************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 tcf1x.phase.inp tcf1x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tcf1x.phase.out_freqs : haplotype frequency estimates tcf1x.phase.out_pairs : most likely haplotype pairs for each individual tcf1x.phase.out_recom : estimates of recombination parameters tcf1x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 76 Positions of loci: 367 745 842 2074 2102 2445 2998 3817 4453 4518 5002 5333 5379 5389 6270 7608 7918 9425 9467 9869 9875 9959 10043 10330 10574 11533 11947 12014 12063 12370 12779 13291 13571 13927 13928 13936 13937 14675 14880 14881 15382 16018 16706 16753 16781 17598 17783 18084 19325 20078 20120 20670 20831 20916 20964 21076 21267 21865 22603 22710 22871 23291 23427 23631 23800 23871 24199 24335 24683 24924 25089 25754 26824 26952 27690 27705 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tcf1x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GATCAADCDTCGCTGDICATGCGAACCGGGAGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 2 GATCAADCDTCGCTGDICATGCGAACCGGGAGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 3 GATCAADCDTTGCTGIDTCTACAGGCCAGGGGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 2.000000 4 GATCAADCDTTGCTGIDTCTACAGGCCAGGGGGGGATCGTACGACGGCGCI 3 CGGGTCGCGGGCCCITGGGGTGAA 1.000000 5 GATCAADCDTTGCTGIDTCTACAGGCCAGGGGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 6 GATCAADCDTTGCTGIDTCTACAGGCCAGGGGGGGGTCGTACGACGGCGCI 3 CGGGTCGCGGGCCCITGGGGTGAA 5.000000 7 GATCAADCDTTGCCGDITCTACAGGCCAGGGGGGGGTTAAACGTCGGCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 8 GATCAADCDTTGTTGIITCTACAGGCCAGGGGGGGGTTAAAAGACCTCGCI 3 CGGGCAGCGAGTCCITGGGACGTG 1.000000 9 GATCAADCDTTGTTGIITCTACAGGCCAGGGGGGGGTCAAACGACGGCGCD 3 CGGGTCGCGGGCCCITGGAGTGAG 1.000000 10 GATCAADCDTTGTTGIDTCTACAGGCCAGGGGGGGGTCAAACGACGGCGCD 3 CGGGTCGCGGGCCCITGGAGTGAG 1.000000 11 GATCAADCDTTGTTGIDTCTACAGGCCAGGGGGGGGTCAAACGACGGCGCI 3 CGGGTCGCGGGCCCITGGAGTGAG 2.000000 12 GATCAADCDTTTCTGIDTCTACAGGCCAGGGGGGGATCAAACATTGGTGCI 3 TAATCCGCGAGCTCICTAGGTTTG 1.000000 13 GATCAADCDTTTCTGIDTCTACAGGCCAGGGGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGAG 3.000000 14 GATCAADCDTTTCTGIDTCTACAGGCCAGGGGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAACCTDTGGGGTGTG 9.000000 15 GATCAADCDTTTCTGIDTCTACAGGCCAGCGGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAACCTDTGGGGTGTG 1.000000 16 GATCAADCDCTGCTGIDTCTACAGGCCAGGGGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 17 GATCAADCDCTGCTGIDTCTACAGGCCAGGGGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 18 GATCAADCDCTGCTGIDTCCACAGGCCAGGGAGATAGTAAAAGACCTCGCI 3 CGGGCAGCGAGTCCITGGGACGTG 3.000000 19 GATCAADCITTGCTGIDTCTACAGGCCAGGGGGGGGTTAAGCGTCCTCGCI 3 CGGGCAACGAGCCTITGGGGTGAG 2.000000 20 GATCAADCITTGCTGIDTCTACAGGCCAGCGGGGGGTTAAGCGTCCTCGCI 3 CGGGCAACGAGCCTITGGGGTGAG 2.000000 21 GATCAADCITTGCTGIDTCTACAGGCCAGCGGGGGGTTAAGCGTCCTCGCI 3 CGGGCAACGAACCTITGGGGTGAG 1.000000 22 GATCAADCITTGCTGIDTCTACAGGTCAGCGGGGGGTTAAGCGTCCTCGCI 3 CGGGCAACGAGCCTITGGGGTGAG 4.000000 23 GATCAADTDTCGCTGDICATGCGAACCGGGAGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 4.000000 24 GATCAADTDTCGCTGDICATGCGAACCGGGAGGGGGTTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 2.000000 25 GATCAADTDTCTCTGDICATGCGAGCCGGGAGGATAGTAAAAGACCTCGCI 3 CGGGCAGCGAGTCCITGGGACGTG 1.000000 26 GATCAAICDCTGCTGIDTCCACAGGCCAGGGGGATAGTAAAAGACCTCGCI 3 CGGGCAGCGAGTCCITGGGACGTG 1.000000 27 GATCAAICDCTGCTGIDTCCACAGGCCAGGGGGATAGTAAAAGACCTCGCI 3 CGGGTAGCGAGTCCITGGGACGTG 1.000000 28 GATCAGICDCTGCCAIICCTATGAGTTAAGGGGGGATCAAACATTGGTGCI 3 TAATCCGCGAGCTCICTAGGTTTG 1.000000 29 GATCAGICDCTGCCAIICCTGTGAGTTAAGGGGGGATCAAACATTGGTGCI 3 TAATCCGCGAGCTCICTAGGTTTG 1.000000 30 GATGAADCITTGCTGIDTCTACAGGCCAGCGGGGGGTTAAGCGTCCTCGCI 3 CGGGCAACGAGCCTITGGGGTGAG 1.000000 31 GATGAGICDCTGCCGIDTCTACAGGCCAGGGGGGGATTAAAAGACCTCGCI 3 CGGGCAGCGAGTCCITGGGGCGTG 1.000000 32 GACCAADCDTTGTTGDDTCTACAGGCCAGGGGGGGGTCAAACGACGGCGCI 3 CGGGCCGCGGGCCCITGGAGTGAG 1.000000 33 GACGAADCDTTGCTGIDCCTACAGGCCAAGGGGGGATTAAACGTCCTCGCI 3 CGGGCAGCGAGCCTITGGGGTGAG 1.000000 34 GGTCAADTDTCGCTGDICATACGAACCGGGAGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 35 GGTCAADTDTCGCTGDICATGCGAACCGGGAGGGGGTCAAACGACGGCGCI 3 CGGGTCGCGGGCCCITGGAGTGAG 1.000000 36 GGTCAADTDTCGCTGDICATGCGAACCGGGAGAGGATTAAACGTCGTCACD 3 CGGGCAGTAAGCCTDTGGGGTGTG 1.000000 37 