************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 ilk22.phase.inp ilk22.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ilk22.phase.out_freqs : haplotype frequency estimates ilk22.phase.out_pairs : most likely haplotype pairs for each individual ilk22.phase.out_recom : estimates of recombination parameters ilk22.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 26 Positions of loci: 206 301 353 523 575 717 997 998 1121 1165 1412 1628 2002 2820 3204 3366 4290 4497 4561 4723 5382 5643 5747 7413 7754 7809 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ilk22.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AACACCCTGTCCAAGACTCTCATATA 1.000000 2 AACACCCTGTCCAAGACTCTCATATT 3.000000 3 AATACCCCTTCCAGGAGTCACATATA 1.000000 4 AATACCCTTTCCAAGCGTCTAGTATA 15.000000 5 AATACCCTTTCCAGGAGTCACATATA 2.000000 6 AATACCCTTACTAGGAGTCACATATA 1.000000 7 AATTTCCCTTCCAAGACTCTCATACT 4.000000 8 AGTACCCCTTCCAAGCGTCTCATATA 4.000000 9 AGTACCCCTTCCAAGCGTCTCATATT 1.000000 10 AGTTCCCCTTTCAAACGTCTCATTTT 1.000000 11 AGTTCCTCTTTCAAGCGTCTCATTTT 7.000000 12 AGTTCCTCTTTCAAACGTCTCATTTT 4.000000 13 AGTTCTCCTTCCAAGACCATCATATT 5.000000 14 AGTTCTCCTTCCAGGACTCTCATATA 3.000000 15 AGTTCTCCTTCCAGGACTCTCATATT 1.000000 16 AGTTCTCCTTCCAGGACTCTCATTTT 1.000000 17 GGTTCTCCTACTAGGAGTCACATATA 30.000000 18 GGTTCTCCTACTGGGAGTCACACATA 9.000000 19 GGTTCTCCTATTAGGAGTCACATATA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,11) D002: (2,5) D003: (14,17) D004: (13,17) D005: (4,5) D006: (13,17) D007: (17,17) D008: (17,17) D009: (4,17) D010: (9,17) D011: (8,8) D012: (13,17) D013: (2,8) D014: (4,11) D015: (7,17) D016: (3,11) D033: (4,14) D034: (2,17) D035: (17,17) D036: (7,13) D037: (8,17) D038: (7,13) D039: (6,14) D040: (12,17) E001: (17,18) E002: (4,17) E003: (12,17) E004: (4,17) E005: (10,18) E006: (12,17) E007: (12,17) E008: (4,17) E009: (17,18) E010: (4,4) E011: (17,19) E012: (11,11) E013: (4,18) E014: (18,18) E015: (17,18) E016: (4,17) E017: (11,18) E018: (15,16) E019: (17,17) E020: (4,4) E021: (4,7) E022: (11,18) E023: (4,17) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A A C A C C C T G T C C A A G A C T C T C A T A T A A G T T C C T C T T T C A A G C G T C T C A T T T T 0 D002 A A C A C C C T G T C C A A G A C T C T C A T A T T A A T A C C C T T T C C A G G A G T C A C A T A T A 0 D003 A G T T C T C C T T C C A G G A C T C T C A T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D004 A G T T C T C C T T C C A A G A C C A T C A T A T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D005 A A T A C C C T T T C C A A G C G T C T A G T A T A A A T A C C C T T T C C A G G A G T C A C A T A T A 0 D006 A G T T C T C C T T C C A A G A C C A T C A T A T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D007 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D008 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D009 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D010 A G T A C C C C T T C C A A G C G T C T C A T A T (T) G G T T C T C C T A C T A G G A G T C A C A T A T (A) 0 D011 A G T A C C C C T T C C A A G C G T C T C A T A T A A G T A C C C C T T C C A A G C G T C T C A T A T A 0 D012 A G T T C T C C T T C C A A G A C C A T C A T A T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D013 A A C A C C C T G T C C A A G A C T C T C A T A T T A G T A C C C C T T C C A A G C G T C T C A T A T A 0 D014 A A T A C C C T T T C C A A G C G T C T A G T A T A A G T T C C T C T T T C A A G C G T C T C A T T T T 0 D015 A A T T T C C C T T C C A A G A C T C T C A T A C T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D016 A A T A C C C C T T C C A G G A G T C A C A T A T A A G T T C C T C T T T C A A G C G T C T C A T T T T 0 D033 A A T A C C C T T T C C A A G C G T C T A G T A T A A G T T C T C C T T C C A G G A C T C T C A T A T A 0 D034 A A C A C C C T G T C C A A G A C T C T C A T A T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D035 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D036 A A T T T C C C T T C C A A G A C T C T C A T A C T A G T T C T C C T T C C A A G A C C A T C A T A T T 0 D037 A G T A C C C C T T C C A A G C G T C T C A T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 D038 A A T T T C C C T T C C A A G A C T C T C A T A C T A G T T C T C C T T C C A A G A C C A T C A T A