************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 luxxx.phase.inp luxxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST luxxx.phase.out_freqs : haplotype frequency estimates luxxx.phase.out_pairs : most likely haplotype pairs for each individual luxxx.phase.out_recom : estimates of recombination parameters luxxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 51 Positions of loci: 85 180 234 518 1722 1946 2128 2237 2315 3221 3317 3919 3941 4452 4497 4971 5323 5649 5743 5898 6280 6537 7008 7011 7293 7342 7358 7394 7508 8357 8389 8555 8768 8921 11008 11314 11530 12045 12109 12948 13277 13386 13447 14342 14578 14724 15518 15546 15600 16426 16873 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file luxxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCGCCGDCGGICTAACTGGGGICCGCTGGTCAAITGGGAATDGGDTACTTC 1.000000 2 GCGCCGDCGGICTAACTGGGGICCGTTGGTCAAITGGAAGTDGGDCGCCCT 1.000000 3 GCGCCGDCGGICTAACTGGGGICCGTTGGTCAAITGGAAATDAGDTACTTC 1.000000 4 GCGCCGDCGGICTAACTGGGGICCGTTGGTCAAITGGAAATDAADTACTTC 1.000000 5 GCGCCGDCGGICTAACTGGGGICCGTTGGTCAAITGGAGACIAGDTGCCTC 2.000000 6 GCGCCGDCGGICTAACTGGGGICCGTTGGTCAAITGGGGATDGGDTACTTC 1.000000 7 GCGGCGDCAGITCAACCGGGGICCCCCGGTCAAITGGGGGTDAGDTATTTC 1.000000 8 GCGGCGDCAGITCAACCGGGGICCCCCGGTCAAITGGGGATDAGDTGCCTC 1.000000 9 GTGCCGDCGGICTAACTGGGGICCGTCGGTCACITGGGGATIAADTGTCTT 2.000000 10 GTGCCGDCGGICTAACTGGGGICCGTTGGTCAAITGGGGGTDGGITGCCTT 1.000000 11 GTGCCGDCGGITCAACCGGGGICCCCCGGTCAAITGGGGATDGGITACTTC 1.000000 12 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGAAGTDGGITGCCTT 1.000000 13 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGAGATDAGDCGCCCT 1.000000 14 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGAGTDGGDTACTTC 1.000000 15 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDGGDCGCCCT 3.000000 16 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDGGDTACCTC 2.000000 17 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDGGDTACTTC 13.000000 18 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDGGDTGCCTC 1.000000 19 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDGGITGCCTT 1.000000 20 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDGADTACTTC 1.000000 21 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTDAGDTACTTC 1.000000 22 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTIAGDCACTTC 1.000000 23 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTIAGDCGCCTC 2.000000 24 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGGTIAADTGTCTC 1.000000 25 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATDGGDTGCCTC 1.000000 26 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATDAGDCACTTC 1.000000 27 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATDAGDCGCCCT 4.000000 28 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATDAGDTGCCTC 1.000000 29 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATDAADCGCCCT 9.000000 30 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATDAADCGCCTC 2.000000 31 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATIAGDCGCCTC 7.000000 32 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATIAADCACTTC 1.000000 33 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATIAADCGCCTC 2.000000 34 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGACIAGDCGCCTC 1.000000 35 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGACIAGDTACTTC 2.000000 36 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGACIAGDTGCTTC 1.000000 37 GTGCCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGACIAADCACTTC 1.000000 38 GTGCCGDCGGITCAACCGGGGICCCCCGAGCAAITGGGGGTDGGDTACTTC 1.000000 39 GTGCCGDCGGITCAACCGGGGICCCCCGAGCAAITGGGGATDAGDTGCCCT 1.000000 40 GTGCCGDCGGITCAACCGGGGICCCCCGAGCAAITGGGGACIAGDTGCTTC 2.000000 41 GTGCCGDCAGICTAACCGGGGICCCCCGGGCAAITGGGGATDAGDCGCCCT 1.000000 42 GTGCCGDCAGICTAACCGATAICCCCCAGTTAADTGGGGACIAGDTGCCTC 2.000000 43 GTGCCGDCAGICTAACCGATAICCCCCAGGTAADTGGGGACIAGDCGCCTC 1.000000 44 GTACCGDCGGITCAACCGGGGICCCCCGGGCAAITGGGGATIAGDCGCCTC 1.000000 