GGTCAADTDTCGCTGDICATGCGAACCGGGAGAGGGTTAAACGTCGTCATD 3 CGGGCAGTAAGCCTDTGGGGTGTG 2.000000 38 GGTCAADTDTCGCTGDICATGCGAACCGGGAAAGGATTAAACGTCGTCATD 3 CGGGCAGTAAGCCTDTGGGGTGTG 3.000000 39 GGCGAADCDTTGTTGDICATGCGAGCCGGGGGGGGATTAAACGTCGTTGCI 1 CGATCCGCGAGCTCICTAGGTTTG 3.000000 40 GGCGAADCDCTGCTGIDTCTACAGGCCAAGGGGGGATTAAACGTCCTCGCI 3 CGGGCAGCGAGCCTITGGGGTGAG 1.000000 41 GGCGCGICDCTGCCAIICCTGCGAGTTAAGGGGGGATCAAACATTGGTGCI 3 TAATCCGCGAGCTCICTAGGTTTG 1.000000 42 AGCCAADCITTGCTGIDTCTACAGGCCAGCGGGGGGTTAAGCGTCCTCGCI 3 CGGGCAACGAGCCTITGGGGTGAG 1.000000 43 AGCGAADCDTTGCTGIDTCTACAGGCCAGGGGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 44 AGCGAADCDTTGCTGIDTCTACAGGCCAGGGGGGGATTAAACGTCGTCGCI 3 TAATCCGCGAGCTCICTAGGTTTG 1.000000 45 AGCGAADCDTTGCTGIDTCTACAGGCCAGGGGGGGGTTAAACGTCGTCACD 3 CGGGCAGCGAGCCTDTGGGGTGTG 1.000000 46 AGCGAADCDTTGCTGIDTCTACAGGCCAGGGGGGGGTTAAACGTCGGCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 1.000000 47 AGCGAADCDTTGCTGIDTCTACAGGCCAGGGAGGGGTTAAACGTCGTCGCI 4 CGGGCAGCGAGCCCITGGGGTGTG 2.000000 48 AGCGAADCDTTGCCGIITCTACAGGCCAGGGGGGGATTAAACGTCGTCACD 3 CGGGCAGTGAGCCTDTGGGGTGTG 2.000000 49 AGCGCADCDCTGCTGIDTCTACAGGCCAAGGGGGGATTAAACGTCCTCGCI 3 CGGGCAGCGAGCCTITGGGGTGAG 1.000000 50 AGCGCGICDCTGCCAIICCTGCGAGTTAAGGGGGGATCAAACATTGGTGCI 3 TAATCCGCGAGCTCICTAGGTTTG 2.000000 51 AGCGCGICDCTGCCAIICCTGTGAGTTAAGGGGGGATCAAACGTCGTCACD 3 CGGGCAGTGAACCTDTGGGGTGTG 1.000000 52 AGCGCGICDCTGCCAIICCTGTGAGTTAAGGGGGGATCAAACATTGGTGCI 3 TAATCCGCGAGCTCICTAGGTTTG 8.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (3,23) DY02: (13,24) DY03: (13,31) DY04: (8,17) DY05: (9,10) DY06: (27,36) DY07: (23,33) DY08: (46,47) DY09: (13,48) DY10: (34,38) DY11: (5,29) DY12: (11,43) DY13: (16,38) DY14: (1,23) DY15: (2,35) DY16: (7,32) DY17: (37,52) DY18: (28,52) DY19: (40,49) DY20: (45,48) DY21: (3,37) DY22: (38,44) DY23: (24,26) DY24: (11,23) E101: (20,52) E102: (6,39) E103: (15,50) E104: (25,47) E105: (14,18) E106: (18,30) E107: (39,52) E108: (14,22) E109: (6,14) E110: (4,22) E111: (14,14) E112: (12,22) E113: (52,52) E114: (14,52) E115: (19,42) E116: (6,6) E117: (18,20) E118: (14,50) E119: (19,22) E120: (51,52) E121: (14,21) E122: (6,39) E123: (14,41) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G A T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 DY02 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G A G G A T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 DY03 G A T (C) A (A) (D) C D (T) T (T) C (T) G I D T C T A C A G G C C A G G G G G G G (G) T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G A G G [A] [T] (G) A (G) (I) C D (C) T (G) C (C) G I D T C T A C A G G C C A G G G G G G G (A) T T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G G C G T G 0 DY04 G A T C A A D C D (T) T G (T) T G I (I) T C T A C A G G C C A G G G G G G G G T T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G [A] C G T G G A T C A A D C D (C) T G (C) T G I (D) T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 DY05 G A T C A A D C D T T G T T G I I T C T A C A G G C C A G G G G G G G G T C A A A C G A C G G C G C D 3 C G G G T C G C G G G C C C I T G G A G T G A G G A T C A A D C D T T G T T G I D T C T A C A G G C C A G G G G G G G G T C A A A C G A C G G C G C D 3 C G G G T C G C G G G C C C I T G G A G T G A G 0 DY06 G A T C A A I C D C T G C T G I D T C C A C A G G C C A G G G G G A T A G T A A A A G A C C T C G C I 3 C G G G T A G C G A G T C C I T G G G A C G T G G G T C A A D T D T C G C T G D I C A T G C G A A C C G G G A [G] [A] G G [A] T T A A A C G T C G T C A C D 3 C G G G C A G T A A G C C T D T G G G G T G T G 0 DY07 G A T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G G G G [A] T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G A C G A A D C D T T G C T G I D C C T A C A G G C C A A G G G G G [G] A T T A A A C G T C C T C G C I 3 C G G G C A G C G A G C C T I T G G G G T G A G 0 DY08 A G C G A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G [G] T T A A A C G T C G G C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G A G C G A A D C D T T G C T G I D T C T A C A G G C C A G G G A G G G G T T A A A C G T C G T C G C I 4 C G G G C A G C G A G C C C I T G G G G T G T G 0 DY09 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G (G) T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G A G A G C G A A D C D T T G C C G I I T C T A C A G G C C A G