************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 itgal.phase.inp itgal.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST itgal.phase.out_freqs : haplotype frequency estimates itgal.phase.out_pairs : most likely haplotype pairs for each individual itgal.phase.out_recom : estimates of recombination parameters itgal.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 32 Positions of loci: 2450 3393 7911 8840 9747 12469 12709 12714 13469 13530 17819 18043 18274 18667 19210 19616 22570 22571 24323 27048 27629 31781 32707 33550 34148 35099 39210 41734 42906 45330 45669 48918 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file itgal.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCGTACGCTCGGCCGTCATCCTCAGCGCDCAA 3.000000 2 GCGTACGCTCGGCCGTCATCCTCAGCGCDCGA 1.000000 3 GCGTATGCTCGACTGTTGGCCTCGGCGCDCGA 1.000000 4 GCGTATGTTCGAACGTCATCCCCAGCGCDCAA 1.000000 5 GCGTATGTTCGAACGTCATCCCCAGCGCDCAG 1.000000 6 GCGTATGTTCGACTGTCAGCTTCGGGGCICAA 1.000000 7 GCGTATGTTCGACTGTCATCCCCAGGACDCAG 1.000000 8 GCGTATGTTCGACTGTCATCCCCGGCGCDCGA 4.000000 9 GCGTATGTTCGACTGTCATCCCCGGGACDCAG 2.000000 10 GCGTATGTTCGACTGTCATCCCCGGGACDCGG 6.000000 11 GCGTATGTTCGACTGTCATCTTCGGGGCICAG 1.000000 12 GCGTATGTTCGACTGTCGTCCCCGGCACDCAG 1.000000 13 GCGTATGTTCGACTGTTGGCCTCGGGGCDCAA 1.000000 14 GCGTATGTTCGACTGTTGTCCCCGGCGCDCGA 1.000000 15 GCGTATGTTCGGCCGTTGGTCTCAGGGCICAA 1.000000 16 GCGTCCGCCCAGCCTTCGGCCTCAGGACDCAA 2.000000 17 GCGTCCGCTTGGCCGTCGGTCTCAGCGCDCGA 1.000000 18 GCGTCCGCTTGGCCGTTGGTCTCAGCGCDCAA 1.000000 19 GCACCTGTTCGAACGCTGGCCCCAGCGCDCAA 4.000000 20 GCACCTGTTCGAACGCTGGCCCCAGGGCICAG 2.000000 21 GCACCTGTTCGAACGCTGGCCCCGGCGCDCAA 1.000000 22 GCACCTGTTCGAACGCTGGCCCCGGGGCICAG 1.000000 23 GCACCTGTTCGAACGCTGGCCTTGGGGCICAA 1.000000 24 GCACCTGTTCGACCGCTGGCCCCAGCGCDCGA 1.000000 25 GCACCTGTTCGACCGCTGGCCCCAGGGTDCAA 1.000000 26 GCACCTGTTCGGCCGTTGGTCTCAGGGCDCAA 1.000000 27 GCATCCGCTTGGCCGTCGGTCTCAGGGCDCAA 1.000000 28 GCATCCGCTTGGCCGTTGGTCTCAGCGCDCAA 4.000000 29 GCATCCGCTTGGCCGTTGGTCTCAGGGCIAAA 1.000000 30 GCATCCGCTTGGCCGTTGGTCTCAGGGCIAAG 2.000000 31 GTGTACGCCCGGCCGTCGGCCTCAGCGCDCAG 2.000000 32 GTGTACGCCCGGCCGTTGGCCCCAGGGCICAA 2.000000 33 GTGTACGCCCGGCCGTTGGTCTTGGCGCDCAA 3.000000 34 GTGTACGCCCGGCCGTTGGTCTTGGCGCDCAG 1.000000 35 GTGTATGTTCGAACGTCATCCCCAGCGCDCAA 2.000000 36 GTGTATGTTCGAACGTCATCCCCAGCGCDCGA 1.000000 37 GTGTATGTTCGAACGTCATCCCCAGCGCDCGG 2.000000 38 GTGTATGTTCGAACGTCATCCCCAGGGCICAA 1.000000 39 GTGTATGTTCGAACGTCATCCCCAGGGCIAAA 1.000000 40 GTGTATGTTCGAACGTCATCCCCAAGGCIAAG 4.000000 41 GTGTATGTTCGAACGTCATCTTCAGGGCIAAA 1.000000 42 GTGTATGTTCGAACGTCATCTTCAGGACDAAA 1.000000 43 GTGTATGTTCGAACGTCATCTTCGGGGTDCAA 1.000000 44 CCGTACGCCCGGCCGTTGGCCTCGGGGCICAA 1.000000 45 CCGTACGCCCGGCCGTTGGCTTCGGCGCDCGA 1.000000 46 CCGTACGCCCGGCCGTTGGTCTCGGGGCICAG 4.000000 47 CCGTACGCCCGGCCGTTGGTCTTGGCGCDCAA 1.000000 48 CCGTACGCCCGGCCGTTGGTCTTGGCGCDCGA 8.000000 49 CCGTACGCCCGGCCGTTGGTCTTGGGGCDCGA 1.000000 50 CCGTACGCCCGGCCGTTGGTCTTGGGGTDCAA 1.000000 51 CCGTACGCCCGGCCGTTGGTCTTGGGACDCAA 2.000000 52 CCGTACGCCCGGCCGTTGGTCTTGGGACDCGG 1.000000 53 CCGTACGCTCAGCCTTCGGCCTCGGCGCDCGA 