45 GTACCGDCGGDCCAACCAGGGICCCCCGGGCGAITGGGGATDAGDCGCCCT 3.000000 46 TTGGTCIGGGICCGATCGGGGDTTCCCGGTCAAITGGGGGTDGGDTACTTC 2.000000 47 TTGGTCIGGGICCGGTCGGGGDTTCCCGGTCAAITGGGGGTDGGDTACTTC 2.000000 48 TTGGTCDGAAICCGGCCGGGGDTCCCCGGTTACICATGGGTDGGDTACTTC 1.000000 49 TTGGTCDGAAICCGGCCGGGGDTCCCCGGTTACICATGGGTDAGDTATTTC 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,47) D002: (15,16) D003: (6,44) D004: (1,28) D005: (16,49) D006: (17,34) D007: (4,15) D008: (40,48) D009: (41,49) D010: (12,42) D011: (10,26) D012: (17,36) D013: (13,31) D014: (35,46) D015: (5,40) D016: (19,43) D033: (3,8) D034: (7,42) D035: (15,29) D036: (31,38) D037: (17,21) D038: (5,30) D039: (29,39) D040: (11,46) E001: (31,31) E002: (29,37) E003: (17,27) E004: (9,14) E005: (17,20) E006: (9,17) E007: (23,23) E008: (17,30) E009: (24,27) E010: (17,33) E011: (29,29) E012: (17,17) E013: (18,45) E014: (25,45) E015: (31,33) E016: (17,27) E017: (29,27) E018: (29,29) E019: (29,31) E020: (17,22) E021: (35,47) E022: (17,31) E023: (32,45) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G C G C C G D C G G I C T A A C T G G G G I C C G T T G G T C A A I T G G A A G T D G G D C G C C C T T T G G T C I G G G I C C G G T C G G G G D T T C C C G G T C A A I T G G G G G T D G G D T A C T T C 0 D002 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C C T C 0 D003 G C (G) C C G D C G G I C T A A C T G G G G I C C G T T G G T C A A I T G G G G A T D G G D T A C T T C G T (A) C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A G D C G C C T C 0 D004 G C G C C G D C G G I C T A A C T G G G G I C C G C T G G T C A A I T G G G (A) A T D (G) G D T (A) C (T) T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G (G) A T D (A) G D T (G) C (C) T C 0 D005 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C C T C T T G G T C D G A A I C C G G C C G G G G D T C C C C G G T T A C I C A T G G G T D A G D T A T T T C 0 D006 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A C I A G D C G C C T C 0 D007 G C G C C G D C G G I C T A A C T G G G G I C C G T T G G T C A A I T G G A A (A) T D (A) (A) D (T) (A) C (T) (T) (C) G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G (G) T D (G) (G) D (C) (G) C (C) (C) (T) 0 D008 G T G C C G D C G G I T C A A C C G G G G I C C C C C G A G C A A I T G G G G (A) (C) (I) (A) G D T (G) C T T C T T G G T C D G A A I C C G G C C G G G G D T C C C C G G T T A C I C A T G G (G) (T) (D) (G) G D T (A) C [T] T C 0 D009 G T G C C G D C A G I C T A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A G D C G C C C [T] T T G G T C D G A A I C C G G C C G G G G D T C C C C G G T T A C I C A T G G G T D A G D T A T T T C 0 D010 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G (G) C A A I T G G A A (G) (T) (D) (G) G (I) T G C C T (T) G T G C C G D C A G I C T A A C C G A T A I C C C C C A G (T) T A A D T G G G G (A) (C) (I) (A) G (D) T G C C T (C) 0 D011 G T G C C G D C G G I (C) (T) A A C (T) G G G G I C C (G) (T) (T) G G (T) C A A I T G G G G G T D G G I T G C C T T G T G C C G D C G G I (T) (C) A A C (C) G G G G I C C (C) (C) (C) G G (G) C A A I T G G G G A T D A G D C A C T T C 0 D012 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A C I A G D T G C T T C 0 D013 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G (A) G A T D A G D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G (G) G A T I A G D C G C C T C 0 D014 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G (A) (C) (I) (A) G D T [A] C [T] T C T T G G T C I G G G I C C G A T C G G G G D T T C C C G G T C A A I T G G G G (G) (T) (D) (G) G D T [A] C [T] T C 0 D015 G C G C C G D C G G I C T A A C T G G G G I C C G T T G G T C A A I T G G A G A C I A G D T G C C T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G A G C A A I T G G G G A C I A G D T G C T T C 0 D016 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G (G) (T) (D) (G) G (I) (T) G C C T (T) G T G C C G D C A G I C T A A C C G A T A I C C C C C A G G T A A D T G G G G (A) (C) (I) (A) G (D) (C) G C C T (C) 0 D033 G C G C C G D C G G I C T A A C T G G G G I C C G T T G G T C A A I T G G A A A T D A [G] D T (A) C (T) T C G C G G C G D C A G I T C A A C C G G G G I C C C C C G G T C A A I T G G G G A T D A G D T (G) C (C) T C 0 D034 G C G G C G D C A G I T C A A C C G G G G I C C C C C G G T C A A I T G G G G (G) (T) (D) A G D T (A) (T) (T) T C G T G C C G D C A G I C T A A C C G A T A I C C C C C A G T T A A D T G G G G (A) (C) (I) A G D T (G) (C) (C) T C 0 D035 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C C T 0 D036 G T G C C G D C G G I T C A A C C G G G G I C C C C C G (G) G C A A I T G G G G A T I A G D C G C C T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G (A) G C A A I T G G G G G T D G G D T A C T T C 0 D037 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D A G D T A C T T C 0 D038 G C G C C G D C G G I C T A A C T G G G G I C C G T T G G T C A A I T G G A G A C I A G D T G C C T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C T C 0 D039 G T G C C G D C G G I T C A A C C G G G G I C C C C C G (G) G C A A I T G G G G A T D A (A) D (C) G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G (A) G C A A I T G G G G A T D A (G) D (T) G C C C T 0 D040 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G T C A A I T G G G G (A) T D G G (I) T A C T T C T T G G T C I G G G I C C G A T C G G G G D T T C C C G G T C A A I T G G G G (G) T D G G (D) T A C T T C 0 E001 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A G D C G C C T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A G D C G C C T C 0 E002 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A (T) (D) A A D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A (C) (I) A A D C A C T T C 0 E003 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A G D C G C C C T 0 E004 G T G C C G D C G G I (C) (T) A A C (T) G G G G I C C (G) (T) C G G (T) C A (C) I T G G G (G) A T I A A D T G T C T T G T G C C G D C G G I (T) (C) A A C (C) G G G G I C C (C) (C) C G G (G) C A (A) I T G G G (A) G T D G G D T A C T T C 0 E005 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G A D T A C T T C 0 E006 G T G C C G D C G G I (C) (T) A A C (T) G G G G I C C (G) (T) C G G (T) C A (C) I T G G G G A T I A A D T G T C T T G T G C C G D C G G I (T) (C) A A C (C) G G G G I C C (C) (C) C G G (G) C A (A) I T G G G G G T D G G D T A C T T C 0 E007 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T I A G D C G C C T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T I A G D C G C C T C 0 E008 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C T C 0 E009 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G (G) T I A (A) D (T) G (T) C T (C) G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G (A) T D A (G) D (C) G (C) C C (T) 0 E010 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G (G) D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A (A) D C G C C T C 0 E011 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C C T 0 E012 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C 0 E013 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D (T) G C C (T) (C) G T A C C G D C G G D C C A A C C A G G G I C C C C C G G G C G A I T G G G G A T D A G D (C) G C C (C) (T) 0 E014 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D (G) G D (T) G C C (T) (C) G T A C C G D C G G D C C A A C C A G G G I C C C C C G G G C G A I T G G G G A T D (A) G D (C) G C C (C) (T) 0 E015 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A G D C G C C T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A A D C G C C T C 0 E016 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A G D C G C C C T 0 E017 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A [A] D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A [G] D C G C C C T 0 E018 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A A D C G C C C T 0 E019 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T D A (A) D C G C