T T 0 D039 A A T A C C C T T A C T A G G A G T C A C A T A T A A G T T C T C C T T C C A G G A C T C T C A T A T A 0 D040 A G T T C C T C T T T C A A A C G T C T C A T T T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E001 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E002 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E003 A G T T C C T C T T T C A A A C G T C T C A T T T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E004 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E005 A G T T C C C C T T T C A A A C G T C T C A T T T T G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E006 A G T T C C T C T T T C A A A C G T C T C A T T T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E007 A G T T C C T C T T T C A A A C G T C T C A T T T T G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E008 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E009 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E010 A A T A C C C T T T C C A A G C G T C T A G T A T A A A T A C C C T T T C C A A G C G T C T A G T A T A 0 E011 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A T T A G G A G T C A C A T A T A 0 E012 A G T T C C T C T T T C A A G C G T C T C A T T T T A G T T C C T C T T T C A A G C G T C T C A T T T T 0 E013 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E014 G G T T C T C C T A C T G G G A G T C A C A C A T A G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E015 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E016 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E017 A G T T C C T C T T T C A A G C G T C T C A T T T T G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E018 A G T T C T C C T T C C A G G A C T C T C A T A T T A G T T C T C C T T C C A G G A C T C T C A T [T] T T 0 E019 G G T T C T C C T A C T A G G A G T C A C A T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 0 E020 A A T A C C C T T T C C A A G C G T C T A G T A T A A A T A C C C T T T C C A A G C G T C T A G T A T A 0 E021 A A T A C C C T T T C C A A G C G T C T A G T A T A A A T T T C C C T T C C A A G A C T C T C A T A C T 0 E022 A G T T C C T C T T T C A A G C G T C T C A T T T T G G T T C T C C T A C T G G G A G T C A C A C A T A 0 E023 A A T A C C C T T T C C A A G C G T C T A G T A T A G G T T C T C C T A C T A G G A G T C A C A T A T A 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 C A = = C T G = C = = = = A C = = = = = = A = A = G T T = = T C T = T = = = = C G = = = = = = T = T 0 D002 = = C = = = = = G = = = = A = = ? = = T = = = = = T = = T = = = = = T = = = = G = = ? = = A = = = = = A 0 D003 A = = = = = = = = T = C = = = = ? = = T = = = = = = G = = = = = = = = A = T = = = = ? = = A = = = = = = 0 D004 A = = = = = = = = T = C = A = = C C A T = = = = = T G = = = = = = = = A = T = G = = G T C A = = = = = A 0 D005 = = = = = = = = = = = = = A = C = = = T A G = = = = = = = = = = = = = = = = = G = A = = = A C A = = = = 0 D006 A = = = = = = = = T = C = A = = C C A T = = = = = T G = = = = = = = = A = T = G = = G T C A = = = = = A 0 D007 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0 D008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D009 A A = A = C = T = T = C = A = C = = = T A G = = = = G G = T = T = C = A = T = G = A = = = A C A = = = = 0 D010 A = = A = C = = = T = C = A = C = = = T = = = = = (T) G = = T = T = = = A = T = G = A = = = A = = = = = (A) 0 D011 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 D012 A = = = = = = = = T = C = A = = C C A T = = = = = T G = = = = = = = = A = T = G = = G T C A = = = = = A 0 D013 = A C = = = = T G = = = = = = A C = = = = = = = = T = G T = = = = C T = = = = = = C G = = = = = = = = A 0 D014 = A = A = = C T = = C = = = = = = = = = A G = A = A = G = T = = T C = = T = = = = = = = = = C A = T = T 0 D015 A A = = T C = = = T = C = A = = C = = T = = = = C T G G = = C T = = = A = T = G = = G = = A = = = = T A 0 D016 = A = A = = C = = = C = = G = A = = = A = = = A = A = G = T = = T = = = T = = A = C = = = T = = = T = T 0 D033 = A = A = C = T = = = = = A = C G = = = A G = = = = = G = T = T = C = = = = = G = A C = = = C A = = = = 0 D034 A A C A = C = T ? ? ? C = A = = C = = T = = = = = T G G T T = T = C ? ? ? T = G = = G = = A = = = = = A 0 D035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D036 = A = = T C = = = = = = = = = = = T C = = = = = C = = G = = C T = = = = = = = = = = = C A = = = = = T = 0 D037 A = = A = C = = = T = C = A = C ? = = T = = = = = = G = = T = T = = = A = T = G = A ? = = A = = = = = = 0 D038 = A = = T C = = = = = = = = = = = T C = = = = = C = = G = = C T = = = = = = = = = = = C A = = = = = T = 0 D039 = A = A = C = T = A = T = = = = G = = A = = = = = = = G = T = T = C = T = C = = = = C = = T = = = = = = 0 D040 A = = = = C T = = T T C = A A C ? = = T = = = T = T G = = = = T C = = A C T = G G A ? = = A = = = A = A 0 E001 = = = = = = = = = = = = A = = = = = = = = = T = = = = = = = = = = = = = = = G = = = = = = = = = C = = = 0 E002 A A = A = C = T = T = C = A = C = = = T A G = = = = G G = T = T = C = A = T = G = A = = = A C A = = = = 0 E003 A = = = = C T = = T T C = A A C = = = T = = = T = T G = = = = T C = = A C T = G G A = = = A = = = A = A 0 E004 A A = A = C = T = T = C = ? = C = = = T A G = = = = G G = T = T = C = A = T = ? = A = = = A C A = = = = 0 E005 A = = = = C = = ? ? ? C A A A C = = = T = = T T = T G = = = = T = = ? ? ? T G G G A = = = A = = C A = A 0 E006 A = = = = C T = = T T ? = A A C = = = T = = = T = T G = = = = T C = = A C ? = G G A = = = A = = = A = A 0 E007 A = = = = C T = = T T C = A A C = = = T = = = T = T G = = = = T C = = A C T = G G A = = = A = = = A = A 0 E008 A A = A = C = T = T = C = A = C = = = T A G = = = = G G = T = T = C = A = T = G = A = = = A C A = = = = 0 E009 = = = = = = = = = = = = A = = = = = = = = = T = = = = = = = = = = = = = = = G = = = = = = = = = C = = = 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 = = = = = = = = = = C = = = = = = = = = ? = = = = = = = = = = = = = = = T = = = = = = = = = ? = = = = = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 A A = A = C = ? = T = C A A = C = = = T ? G T = = = G G = T = T = ? = A = T G G = A = = = A ? A C = = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0 E015 = = = = = = = = = = = = A = = = = = = = ? = T = = = = = = = = = = = = = = = G = = = = = = = ? = C = = = 0 E016 A A = A = C = T = T = C = A = C = = = T ? G = = = = G G = T = T = C = A = T = G = A = = = A ? A = = = = 0 E017 A = = = = C T = = T T C A A = C = = = T = = T T = T G = = = = T C = = A C T G G = A = = = A = = C A = A 0 E018 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 0 E019 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 E020 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 E021 = = = A C = = T = = = = = = = C G = = = A G = = T A = = = T T = = C = = = = = = = A C = = = C A = = C T 0 E022 A = = = = C T = = T T C A A = C = = = T = = T T = T G = = = = T C = = A C T G G = A = = = A = = C A = A 0 E023 A A = A = C = T = T = ? = A ? C = = = T A G = = = = G G = T = T = C = A = ? = G ? A = = = A C 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 = = = = = 1.00 1.00 = = = = = = = = 1.00 = 1.00 = = = = ? = = 1.00 = = = = = = 1.00 = = = = = = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 = = = = = = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = 0.55 = = = = = = = = = = = = = ? = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = = 0.92 = 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 = 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = = = 1.00 = = 1.00 = 1.00 = = = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 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 = = 0.97 = 0.97 = 0.97 = 0.97 = 0.99 = 0.99 = = = = 1.00 = = 1.00 = = = = = = 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 0.93 1.00 ? = = 1.00 = = = 1.00 = 1.00 = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 0.93 1.00 = = = 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = ? = 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 = = = = 1.00 = = ? ? ? 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 ? = 1.00 0.93 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 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 = ? = 1.00 = 1.00 1.00 1.00 = 1.00 = = = 1.00 ? 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 1.00 = = = = = = = ? = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 ? 1.00 = = = = 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = = = = = 1.00 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 = 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