G G G G G G (A) T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 DY10 G G T C A A D T D T C G C T G D I C A T (A) C G A A C C G G G A G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G G T C A A D T D T C G C T G D I C A T (G) C G A A C C G G G A [A] A G G A T T A A A C G T C G T C A T D 3 C G G G C A G T A A G C C T D T G G G G T G T G 0 DY11 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G A T C A G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 DY12 (G) (A) (T) (C) A A D C D T T G T T G I [D] T C T A C A G G C C A G G G G G G G G T C A A A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G A G T G A G (A) (G) (C) (G) A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 DY13 G A T C A A D C D (C) T G C T G I D T C T A C A G G C C A G G G G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G G T C A A D T D (T) C G C T G D I C A T G C G A A C C G G G A [A] A G G A T T A A A C G T C G T C A T D 3 C G G G C A G T A A G C C T D T G G G G T G T G 0 DY14 G A T C A A D C D T C G C T G D I C A T G C G A A C C G G G A G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G A T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 DY15 G A T C A A D (C) D T C G C T G D I C A T G C G A A C C G G G A G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G G T C A A D (T) D T C G C T G D I C A T G C G A A C C G G G A G [G] G G G T [C] A A A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G A G T G A G 0 DY16 G A (T) C A A D C D T T G C (C) G D (I) T C T A C A G G C C A G G G G G G G G T T A A A C G T C G G C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G A (C) C A A D C D T T G T (T) G D (D) T C T A C A G G C C A G G G G G G G G T C A A A C G A C G G C G C I 3 C G G G C C G C G G G C C C I T G G A G T G A G 0 DY17 G G T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G A G G G T T A A A C G T C G T C A T D 3 C G G G C A G T A A G C C T D T G G G G T G T G A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 DY18 G A T C A G I C D C T G C C A I I C C T (A) T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G A G C G C G I C D C T G C C A I I C C T (G) T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 DY19 (G) G C G A A D C D C T G C T G I D T C T A C A G G C C A A G G G G G [G] A T T A A A C G T C C T C G C I 3 C G G G C A G C G A G C C T I T G G G G T G A G (A) G C G C A D C D C T G C T G I D T C T A C A G G C C A A G G G G G [G] A T T A A A C G T C C T C G C I 3 C G G G C A G C G A G C C T I T G G G G T G A G 0 DY20 A G C G A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G (G) T T A A A C G T C G T C A C D 3 C G G G C A G (C) G A G C C T D T G G G G T G T G A G C G A A D C D T T G C C G I I T C T A C A G G C C A G G G G G G G (A) T T A A A C G T C G T C A C D 3 C G G G C A G (T) G A G C C T D T G G G G T G T G 0 DY21 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G G T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G A G G G T T A A A C G T C G T C A T D 3 C G G G C A G T A A G C C T D T G G G G T G T G 0 DY22 G G T C A A D T D T C G C T G D I C A T G C G A A C C G G G A A A G G A T T A A A C G T C G T C A T D 3 C G G G C A G T A A G C C T D T G G G G T G T G A G C G A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G A T T A A A C G T C G T C G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 DY23 G A T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G G A T C A A I C D C T G C T G I D T C C A C A G G C C A G G G G G A T A G T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G A C G T G 0 DY24 G A T C A A D C D T T G T T G [I] D T C T A C A G G C C A G G G G G G G G T C A A A C G A C G G C G C I 3 C G G G [T] C G C G G G C C C I T G G A G T G A G G A T C A A D T D T C G C T G D I C A T G C G A A C C G G G A G G G G A T T A A A C G T C G T C A C D 3 C G G G C A G T G A G C C T D T G G G G T G T G 0 E101 G A T C A A D C I T T G C T G I D T C T A C A G G C C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E102 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G G T C G T A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G G G T G A A G G C G A A D C D T T G [T] T G D I C A T G C G A G C C G G G G G G G G A T T A A A C G T C G T T G C I 1 C G A T C C G C G A G C T C I C T A G G T T T G 0 E103 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G (C) G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G A G C G C G I C D C T G C C A I I C C T G C G A G T T A A (G) G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E104 G A T C A A D T D T C (T) C T G D I C A T G C G A G C C G G G A G G A T A G T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G A C G T G A G C G A A D C D T T (G) C T G I D T C T A C A G G C C A G G G A G G G G T T A A A C G T C G T C G C I 4 C G G G C A G C G A G C C C I T G G G G T G T G 0 E105 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G G A T C A A D C D C T G C T G I D T C C A C A G G C C A G G G A G A T A G T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G A C G T G 0 E106 G A T (C) A A D C D C T G C T G I D T C C A C A G G C C A G G G A G A T A G T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G A C G T G G A T (G) A A D C I T T G C T G I D T C T A C A G G C C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E107 G G C G A A D C D T T G [T] T G D I C A T G C G A G C C G G G G G G G G A T T A A A C G T C G T T G C I 1 C G A T C C G C G A G C T C I C T A G G T T T G A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E108 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G G A T C A A D C I T T G C T G I D T C T A C A G G T C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E109 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G G T C G T A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G G G T G A A G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G 0 E110 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G (A) T C G T A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G G G T G A A G A T C A A D C I T T G C T G I D T C T A C A G G [T] C A G C G G G G G (G) T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E111 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G 0 E112 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G G A T C A A D C I T T G C T G I D T C T A C A G G T C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E113 A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E114 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E115 G A T C A A D C I T T G C T G I D T C T A C A G G C C A G (G) G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G A G C C A A D C I T T G C T G I D T C T A C A G G C C A G (C) G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E116 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G G T C G T A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G G G T G A A G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G G T C G T A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G G G T G A A 0 E117 G A T C A A D C D C T G C T G I D T C C A C A G G C C A G G G A G A T A G T A A A A G A C C T C G C I 3 C G G G C A G C G A G T C C I T G G G A C G T G G A T C A A D C I T T G C T G I D T C T A C A G G C C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E118 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G A G C G C G I C D C T G C C A I I C C T G C G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E119 G A T C A A D C I T T G C T G I D T C T A C A G G C C A G G G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G G A T C A A D C I T T G C T G I D T C T A C A G G T C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A G C C T I T G G G G T G A G 0 E120 A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G A G C G C G I C D C T G C C A I I C C T G T G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T G 0 E121 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G G A T C A A D C I T T G C T G I D T C T A C A G G C C A G C G G G G G G T T A A G C G T C C T C G C I 3 C G G G C A A C G A A C C T I T G G G G T G A G 0 E122 G A T C A A D C D T T G C T G I D T C T A C A G G C C A G G G G G G G G T C G T A C G A C G G C G C I 3 C G G G T C G C G G G C C C I T G G G G T G A A G G C G A A D C D T T G [T] T G D I C A T G C G A G C C G G G G G G G G A T T A A A C G T C G T T G C I 1 C G A T C C G C G A G C T C I C T A G G T T T G 0 E123 G A T C A A D C D T T T C T G I D T C T A C A G G C C A G G G G G G G G T T A A A C G T C G T C A C D 3 C G G G C A G T G A A C C T D T G G G G T G T G G G C G C G I C D C T G C C A I I C C T G C G A G T T A A G G G G G G A T C A A A C A T T G G T G C I 3 T A A T C C G C G A G C T C I C T A G G T T T 