 861 2653 3435 3673 5808 6009 6191 6484 6853 6915 7566 8773 9041 10212 10424 10719 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file vkrc1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCGAGTCCCGTTCGAGG 5.000000 2 CCGAGTCTCGTCCGAGG 3.000000 3 CCGAATCCTCTTCGAGG 10.000000 4 CCGAAGCCTCTTCGAGG 17.000000 5 CCGGGTCCCCTCCGAGG 3.000000 6 CCGGGTCCCGTCTAAGG 5.000000 7 TCGAGTCCCGTCCAAGG 17.000000 8 TCGAGTCCCGTCCGCAG 1.000000 9 TCGAGTCCCGCCCGCAC 4.000000 10 TCGGGTCCCGTCTAAGG 5.000000 11 TAGAGTCCCGTCCAAGG 8.000000 12 TACAGTCCCGTCCAAGG 1.000000 13 TACAGTTCCGTCCGAGG 15.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (5,7) D002: (10,10) D003: (2,13) D004: (1,6) D005: (7,13) D006: (8,10) D007: (4,6) D008: (1,3) D009: (2,3) D010: (4,6) D011: (7,9) D012: (7,12) D013: (1,4) D014: (1,7) D015: (6,9) D016: (9,13) D033: (7,7) D034: (5,7) D035: (5,9) D036: (3,13) D037: (7,10) D038: (1,10) D039: (2,6) D040: (7,13) E001: (4,7) E002: (3,4) E003: (13,13) E004: (3,7) E005: (3,7) E006: (4,13) E007: (7,13) E008: (3,13) E009: (3,11) E010: (7,13) E011: (3,4) E012: (7,13) E013: (4,4) E014: (3,11) E015: (4,7) E016: (4,13) E017: (4,4) E018: (4,4) E019: (4,11) E020: (11,11) E021: (4,13) E022: (11,13) E023: (11,11) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C C G G G T C C C C T C C G A G G T C G A G T C C C G T C C A A G G 0 D002 T C G G G T C C C G T C T A A G G T C G G G T C C C G T C T A A G G 0 D003 C C G A G T C T C G T C C G A G G T A C A G T T C C G T C C G A G G 0 D004 C C G A G T C C C G T T C G A G G C C G G G T C C C G T C T A A G G 0 D005 T C G A G T C C C G T C C A A G G T A C A G T T C C G T C C G A G G 0 D006 T C G A G T C C C G T C C G C A G T C G G G T C C C G T C T A A G G 0 D007 C C G A A G C C T C T T C G A G G C C G G G T C C C G T C T A A G G 0 D008 C C G A G T C C C G T T C G A G G C C G A A T C C T C T T C G A G G 0 D009 C C G A G T C T C G T C C G A G G C C G A A T C C T C T T C G A G G 0 D010 C C G A A G C C T C T T C G A G G C C G G G T C C C G T C T A A G G 0 D011 T C G A G T C C C G T C C A A G G T C G A G T C C C G C C C G C A C 0 D012 T (C) G A G T C C C G T C C A A G G T (A) C A G T C C C G T C C A A G G 0 D013 C C G A G T C C C G T T C G A G G C C G A A G C C T C T T C G A G G 0 D014 C C G A G T C C C G T T C G A G G T C G A G T C C C G T C C A A G G 0 D015 C C G G G T C C C G T C T A A G G T C G A G T C C C G C C C G C A C 0 D016 T C G A G T C C C G C C C G C A C T A C A G T T C C G T C C G A G G 0 D033 T C G A G T C C C G T C C A A G G T C G A G T C C C G T C C A A G G 0 D034 C C G G G T C C C C T C C G A G G T C G A G T C C C G T C C A A G G 0 D035 C C G G G T C C C C T C C G A G G T C G A G T C C C G C C C G C A C 0 D036 C C G A A T C C T C T T C G A G G T A C A G T T C C G T C C G A G G 0 D037 T C G A G T C C C G T C C A A G G T C G G G T C C C G T C T A A G G 0 D038 C C G A G T C C C G T T C G A G G T C G G G T C C C G T C T A A G G 0 D039 C C G A G T C T C G T C C G A G G C C G G G T C C C G T C T A A G G 0 D040 T (C) G A G T C C C G T C C A A G G [T] (A) [C] A G T [T] C C G T C C G A G G 0 E001 C C G A A G C C T C T T C G A G G T C G A G T C C C G T C C A A G G 0 E002 C C G A A T C C T C T T C G A G G C C G A A G C C T C T T C G A G G 0 E003 T A C A G T T C C G T C C G A G G T A C A G T T C C G T C C G A G G 0 E004 C C G A A T C C T C T T C G A G G T C G A G T C C C G T C C A A G G 0 E005 C C G A A T C C T C T T C G A G G T C G A G T C C C G T C C A A G G 0 E006 C C G A A G C C T C T T C G A G G T A C A G T T C C G T C C G A G G 0 E007 T C G A G T C C C G T C C A A G G T A C A G T T C C G T C C G A G G 0 E008 C C G A A T C C T C T T C G A G G T A C A G T T C C G T C C G A G G 0 E009 C C G A A T C C T C T T C G A G G T A G A G T C C C G T C C A A G G 0 E010 T C G A G T C C C G T C C A A G G T A C A G T T C C G T C C G A G G 0 E011 C C G A A T C C T C T T C G A G G C C G A A G C C T C T T C G A G G 0 E012 T C G A G T C C C G T C C A A G G T A C A G T T C C G T C C G A G G 0 E013 C C G A A G C C T C T T C G A G G C C G A A G C C T C T T C G A G G 0 E014 C C G A A T C C T C T T C G A G G T A G A G T C C C G T C C A A G G 0 E015 C C G A A G C C T C T T C G A G G T C G A G T C C C G T C C A A G G 0 E016 C C G A A G C C T C T T C G A G G T A C A G T T C C G T C C G A G G 0 E017 C C G A A G C C T C T T C G A G G C C G A A G C C T C T T C G A G G 0 E018 C C G A A G C C T C T