1.000000 54 CCGTACGCTCAGCCTTCGGCCTCGGGACDCAG 3.000000 55 CCGTACGCTCAGCCTTCGGCTTCAGGGTDCAA 4.000000 56 CCGTACGCTCAGCCTTCGGCTTCAAGGCICAA 2.000000 57 CCGTACGCTCAGCCTTCGGCTTCGGCGCDCGA 2.000000 58 CCGTACGCTCAGCCTTCGGCTTCGGGGCICAG 1.000000 59 CCGTACGCTCAGCCTTCGGCTTCGGGGTDCAA 13.000000 60 CCGTACGCTCAGCCTTCGGCTTCGGGGTDCAG 2.000000 61 CCGTACGCTCAGCCTTCGGCTTCGGGACDCAG 1.000000 62 CCGTACGCTCAGCCTTCGGCTTCGAGGCIAAG 1.000000 63 CCGTACGCTCAGCCTTCGGTCTCAAGGCICAA 1.000000 64 CCGTACGCTCAGCCTTCGGTCTTGGGGTDCAA 1.000000 65 CCGTACACTCGGCCGTCGGCCTCAAGGCICAA 1.000000 66 CCGTACACTCAGCCTTCGGCTCCAGGACDCAG 1.000000 67 CCGTACACTCAGCCTTCGGCTTCAAGGCICAA 2.000000 68 CCGTACACTCAGCCTTCGGCTTCGGGGCICAA 3.000000 69 CCGTACACTCAGCCTTCGGCTTCGGGGTDCAA 24.000000 70 CCGTACACTCAGCCTTCGGCTTCGGGGTICAA 1.000000 71 CCGTACACTCAGCCTTCGGCTTCGAGGCICAA 1.000000 72 CCGTATGTTCGAACGTCATCCCCAGGGCIAAA 5.000000 73 CCGTCCACTCGGCCGTCGGCCTCAAGGCDCAA 1.000000 74 CCGTCCACTCGGCCGTCGGCCTCAAGGCICAA 21.000000 75 CCGTCCACTCGGCCGTCGGCCTCAAGGTDCAA 1.000000 76 CCGTCCACTCGGCCGTCGGCCTCGGGGTDCAA 2.000000 77 CCGTCCACTCGGCCGTCGGCCTTGGCGCDCGA 2.000000 78 CCGTCCACTCGGCCGTCGGCTTCGGGGTDCAA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (8,31) D002: (30,72) D003: (18,23) D004: (1,42) D005: (33,54) D006: (1,30) D007: (11,40) D008: (2,67) D009: (37,69) D010: (5,13) D011: (39,72) D012: (3,72) D013: (34,62) D014: (6,33) D015: (28,32) DY01: (16,35) DY02: (27,51) DY03: (26,37) DY04: (33,38) DY05: (29,72) DY06: (10,15) DY07: (28,52) DY08: (16,28) DY09: (7,31) DY10: (32,41) DY11: (28,72) DY12: (1,35) E101: (10,22) E102: (48,59) E103: (48,60) E104: (59,66) E105: (21,48) E106: (4,24) E107: (46,46) E108: (20,54) E109: (10,47) E110: (46,58) E111: (8,19) E112: (55,69) E113: (8,43) E114: (19,40) E115: (14,40) E116: (19,59) E117: (59,60) E118: (8,55) E119: (19,68) E120: (54,55) E121: (25,36) E122: (51,53) H101: (48,68) H102: (74,74) H103: (56,74) H104: (74,74) H105: (48,68) H106: (10,56) H107: (46,57) H108: (9,59) H109: (69,74) H110: (44,74) H111: (61,69) H112: (12,69) H113: (48,74) H114: (17,74) H115: (20,74) H116: (69,77) H117: (74,74) H118: (10,55) H119: (9,48) H120: (74,77) H121: (48,59) H122: (10,40) X101: (74,76) X102: (69,69) X103: (59,69) X104: (69,78) X105: (59,69) X106: (59,74) X107: (69,74) X108: (65,70) X109: (69,69) X110: (64,69) X111: (49,76) X112: (67,71) X113: (45,69) X114: (69,74) X115: (59,59) X116: (63,69) X117: (69,69) X118: (73,74) X119: (50,74) X120: (59,69) X121: (59,74) X122: (69,75) X123: (57,69) X124: (69,74) 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 T A T G T T C G A C T G T C A T C C C C G G C G C D C G A G T G T A C G C C C G G C C G T C G G C C [T] C A G C G C D C A [G] 0 D002 G C A T C C G C T T G G C C G T T G G T C T C A G G G C I A A G C C G T A T G T T C G A A C G T C A T C C C C A G G G C I A A A 0 D003 G C (G) T C C G C T T G G C C G T T G G T C T (C) (A) G (C) G C (D) C A A G C (A) C C T G T T C G A A C G C T G G C C T (T) (G) G (G) G C (I) C A A 0 D004 G C G T A C G C T C G G C C G T C A T C C T C A G C G C D (C) A A G T G T A T G T T C G A A C G T C A