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 DY01 = = = = = = = C = = T ? ? ? = I ? T C = A = A G G ? = A = ? G = = = = = = ? ? ? = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = C ? ? ? = D ? C A = G = G A A ? = G = ? A = = = = = = ? ? ? = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY02 = ? = = = = = C = = T T = = = I D ? ? = A = A G G = = A = = G ? ? = = = = ? ? ? = ? = = = = = = ? = ? = = = = = = = = = = = = = = = = = = = = ? = = A = = ? = = = = = T = = C G = = = D I ? ? = G = G A A = = G = = A ? ? = = = = ? ? ? = ? = = = = = = ? = ? = = = = = = = = = = = = = = = = = = = = ? = = T = 0 DY03 = ? ? (C) = (A) (D) = = (T) = (T) = (T) = = = = = = = = = = = ? = = ? = = = = ? ? (G) = = = = = C = T = G = ? A = D = = = = = = = = T = = = C = T D = = = = = T = A = = ? ? (G) = (G) (I) = = (C) = (G) = (C) = = = = = = = = = = = ? = = ? = = = = ? ? (A) = = = = = A = A = C = ? G = I = = = = = = = = C = = = T = C I = = = = = C = T = 0 DY04 = = ? = = = = = = (T) = = (T) = = = (I) = = = = = = = = = = = = = = = = = = = = = = = = A = A = C = ? G = I = = = = = = = = C = = = T = C ? ? = = = ? C = = = = = ? = = = = = = (C) = = (C) = = = (D) = = = = = = = = = = = = = = = = = = = = = = = = C = T = G = ? A = D = = = = = = = = T = = = C = T ? ? = = = ? T = = = 0 DY05 = = = = = = = = = = = = = = = = I = = = = = = = = ? = = = = = = = ? ? ? ? = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D = = = = = = = = ? = = = = = = = ? ? ? ? = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY06 = A = = = = I C = C T = = = = I D ? ? C A = A G G ? = A = = ? ? ? ? ? ? ? = = = ? ? = A = C = ? G = ? = = = = = T = = C G = = T = C I = = = = A C = = = = G = = = = D T = T C = = = = D I ? ? T G = G A A ? = G = = ? ? ? ? ? ? ? = = = ? ? = T = G = ? A = ? = = = = = C = = T A = = C = T D = = = = G T = = = 0 DY07 = = T C = = = T = = C = = = = D I = A = G = ? A A = = G G ? ? = = ? ? ? ? = = = = = = = = G = = A ? ? = = = = = ? = = T = = = = = = D = = = = = = = T = = = C G = = = C = = T = = = = I D = C = A = ? G G = = A A ? ? = = ? ? ? ? = = = = = = = = C = = G ? ? = = = = = ? = = C = = = = = = I = = = = = = = A = 0 DY08 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = G = ? ? ? ? = = = ? = = = = = G ? A = D 3 = = = = ? = = T = = = = = T D = = = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = A = ? ? ? ? = = = ? = = = = = T ? G = I 4 = = = = ? = = C = = = = = C I = = = = ? = = = = 0 DY09 G A T C = = = = = = = T = T = = D = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = A = A G C G = = = = = = = G = C = = I = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = T = 0 DY10 = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = C = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = T = = = = = = = = = = A = = = = = = = = = = = = = = = 0 DY11 = = = = = A D = = T = = = T G = D T = = A C A G = ? C = G = = = = = = G = T = = = = G = C ? ? C A = D = C G G G = A = T = = = = C T D T G G = = = G = = = = = = = G I = = C = = = C A = I C = = G T G A = ? T = A = = = = = = A = C = = = = A = T ? ? T G = I = T A A T = C = C = = = = T C I C T A = = = T = = 0 DY12 (G) (A) (T) (C) = = = = = = = = T = = = ? = = = = = = = = = = = = = = = = = = G = C = = = = = A = = G = G = I = = = = = T C = C = G = = = C I = = = A = = = A = (A) (G) (C) (G) = = = = = = = = C = = = ? = = = = = = = = = = = = = = = = = = A = T = = = = = T = = T = A = D = = = = = C A = T = A = = = T D = = = G = = = T = 0 DY13 = A = = = = = C = (C) T = = = = ? D T C = A = A G G = = A = = G ? G = = = = = = = = = = = = ? ? = = C = = = = = = = = = = G = = = = = = = = = = = = = = = = G = = = = = T = (T) C = = = = ? I C A = G = G A A = = G = = A ? A = = = = = = = = = = = = ? ? = = T = = = = = = = = = = A = = = = = = = = = = = = = = = 0 DY14 = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY15 = A = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? = = = T = = T = A = D = = = = = C A = T = A = = = T D = = = G = = = T = = G = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? = = = A = = G = G = I = = = = = T C = C = G = = = C I = = = A = = = A = 0 DY16 = = (T) = = = = = = = = = C (C) = = (I) = = = = = = = = = = = = = = = = = = = = T = = = ? = T = = = = A = D = = = = = = A = T = A = = = T D = = = G = = = T = = = (C) = = = = = = = = = T (T) = = (D) = = = = = = = = = = = = = = = = = = = = C = = = ? = A = = = = G = I = = = = = = C = C = G = = = C I = = = A = = = A = 0 DY17 G = T C A A D T = T C = = T G D = = A = = C = = A C C G G = A = A = = G = ? ? ? = = G = C = T C A T D = C G G G = A = T A = = = C T D T G G = = = G = = A = C G C G I C = C T = = C A I = = C = = T = = G T T A A = G = G = = A = ? ? ? = = A = T = G T G C I = T A A T = C = C G = = = T C I C T A = = = T = = 0 DY18 G ? ? C A = = = = = = = = = = = = = = = (A) = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A ? ? G C = = = = = = = = = = = = = = = (G) = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY19 (G) = = = A = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = C = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 = = = = = = = = = = = = = T = = ? = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = ? = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = ? = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = ? = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = 0 DY21 = A = = = = = C = = T = = = = I D T C = A = A G G = = A = = G = G = = A = = = = = = = = = = = = = C = = = = = = = = = = G = = = = = = = = = = = = = = = = G = = = = = T = = C = = = = D I C A = G = G A A = = G = = A = A = = G = = = = = = = = = = = = = T = = = = = = = = = = A = = = = = = = = = = = = = = = 0 DY22 G = ? C = = = T = = C = = = = D I C A = G = G A A = = G = = A A A = = = = = = = = = = = = = = = A T D = C G G G = A = T A = = = C T D T G G = = ? G = = A = ? G = = = C = = T = = = = I D T C = A = A G G = = A = = G G G = = = = = = = = = = = = = = = G C I = T A A T = C = C G = = = T C I C T A = = ? T = = 0 DY23 = = = = = = D T = T C = = = = D I C A T G = G A A = = G = = A = = G G G T = = = = C = T = G = = A = D = = = = = = = = T = = = C = T D = = = = G T = = = = = = = = = I C = C T = = = = I D T C C A = A G G = = A = = G = = A T A G = = = = A = A = C = = G = I = = = = = = = = C = = = T = C I = = = = A C = = = 0 DY24 = ? = = = = = C = = T = T = = ? D T C = A = ? G G ? = A = = G = = = = G = ? ? ? = = = A = = G = G = I = = = = = ? C = C = G = = = C I = = = A = = = A = = ? = = = = = T = = C = C = = ? I C A = G = ? A A ? = G = = A = = = = A = ? ? ? = = = T = = T = A = D = = = = = ? A = T = A = = = T D = = = G = = = T = 0 E101 G ? T C A A D = I T = = = T G = D T = = A C A G = C C = G C = ? = = = G = T = = G = G = C C T C = = = = C G G G = A A = = = = = C T = T G G = = = G A = A ? C G C G I = D C = = = C A = I C = = G T G A = T T = A G = ? = = = A = C = = A = A = T G G T = = = = T A A T = C G = = = = = T C = C T A = = = T T = 0 E102 = A T C = = = = = = = = ? = = I D T C = A = A G = = = A = = = = = = = G = C G T = = = A = = G C = = = 3 = = G G T = = = = G = = C = = T G G = = = G A A = G C G = = = = = = = = ? = = D I C A = G = G A = = = G = = = = = = = A = T A A = = = T = = T T = = = 1 = = A T C = = = = A = = T = = C T A = = = T T G 0 E103 G A T C A A D = = T = T = T G = ? T = = A = A G = C C = G (C) = = = = = G = T = = = = G = C = T C A = D = C G G G = A = T = = A = C T D T G G = = = G = = A G C G C G I = = C = G = C A = ? C = = G = G A = T T = A (G) = = = = = A = C = = = = A = T = G T G = I = T A A T = C = C = = G = T C I C T A = = = T = = 0 E104 G A T C = = = T = = C (T) = = = D I C A = G = G A = = = G = = A G = A T A G = ? ? = A = A = C = = = = = 3 = = = = = = = = = ? = T = = = = = = = A C = = = A G C G = = = C = = T (G) = = = I D T C = A = A G = = = A = = G A = G G G T = ? ? = C = T = G = = = = = 4 = = = = = = = = = ? = C = = = = = = = G T = = = 0 E105 = = = = = = = = = T = T = = = = = = = T = = = = = = = = = = = G = G G G T = = = = C = T = G = ? A = D = = = = = = = = T = = A C = T D = = = = G T = = = = = = = = = = = = C = G = = = = = = = C = = = = = = = = = = = A = A T A G = = = = A = A = C = ? G = I = = = = = = = = C = = G T = C I = = = = A C = = = 0 E106 = = = (C) = = = = D C = = = = = = = = = C = = = = = = = = = G = ? = A T A G = = = A A = A = = = = = = = = = = = = = = G = = = = T = C = = = = = A C = T = = = = (G) = = = = I T = = = = = = = = = T = = = = = = = = = C = ? = G G G T = = = G C = T = = = = = = = = = = = = = = A = = = = C = T = = = = = G T = A = 0 E107 G = = = A A D = = T = = ? ? G D = = A = = C = = = C C G G = = = = ? ? = = T = = = = G = C = T ? = = = 1 C G = = = = = = = = = = = = = = = = = = = = = = A = = = C G I = = C = = ? ? A I = = C = = T = = = T T A A = = = = ? ? = = C = = = = A = T = G ? = = = 