T C G A G G C C G A A G C C T C T T C G A G G 0 E019 C C G A A G C C T C T T C G A G G T A G A G T C C C G T C C A A G G 0 E020 T A G A G T C C C G T C C A A G G T A G A G T C C C G T C C A A G G 0 E021 C C G A A G C C T C T T C G A G G T A C A G T T C C G T C C G A G G 0 E022 T A G A G T C C C G T C C A A G G T A C A G T T C C G T C C G A G G 0 E023 T A G A G T C C C G T C C A A G G T A G A G T C C C G T C C A A 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 = = G = = = = = C = = = G = = = T = = A = = = = = G = = = A = = = 0 D002 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = 0 D003 C C G = = = C T = = = = = = = = = T A C = = = T C = = = = = = = = = 0 D004 = = = A = = ? ? ? = = T C G = = = = = = G = = ? ? ? = = C T A = = = 0 D005 = C G = = = ? ? ? = = = = A = = = = A C = = = ? ? ? = = = = G = = = 0 D006 = = = A = = = = = = = = C G C A = = = = G = = = = = = = = T A A G = 0 D007 = = = A A G = = T C = T C G = = = = = = G G T = = C G = C T A = = = 0 D008 = = = = G = = = C G = = = = = = = = = = = A = = = T C = = = = = = = 0 D009 = = = = G = = T C G = C = = = = = = = = = A = = C T C = T = = = = = 0 D010 = = = A A G = = T C = T C G = = = = = = G G T = = C G = C T A = = = 0 D011 = = = = = = = = = = T = = A A G G = = = = = = = = = = C = = G C A C 0 D012 = (C) G = = = = = = = = = = = = = = = (A) C = = = = = = = = = = = = = = 0 D013 = = = = ? T = = C G = = = = = = = = = = = ? G = = T C = = = = = = = 0 D014 C = = = = = = = = = = T = G = = = T = = = = = = = = = = C = A = = = 0 D015 C = = G = = = = = = T = T A A G G T = = A = = = = = = C = C G C A C 0 D016 = C G = = = C = = = C = = = C A C = A C = = = T = = = T = = = A G G 0 D033 = = ? ? ? = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = 0 D034 C = = G ? = = = = C = = = G = = = T = = A ? = = = = G = = = A = = = 0 D035 C = = G = = = = = C T = = = A G G T = = A = = = = = G C = = = C A C 0 D036 C C G = A = C = T C = T = = = = = T A C = G = T = C G = C = = = = = 0 D037 = = = A = = = = = = = = C = = = = = = = G = = = = = = = = T = = = = 0 D038 C = ? A = = = = = = = T C G = = = T = ? G = = = = = = = C T A = = = 0 D039 = = = A ? = = T = = = = C G = = = = = = G ? = = C = = = = T A = = = 0 D040 ? (C) ? ? = = ? ? ? = = ? = A ? ? ? ? (A) ? ? = = ? ? ? = = ? = G ? ? ? 0 E001 C = ? = A G = = T C = T = G = = = T = ? = G T = = C G = C = A = = = 0 E002 = = = = = T = = = = = = = = = = = = = = = = G = = = = = = = = = = = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 C = = = A = = = T C = T = G = = = T = = = G = = = C G = C = A = = = 0 E005 C = = = A = = = T C = ? = G = = = T = = = G = = = C G = ? = A = = = 0 E006 C C G = A G C = T C = T = = = = = T A C = G T T = C G = C = = = = = 0 E007 = C G = = = C = = = = = = A = = = = A C = = = T = = = = = = G = = = 0 E008 C C G = A = ? ? T C = T = = = = = T A C = G = ? ? C G = C = = = = = 0 E009 C C = = A = = = T C = T = G = = = T A = = G = = = C G = C = A = = = 0 E010 = C G = = = C = = = = = = A = = = = A C = = = T = = = = = = G = = = 0 E011 = = = = = T = = = = = = = = = = ? = = = = = G = = = = = = = = = = ? 0 E012 = C G = = = C = = = = = = A = = = = A C = = = T = = = = = = G = = = 0 E013 = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 E014 C C = = A = = = T C = T = G = = = T A = = G = = = C G = C = A = = = 0 E015 C = = = A G = = T C = T = G = = = T = = = G T = = C G = C = A = = = 0 E016 C C G = A G C = T C = T = = = = = T A C = G T T = C G = C = = = = = 0 E017 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 C C = = A G = = T C = T = G = = = T A = = G T = = C G = C = A = = = 0 E020 = = = = = = ? ? ? = = = = = = = = = = = = = = ? ? ? = = = = = = = = 0 E021 C C G = A G C = T C = T = = = = = T A C = G T T = C G = C = = = = = 0 E022 = = G = = = C = = = = = = A = = = = = C = = = T = = = = = = G = = = 0 E023 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? 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 = = = ? ? ? = = = = 1.00 = = = = = = 0.94 = = = = = = = = 0.94 1.00 0.98 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 = 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 = 0.76 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 = = = = 0.96 = ? 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = 1.00 ? = = 1.00 = = = = 1.00 1.00 = = = ? 0.78 ? ? = = ? ? ? = = ? = 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 = = = 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