C C T G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A (G) D C G C C T C 0 E020 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T I A G D C A C T T C 0 E021 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G (A) (C) (I) (A) G D T A C T T C T T G G T C I G G G I C C G G T C G G G G D T T C C C G G T C A A I T G G G G (G) (T) (D) (G) G D T A C T T C 0 E022 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G G T D G G D T A C T T C G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T I A G D C G C C T C 0 E023 G T G C C G D C G G I T C A A C C G G G G I C C C C C G G G C A A I T G G G G A T (I) A (A) D C (A) C (T) (T) (C) G T A C C G D C G G D C C A A C C A G G G I C C C C C G G G C G A I T G G G G A T (D) A (G) D C (G) C (C) (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 G C = C C G D C = = = = T A A C T = = = = I C C G T T = = = = = = = = = = A A = = = = = ? C G = C ? T T T = G T C I G = = = = C G G T C = = = = D T T C C C = = = = = = = = = = G G = = = = = ? T A = T ? C 0 D002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C G = = C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A = = T C 0 D003 = C (G) = = = = = = = = C T = = = T = = = = = = = G T T = = T = = = = = = = = = = = D G = = T A = ? = = = T (A) = = = = = = = = T C = = = C = = = = = = = C C C = = G = = = = = = = = = = = I A = = C G = ? = = 0 D004 = C = = = = = = = = = C T = = = T = = = = = = = G = T = = T = = = = = = = = (A) = = = (G) = = = (A) = (T) = = = T = = = = = = = = = T C = = = C = = = = = = = C = C = = G = = = = = = = = (G) = = = (A) = = = (G) = (C) = = 0 D005 G = = C C G = C G G = T = ? ? = = = = = = I C = = = = = = G C = A = T G G = = = = = G = = = = C C = = T = = G T C = G A A = C = ? ? = = = = = = D T = = = = = = T T = C = C A T = = = = = A = = = = T T = = 0 D006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T D G = = T A = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C I A = = C G = C = = 0 D007 = C = = = = = = = = = C T = = = T = = = = = = = G T T = = T = = = = = = = A A (A) = = (A) (A) = (T) (A) = (T) (T) (C) = T = = = = = = = = = T C = = = C = = = = = = = C C C = = G = = = = = = = G G (G) = = (G) (G) = (C) (G) = (C) (C) (T) 0 D008 G = = C C G = C G G = T = A A = = = = = = I C = = = = = A G C = A = T G G = = (A) (C) (I) (A) = = = (G) = ? = = T = = G T C = G A A = C = G G = = = = = = D T = = = = = G T T = C = C A T = = (G) (T) (D) (G) = = = (A) = ? = = 0 D009 G = = C C G = C = G = = T A A = = = = = = I C = = ? ? ? ? G C = A = T G G = = A = = = = ? C G C C ? ? T = = G T C = G = A = = C G G = = = = = = D T = = ? ? ? ? T T = C = C A T = = G = = = = ? T A T T ? ? 0 D010 = = = = = = = = G = = T C = = = = = G G G = = = = = = G = (G) C = = I = = = A A (G) (T) (D) (G) = (I) = = = ? = (T) = = = = = = = = A = = C T = = = = = A T A = = = = = = A = (T) T = = D = = = G G (A) (C) (I) (A) = (D) = = = ? = (C) 0 D011 = = = = ? = = = = = = (C) (T) = = = (T) = = = = = = = (G) (T) (T) = = (T) = = = = = = = = = G = = G = I T G = C = T = = = = ? = = = = = = (T) (C) = = = (C) = = = = = = = (C) (C) (C) = = (G) = = = = = = = = = A = = A = D C A = T = C 0 D012 = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T D G = = = A = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C I A = = = G = = = = 0 D013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = D = = = = = = = C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = I = = = = = = = T C 0 D014 ? = = C ? G D C = = = T = ? = C = = = = = I C C = = = = = G = = = = = = = = = (A) (C) (I) (A) = = = ? ? ? = = ? = = G ? C I G = = = C = ? = T = = = = = D T T = = = = = T = = = = = = = = = (G) (T) (D) (G) = = = ? ? ? = = 0 D015 = C = = ? = = = = = = C T = = = T = = = = = = = G T T = G T = = = = = = = A = = = = = = = = = = C = = = T = = ? = = = = = = T C = = = C = = = = = = = C C C = A G = = = = = = = G = = = = = = = = = = T = = 0 D016 = = = = ? = = = G = = T C = = = = = G G G = = = = = = G = = C = = I = = = = = (G) (T) (D) (G) = (I) (T) = = = = (T) = = = = ? = = = A = = C T = = = = = A T A = = = = = = A = = T = = D = = = = = (A) (C) (I) (A) = (D) (C) = = = = (C) 0 D033 = = = C = = = = G = = C T = = = T = = = = = = = G T T = = ? = = = = = = = A A = = = = ? ? = (A) = (T) = = = = = G = = = = A = = T C = = = C = = = = = = = C C C = = ? = = = = = = = G G = = = = ? ? = (G) = (C) = = 0 D034 = C = G = = = = = = = T C = = = = = G G G = = = = = = G = = C = = I = = = = = (G) (T) (D) = = = = (A) (T) (T) = = = T = C = = = = = = = C T = = = = = A T A = = = = = = A = = T = = D = = = = = (A) (C) (I) = = = = (G) (C) (C) = = 0 D035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = G G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = A A = = = = = = = 0 D036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = A = I A = = C G = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = G = D G = = T A = T = = 0 D037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = 0 D038 = C = = = = = = = = = C T = = = T = = = = = = = G T T = = T = = = = = = = A = = C I = G = T = = = = = = T = = = = = = = = = T C = = = C = = = = = = = C C C = = G = = = = = = = G = = T D = A = C = = = = = 0 D039 = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = (A) = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = (G) = (T) = = = = = 0 D040 G = = C C G D ? = = = T = ? = C = = = = ? I C C = = = = = = = = = = = = = = = (A) = = = = (I) = = = = = = T = = G T C I ? = = = C = ? = T = = = = ? D T T = = = = = = = = = = = = = = = (G) = = = = (D) = = = = = = 0 E001 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) (D) = = = = G = C C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) (I) = = = = A = T T C 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = G = = G = = T A = T T C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = A = = A = = C G = C C T 0 E004 = = = = = = = = = = = (C) (T) = = = (T) = = = = = = = (G) (T) = = = (T) = = (C) = = = = = (G) A = I A A = = G T C = T = = = = = = = = = = = (T) (C) = = = (C) = = = = = = = (C) (C) = = = (G) = = (A) = = = = = (A) G = D G G = = A C T = C 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = 0 E006 = = = = = = = = = = ? (C) (T) = = = (T) = = = = = = = (G) (T) = = = (T) = = (C) = = = = = = A = I A A = = G T C = T = = = = = = = = = = ? (T) (C) = = = (C) = = = = = = = (C) (C) = = = (G) = = (A) = = = = = = G = D G G = = A C T = C 0 E007 = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = G G = T A = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = A A = C G = C = = 0 E009 = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = I = (A) ? (T) = (T) = T (C) = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = D = (G) ? (C) = (C) = C (T) 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = D ? (G) = T A = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = I ? (A) = C G = C = = 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = G = = = = = = = I T = = = = = G = = = = = = = = = = = = = A = = = = = = = G = = G = = (T) = = = (T) (C) = = A = = = = = = = D C = = = = = A = = = = = = = = = = = = = G = = = = = = = A = = A = = (C) = = = (C) (T) 0 E014 = = G = = = = = = = I T = = = = = G = = = = ? ? = = = = = = = A = = = = = = = = = = (G) = = (T) = = = (T) (C) = = A = = = = = = = D C = = = = = A = = = = ? ? = = = = = = = G = = = = = = = = = = (A) = = (C) = = = (C) (T) 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = 0 E016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = G = = T A = T T C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = A = = C G = C C T 0 E017 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D = (A) = = = = = C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = (G) = = = = = T C 0 E020 = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = D G = = T = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = I A = = C = = = = = 0 E021 G = = C C G D C = = = T = A A C = = = = = I C C = = = = = G = = = = = = = = = (A) (C) (I) (A) = = = = = = = = T = = G T C I