3 T A = = = = = = = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = D = = T = = = = = = = = = = = = = C ? ? ? G = = = = = = = = = = A = = = = G = ? A = D = = = = = ? = G T = = A = = = D = = ? ? ? = = T = = = = = = = = = I = = G = = = = = = = = = = = = = T ? ? ? C = = = = = = = = = = G = = = = C = ? G = I = = = = = ? = A C = = G = = = I = = ? ? ? = = A = 0 E109 = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = ? = = = = = C G T = = = A = = G = ? = I = = = = = T C = C = G G = = C I = = = = = = = A A = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = ? = = = = = T A A = = = T = = T = ? = D = = = = = C A = T = A A = = T D = = = = = = = T G 0 E110 = ? ? = = = ? = D = = = = = = = = = = = = = = = = ? = = = G = = = = = (A) = C G T A = = A = G G = = = = = = = = = T C G = = G = = = C = = = = = = = = = A = ? ? = = = ? = I = = = = = = = = = = = = = = = = ? = = = C = = = = = (G) = T A A G = = T = C T = = = = = = = = = C A A = = A = = = T = = = = = = = = = G 0 E111 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E112 = = = = = = = = D = = T = = = = = = = = = = = = = C = = = G = = = = = A = C = = A = A = T G G ? = = = = T A A T = C G = = = = = T C = C T A = = = T T = = = = = = = = = I = = G = = = = = = = = = = = = = T = = = C = = = = = G = T = = G = G = C C T ? = = = = C G G G = A A = = = = = C T = T G G = = = G A = 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 G A T C A A D = = T = T = T G = D T = = A C A G = C C = G = = ? = = = G = T = = ? = G = C = T C A = D = C G G G = A = T = = A = ? ? D T G G = = = G = = A G C G C G I = = C = G = C A = I C = = G T G A = T T = A = = ? = = = A = C = = ? = A = T = G T G = I = T A A T = C = C = = G = ? ? I C T A = = = T = = 0 E115 G A T = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G C = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = = = D C = = = = = = = = = C = = = = = = = = = G = A = A T A G = = = ? A = A = = = ? = = = = = = = ? ? = G = = = = T = C = = = = = A C = T = = = = = = = = = I T = = = = = = = = = T = = = = = = = = = C = G = G G G T = = = ? C = T = = = ? = = = = = = = ? ? = A = = = = C = T = = = = = G T = A = 0 E118 G ? ? ? ? A D = = T = T = ? ? ? D T = = A = A G = ? C = G = = = ? = = G = T = = = = G = C = T C A = D = C G G G = A = T = = A = C T D T G G = = = G = = A ? ? ? ? G I = = C = G = ? ? ? I C = = G = G A = ? T = A = = = ? = = A = C = = = = A = T = G T G = I = T A A T = C = C = = G = T C I C T A = = = T = = 0 E119 = = = = = = = = = = = = = = = = = = = = = = = ? ? C = = = G = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? T = = = C = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = ? ? ? ? ? = = = = = G = C = T ? A = D = C G G G = A = T = = A = C T D T G G = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = ? ? ? ? ? = = = = = A = T = G ? G = I = T A A T = C = C = = G = T C I C T A = = = T = = 0 E121 = = = = = = = = D = = T = = = = = = = = = = = = = = = = = G = = ? ? ? ? ? = = = ? = = = = G = = A = D = = = = = = = G T = = = = = = D = = = = ? = = T = = = = = = = = = I = = G = = = = = = = = = = = = = = = = = C = = ? ? ? ? ? = = = ? = = = = C = = G = I = = = = = = = A C = = = = = = I = = = = ? = = A = 0 E122 = A ? C = = = = = = = = ? = = I D T ? = A = A G = = = A = = = = = ? ? ? ? C G T = = = A = = G C = = = 3 = = G G T = = = = G = = C = = T G G = = = G A A = G ? G = = = = = = = = ? = = D I C ? = G = G A = = = G = = = = = ? ? ? ? T A A = = = T = = T T = = = 1 = = A T C = = = = A = = T = = C T A = = = T T G 0 E123 = A T C A A D = = T = T = T G = D T = = A = A G = C C = G = ? = ? ? ? G = T = = = = G = C = T C A = D = C G G ? ? A = T = = A = C T D T G G = = = G = = = G C G C G I = = C = G = C A = I C = = G = G A = T T = A = ? = ? ? ? A = C = = = = A = T = G T G = I = T A A ? ? C = C = = G = T C I C T A = = = 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 ? ? = = = = ? ? ? = ? = = = = = = ? = ? = = = = = = = = = = = = = = = = = = = = ? = = 0.99 = = ? ? 0.70 = 0.89 0.89 = = 0.89 = 0.89 = 0.89 = = = = = = = = = = = ? = = ? = = = = ? ? 0.77 = = = = = 1.00 = 1.00 = 1.00 = ? 1.00 = 1.00 = = = = = = = = 1.00 = = = 1.00 = 1.00 1.00 = = = = = 1.00 = 0.99 = = = ? = = = = = = 0.70 = = 0.86 = = = 0.86 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = ? 1.00 = 1.00 = = = = = = = = 1.00 = = = 1.00 = 1.00 ? ? = = = ? 