T C T T C A G G A C D (A) A A 0 D005 G T G T A C G C C C G G C C G T T G G T C T T G G C G C D C A (A) C C G T A C G C T C A G C C T T C G G C C T C G G G A C D C A (G) 0 D006 G C G T A C G C T C G G C C G T C A T C C T C A G C G C D C A A G C A T C C G C T T G G C C G T T G G T C T C A G G G C I A A G 0 D007 G C G T A T G T T C G A C T G T C A T C T T C G G G G C I C A G G T G T A T G T T C G A A C G T C A T C C C C A A G G C I A A G 0 D008 G C G T A C G C T C G G C C G T C A T C C T C A G C G C D C G A C C G T A C A C T C A G C C T T C G G C T T C A A G G C I C A A 0 D009 G T G T A T G T T C G A A C G T C A T C C C C A G C G C D C G G C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 D010 G C G T A T G T T C G A A C G T C A T C C C C A G (C) G C D C A (G) G C G T A T G T T C G A C T G T T G G C C [T] C G G (G) G C D C A (A) 0 D011 G T G T A T G T T C G A A C G T C A T C C C C A G G G C I A A A C C G T A T G T T C G A A C G T C A T C C C C A G G G C I A A A 0 D012 G C G T A T G (C) T C G A C T G T T G G C C T C G G C G C D C G A C C G T A T G (T) T C G A A C G T C A T C C C C A G G G C I A A A 0 D013 G T G T A C G C C C G G C C G T T G G T C T T G (G) (C) G C (D) (C) A G C C G T A C G C T C A G C C T T C G G C T T C G (A) (G) G C (I) (A) A G 0 D014 G C G T A T G T T C G A C T G T C A G C T T C G G G G C I C A A G T G T A C G C C C G G C C G T T G G T C T T G G C G C D C A A 0 D015 G C [A] T C C G C T T G G C C G T T G G T C T C A G C G C D C A A G T G T A C G C C C G G C C G T T G G C C C C A G G G C I C A A 0 DY01 G C G T C C G C C C A G C C T T C G G C C T C A G G A C D C A A G T G T A T G T T C G A A C G T C A T C C C C A G C G C D C A A 0 DY02 G C A T C C G C T T G G C C G T C G G T C T C A G G G C D C A A C C G T A C G C C C G G C C G T T G G T C T [T] G G G A C D C A A 0 DY03 G C A [C] [C] T G T T C G G C C G T T G G T C T C A G G G C D C (A) (A) G T G T A T G T T C G A A C G T C A T C C C C A G C G C D C (G) (G) 0 DY04 G T G T A C G C C C G G C C G T T G G T C T T G G (C) G C (D) C A A G T G T A T G T T C G A A C G T C A T C C C C A G (G) G C (I) C A A 0 DY05 G C A T C C G C T T G G C C G T T G G T C T C A G G G C I A A A C C G T A T G T T C G A A C G T C A T C C C C A G G G C I A A A 0 DY06 G C G T A T G T T C G A C T G T C A T C C C C G G G A C D C G G G C G T A T G T T C G G C C G T T G G T C T C A G G G C I C A [A] 0 DY07 G C [A] T C C G C T T G G C C G T T G G T C T C A G C G C D C (A) (A) C C G T A C G C C C G G C C G T T G G T C T T G G G A C D C (G) (G) 0 DY08 G C G T C C G C C C A G C C T T C G G C C T C A G G A C D C A A G C A T C C G C T T G G C C G T T G G T C T C A G C G C D C A A 0 DY09 G C G T A T G T T C G A C T G T C A T C C C C A G G A C D C A G G T G T A C G C C C G G C C G T C G G C C [T] C A G C G C D C A G 0 DY10 G T G T A C G C C C G G C C G T T G G C C C C A G G G C I C A A G T G T A T G T T C G A A C G T C A T C T T C A G G G C I A A A 0 DY11 G C A T C C G C T T G G C C G T T G G T C T C A G C G C D C A A C C G T A T G T T C G A A C G T C A T C C C C A G G G C I A A A 0 DY12 G C G T