G = = = C = G G T = = = = = D T T = = = = = T = = = = = = = = = (G) (T) (D) (G) = = = = = = = = 0 E022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = D G = = T A = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = I A = = C G = C = = 0 E023 = = G = = = = = = = I T = = = = = G = = = = ? ? = = = = = = = A = = = = = = = = = (I) = (A) = = (A) = (T) (T) (C) = = A = = = = = = = D C = = = = = A = = = = ? ? = = = = = = = G = = = = = = = = = (D) = (G) = = (G) = (C) (C) (T) 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 0.59 = = = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = 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 = = = 0.74 = = = 0.67 = 0.67 = = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = ? ? = = = = = = 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 = = 0.90 0.93 = 0.93 = = = 1.00 = = = = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = 1.00 1.00 0.53 = = 0.53 0.52 = 0.62 0.62 = 0.62 0.62 0.62 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 0.84 0.84 0.84 0.84 = = = 0.84 = ? = = 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = ? ? ? ? 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = = = = ? 1.00 1.00 1.00 1.00 ? ? = = = = = = = = 1.00 = = 1.00 1.00 = = = = = 1.00 1.00 1.00 = = = = = = 1.00 = 0.74 1.00 = = 1.00 = = = 1.00 1.00 0.74 0.74 0.74 0.74 = 0.74 = = = ? = 0.74 = = = = ? = = = = = = 0.58 0.58 = = = 0.58 = = = = = = = 0.58 0.58 0.58 = = 0.58 = = = = = = = = = 1.00 = = 1.00 = 1.00 1.00 0.94 = 0.94 = 0.94 = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 = = = 1.00 = = = = = = = 1.00 1.00 ? = = 1.00 ? 1.00 1.00 1.00 = = = 1.00 = ? = 1.00 = = = = = 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = = = 0.58 0.58 0.58 0.58 = = = ? ? ? = = = 1.00 = = ? = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 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 = = = = = 0.53 0.53 0.53 0.53 = 0.53 0.53 = = = = 0.53 = = = 1.00 = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = ? = = = = = = = 1.00 1.00 = = = = ? ? = 0.67 = 0.67 = = = 1.00 = 1.00 = = = = = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 = = = = = = 1.00 = = 1.00 = = 1.00 = = = = = 0.82 0.82 0.82 = = = = 0.82 0.82 0.82 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.55 = = = = = = = = = = 0.97 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.77 = = = = = = = = = = = = = = 0.85 = 0.82 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 ? = = = 1.00 = ? = 1.00 = = = = ? 1.00 1.00 1.00 = = = = = = = = = = = = = = = 0.71 = = = = 0.55 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.60 0.75 = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0.96 = = 0.95 = = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = 0.83 0.83 = = = 0.83 = = = = = = = 0.83 0.83 = = = 0.83 = = 0.83 = = = = = 0.57 0.97 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = ? 0.84 0.84 = = = 0.84 = = = = = = = 0.84 0.84 = = = 0.84 = = 0.84 = = = = = = 0.97 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = 0.99 0.97 = 1.00 0.97 = 0.97 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.78 = 1.00 = 0.56 ? 0.79 = 0.78 = 1.00 0.84 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 ? 0.71 = 1.00 0.97 = 0.97 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = = = = = = = 0.96 0.96 = = = = = 0.96 = = = = = = = = = = = = = 0.96 = = = = = = = 0.97 = = 0.91 = = 0.56 = = = 0.56 0.56 = = 1.00 = = = = = = = 1.00 1.00 = = = = = 1.00 = = = = ? ? = = = = = = = 1.00 = = = = = = = = = = 0.74 = = 0.51 = = = 0.51 0.51 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.95 = = 0.95 = = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = 0.85 = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = 0.85 0.85 0.85 0.85 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 = 1.00 1.00 = = 1.00 0.99 = 0.99 = = = = 0.96 = = = = = = = 0.96 0.96 = = = = = 0.96 = = = = ? ? = = = = = = = 0.96 = = = = = = = = = 0.72 = 0.76 = = 0.67 = 0.67 0.67 0.67 END PHASEPROBS