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = ? = = = = = = = ? ? ? ? = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = = = 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 = = = = = 0.99 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 = = 0.99 = = = = = = = = = = = = = = = = = = 0.84 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = = = = = = = = = = = = = = = = = = = = = 0.54 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = 1.00 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 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = 0.86 0.86 0.86 0.86 = = = = = = = = 1.00 = = = ? = = = = = = = = = = = = = = = = = = 0.96 = 1.00 = = = = = 1.00 = = 1.00 = 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 1.00 = = = = ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = = 1.00 ? 0.96 = = = = = = = = = = = = ? ? = = 0.96 = = = = = = = = = = 0.96 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = = = 0.76 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? = = = 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 = = = = = = = = = 1.00 0.83 = = 0.88 = = = = = = = = = = = = = = = = = = = = 1.00 = = = ? = 1.00 = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = = = 1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 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 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 ? ? 1.00 1.00 = = = = = = = = = = = = = = = 0.51 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.84 = = = 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = ? = = = = = = = = = = = = = = = = = = 0.70 = = = = = = = = = = = ? = = = = = = = = = = = 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 = 1.00 = = 0.91 = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = 0.95 = ? 0.95 = = = 0.96 = = 0.96 = = = = 0.96 0.96 0.96 0.96 = 0.96 = 0.96 0.96 0.96 = = 0.96 = = 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 = = = 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 = = = = = = = 1.00 = 1.00 1.00 1.00 = = = 1.00 = = 1.00 1.00 = = = 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 = = 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 = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = 0.98 0.98 0.98 0.98 = = = 0.95 = = 0.95 0.63 = = = 0.95 0.95 0.95 0.95 = 0.95 = 0.95 0.95 = = = 0.95 = = 0.95 0.95 = 0.94 0.94 0.94 0.94 = ? ? = 0.94 = 0.94 = 0.94 = = = = = 0.94 = = = = = = = = = ? = 0.94 = = = = = = = 0.94 0.94 = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = 1.00 = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 = ? 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = = = 0.50 = = = = 1.00 1.00 = = = = = = = = = 1.00 = = = = = = = = = 1.00 = ? = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 = = = = 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = ? ? 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = ? ? = = 1.00 = = = = 1.00 = 1.00 = 1.00 ? = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = 1.00 ? ? ? 1.00 = = = = = = = = = = 1.00 = = = = 1.00 = ? 1.00 = 1.00 = = = = = ? = 1.00 1.00 = = 1.00 = = = 1.00 = = ? ? ? = = 1.00 = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = ? = = = = = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = ? = 1.00 = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = = 1.00 1.00 = ? ? = = = ? = 1.00 = = = = = = = = = = = = = = = = ? = = = 1.00 = = = = = 0.51 = 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 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = 0.99 = = = = = = = = = = = = = 0.99 = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.50 = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 = 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 = = 1.00 = 1.00 = ? ? ? 1.00 1.00 = = 1.00 = 1.00 1.00 = ? 1.00 = 1.00 = = = ? = = 1.00 = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 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 = 1.00 = 1.00 ? 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 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 = = = = ? = = 1.00 = = 1.00 ? 1.00 = = = = = = = = ? = = 1.00 1.00 1.00 ? = 1.00 = 1.00 1.00 = = = 1.00 = = = = = ? ? ? ? 1.00 1.00 1.00 = = = 1.00 = = 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = ? = ? ? ? 1.00 = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 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