A C G C T C G G C C G T C A T C C T C A G C G C D C A A G T G T A T G T T C G A A C G T C A T C C C C A G C G C D C A A 0 E101 G C G T A T G T T C G A C T G T C A T C C C C G G G A C D C G G G C A C C T G T T C G A A C G C T G G C C C C G G G G C I C A G 0 E102 C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C G A C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A 0 E103 C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C G (A) C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A (G) 0 E104 C C G T A C (G) C T C A G C C T T C G G C T T C (G) G G G T D C A A C C G T A C (A) C T C A G C C T T C G G C T C C (A) G G A C D C A G 0 E105 G C A C C T G T T C G A A C G C T G G C C C C G G C G C D C (A) A C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C (G) A 0 E106 G C G T A T G T T C G A A C G T C A T C C C C A G C G C D C (A) A G C A C C T G T T C G A C C G C T G G C C C C A G C G C D C (G) A 0 E107 C C G T A C G C C C G G C C G T T G G T C T C G G G G C I C A G C C G T A C G C C C G G C C G T T G G T C T C G G G G C I C A G 0 E108 G C A C C T G T T C G A A C G C T G G C C C C A G [G] G C I C A [G] C C G T A C G C T C A G C C T T C G G C C T C G G G A C D C A G 0 E109 G C G T A T G T T C G A C T G T C A T C C C C G G (G) (A) C D C (G) [G] C C G T A C G C C C G G C C G T T G G T C T T G G (C) (G) C D C (A) A 0 E110 C C G T A C G C C C G G C C G T T G G T C T C G G G G C I C A G C C G T A C G C T C A G C C T T C G G C T T C G G G G C I C A G 0 E111 G C G T A T G T T C G A C T G T [C] [A] T C C C C G G C G C D C G A G C A C C T G T T C G A A C G C T G G C C C C A G C G C D C A A 0 E112 C C G T A C G C T C A G C C T T C G G C T T C A G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 E113 G C G T A T G T T C G A C T G T C A T C C C C G G C G C D C G A G [T] G T A T G T T C G A A C G T C A T C [T] T C G G G G T D C A A 0 E114 G C A C C T G T T C G A A C G C T G G C C C C A G C G C D C A A G T G T A T G T T C G A A C G T C A T C C C C A A G G C I A A G 0 E115 G C G T A T G T T C G A C T G T T G T C C [C] C G G C G C D C G A G T G T A T G T T C G A A C G T C A T C C C C A A G G C I A A G 0 E116 G C A C C T G T T C G A A C G C T G G C C C C (A) G C G C D C A A C C G T A C G C T C A G C C T T C G G C T T C (G) G G G T D C A A 0 E117 C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A G 0 E118 G C G T A T G T T C G A C T G T [C] [A] T C C C C G G C G C D C G A C C G T A C G C T C A G C C T T C G G C T T C A G G G T D C A A 0 E119 G C A C C T G T T C G A A C G C T G G C C C C A G C G C D C A A C C G T A C [A] C T C A G C C T T C G G C T T C G G G G C I C A [A] 0 E120 C C G T A C G C T C A G C C T T C G G C C T C G G G A C D C A G C C G T A C G C T C A G C C T T C G G C T T C A G G G T D C A A 0 E121 G C A C C T G T T C G A C C G C T G G C C C C A G (G) G (T) D C A A G [T] G T A T G T T C G A A C G T C A T C C C C A G (C) G (C) D C G A 0 E122 C C G T A C G C C C G G C C G T T G G T C T [T] G G G A C D C A A C C G T A C G C T C A G C C T T C G G C C [T] C [G] G C G C D C G A 0 H101 C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C G A C C G T A C A C T C A G C C T T C G G C T T C G G G G C I C A A 0 H102 C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H103 C C G T A C G C T C A G C C T T C G G C T T C A A G G C I C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H104 C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A C C G T [C] C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H105 C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C G A C C G T A C [A] C T C A G C C T T C G G C T T C G G G G C I C A [A] 0 H106 G C G T A T G T T C G A C T G T C A T C C C C G G G A C D C G G C C G T A C G C T C A G C C T T C G G C T T C A A G G C I C A A 0 H107 C C G T A C G C C C G G C C G T T G G T C T C G G G G C I C A G C C G T A C G C T C A G C C T T C G G C T T C G G C G C D C G A 0 H108 G C G T A T G T T C G A C T G T C A T C C C C G G G (A) (C) D C A (G) C C G T A C G C T C A G C C T T C G G C [T] T C G G G (G) (T) D C A (A) 0 H109 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H110 C C G T A C G C C C G G C C G T T G G C C [T] C (G) (G) G G C I C A A C C G T C C A C T C G G C C G T C G G C C T C (A) (A) G G C I C A A 0 H111 C C G T A C (G) C T C A G C C T T C G G C T [T] C G G G A C D C A G C C G T A C (A) C T C A G C C T T C G G C T T C G G G G T D C A A 0 H112 G C G T A T G T T C G A C T G T C G [T] C C C C G G C A C D C A G C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 H113 C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C G A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H114 G C G T C C G C T T G G C C G T C G G T C T C A G C G C D C G A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H115 G C A C C T G T T C G A A C G C T G G C C C C A G [G] G C I C A G C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H116 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T T G G C G C D C G A 0 H117 C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 H118 G C G T A T G T T C G A C T G T C A T C C C C G G G A C D C G G C C G T A C G C T C A G C C T T C G G C T T C A G G G T D C A A 0 H119 G C G T A T G T T C G A C T G T C A T C C C C G G G A C D C (A) G C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C (G) A 0 H120 C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A C C G T C C A C T C G G C C G T C G G C C T T G G C G C D C G A 0 H121 C C G T A C G C C C G G C C G T T G G T C T T G G C G C D C G A C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A 0 H122 G C G T A T G T T C G A C T G T C A T C C C C G G G A C D C G G G T G T A T G T T C G A A C G T C A T C C C C A A G G C I A A G 0 X101 C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A C C G T C C A C T C G G C C G T C G G C C T C G G G G T D C A A 0 X102 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 X103 C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 X104 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C T T C G G G G T D C A A 0 X105 C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 X106 C C G T A C G C T C A G C C T T C G G C T T C [G] G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 X107 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 X108 C C G T A C A C T C G G C C G T C G G C C T C A A G G C I C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T I C A A 0 X109 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 X110 C C G T A C (G) C T C A G C C T T C G G T C T T G G G G T D C A A C C G T A C (A) C T C A G C C T T C G G C T T C G G G G T D C A A 0 X111 C C G T A C G C C C G G C C G T T G G T C T T G G G G (C) D C (G) A C C G T C C A C T C G G C C G T C G G C [C] T C G G G G (T) D C (A) A 0 X112 C C G T A C A C T C A G C C T T C G G C T T C A A G G C I C A A C C G T A C A C T C A G C C T T C G G C T T C G A G G C I C A A 0 X113 C C G T A C G C C C G G C C G T T G G C T T C G G (C) G (C) D C (G) A C C G T A C A C T C A G C C T T C G G C T T C G G (G) G (T) D C (A) A 0 X114 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 X115 C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A 0 X116 C C G T A C (G) C T C A G C C T T C G G (T) (C) T C A A G G C I C A A C C G T A C (A) C T C A G C C T T C G G (C) (T) T C G G G G T D C A A 0 X117 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 X118 C C G T C C A C T C G G C C G T C G G C C T C A A G G C D C [A] A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 X119 C C G T A C G C C C G G C C G T T G G T C T T G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 X120 C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A 0 X121 C C G T A C G C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A A 0 X122 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G T D C A A 0 X123 C C G T A C (G) C T C A G C C T T C G G C T T C G G C G C D C G A C C G T A C (A) C T C A G C C T T C G G C T T C G G G G T D C A A 0 X124 C C G T A C A C T C A G C C T T C G G C T T C G G G G T D C A A C C G T C C A C T C G G C C G T C G G C C T C A A G G C I C A 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 = ? = ? = T = T T = = A ? T = = = A T = = ? ? ? = = = = = = G ? = ? = ? = C = C C = = G ? C = = = G G = = ? ? ? = = = = = = A ? 0 D002 G = A ? C C = C = T = G ? = ? = T G G T = T = = = = = = = = = G C = G ? A T = T = C = A ? = ? = C A T C = C = = = = = = = = = A 0 D003 = = (G) T = C = C = T = G C = = T = = = T = = (C) (A) = (C) = = (D) = = = = = (A) C = T = T = C = A A = = C = = = C = = (T) (G) = (G) = = (I) = = = 0 D004 = C = = = C = C = = = G C = = ? = = = = C ? = = = C G = = (C) = = = T = = = T = T = = = A A = = ? = = = = T ? = = = G A = = (A) = = 0 D005 G T = ? = = = = C = G = = = G = ? ? = T = ? T = = C G = = = = (A) C C = ? = = = = T = A = = = T = ? ? = C = ? C = = G A = = = = (G) 0 D006 = = G = A = = = = C = ? = = = ? C A T C = ? = = = C = = D C = A = = A = C = = = = T = ? = = = ? T G G T = ? = = = G = = I A = G 0 D007 = ? = = = = = = = = = = C T ? = = = = = T ? = G G = = = = C = = = ? = = = = = = = = = = A C ? = = = = = C ? = A A = = = = A = = 0 D008 G = = = = = G = = = G ? = ? ? ? ? ? T = C ? = = G C = = D = G ? C = = = = = A = = = A ? = ? ? ? ? ? G = T ? = = A G = = I = A ? 0 D009 ? T = = = T G T = = G ? ? = G = = ? T = C C = A = C = C = = G G ? C = = = C A C = = A ? ? = T = = ? G = T T = G = G = T = = A A 0 D010 = = ? ? ? = = = = = = = A C = = C A T = = ? = A = (C) = = = = = (G) = = ? ? ? = = = = = = = C T = = T G G = = ? = G = (G) = = = = = (A) 0 D011 G T = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D012 G = = = = = = (C) = = = = C T = = T G G = = T = G = C = = D C G = C = = = = = = (T) = = = = A C = = C A T = = C = A = G = = I A A = 0 D013 G ? ? ? ? = = = C = ? = = = G = T = ? T ? = T = (G) (C) = = (D) (C) = = C ? ? ? ? = = = T = ? = = = T = C = ? C ? = C = (A) (G) = = (I) (A) = = 0 D014 = ? = ? = ? ? ? T = = A = T = = C A = C T = C = = G = ? I = = = = ? = ? = ? ? ? C = = G = C = = T G = T C = T = = C = ? D = = = 0 D015 = C ? = C = = = T T = = = = = = = = = T = T = = = C = = ? = = = = T ? = A = = = C C = = = = = = = = = C = C = = = G = = ? = = = 0 DY01 = C = = C C = C C = A G C = T = = G G = = T = = = G A = = = = = = T = = A T = T T = G A A = G = = A T = = C = = = C G = = = = = 0 DY02 G = A ? ? = = = T T = = = = = = C = = = = ? ? ? = = G = = = = = C = G ? ? = = = C C = = = = = = T = = = = ? ? ? = = A = = = = = 0 DY03 = C A ? ? = = = = = = G C = = = T G G T = T = = = G = = = = (A) (A) = T G ? ? = = = = = = A A = = = C A T C = C = = = C = = = = (G) (G) 0 DY04 = = = ? ? C = C C ? = G C = = = T G G T = T T G = (C) = = (D) = = = = = = ? ? T = T T ? = A A = = = C A T C = C C A = (G) = = (I) = = = 0 DY05 G = A = C C = C = T = G C = = = T G G T = T = = ? ? = = = = = = C = G = A T = T = C = A A = = = C A T C = C = = ? ? = = = = = = 0 DY06 = = = ? ? = = = = = = A = T = = C A T C = C = G = = A = D = G ? = = = ? ? = = = = = = G = C = = T G G T = T = A = = G = I = A ? 0 DY07 G = ? ? ? = = = T T = = = = = = = = = = ? = C A = C G = = = (A) (A) C = ? ? ? = = = C C = = = = = = = = = = ? = T G = G A = = = (G) (G) 0 DY08 = = G = = ? ? ? C C A = = = T = C = = C = = = = = G A = = = = = = = A = = ? ? ? T T G = = = G = T = = T = = = = = C G = = = = = 0 DY09 = C = ? ? T = T T = = A = T = = ? ? ? = ? ? = = = G A = = = = = = T = ? ? C = C C = = G = C = = ? ? ? = ? ? = = = C G = = = = = 0 DY10 = = = = = C = C C = = G C = = = T G G = C C = = = ? = = = C = = = = = = = T = T T = = A A = = = C A T = T T = = = ? = = = A = = 0 DY11 G ? A = C C = C = T = G C = = = T G G T = T = = = C = = D C = = C ? G = A T = T = C = A A = = = C A T C = C = = = G = = I A = = 0 DY12 = C = = = C = C = = = G C = = = = = = = = T = = = = = = = = = = = T = = = T = T = = = A A = = = = = = = = C = = = = = = = = = = 0 E101 = = G T A = = = = = = = C T = T ? ? T = = = = = = = A = D = G = = = A C C = = = = = = = A C = C ? ? G = = = = = = = G = I = A = 0 E102 = = = = = = = = C = G = = = G = T = = T C = T = = C = C = = G = = = = = = = = = T = A = = = T = C = = C T = C = = G = T = = A = 0 E103 = ? = ? ? = = = C = G = = = G = T = = T C ? ? = = C = C = = G (A) = ? = ? ? = = = T = A = = = T = C = = C T ? ? = = G = T = = A (G) 0 E104 = = ? ? ? = (G) = = = = = = = = = = = = = = T = (G) = = G ? = = = A = = ? ? ? = (A) = = = = = = = = = = = = = = C = (A) = = A ? = = = G 0 E105 G = A C C T = T T = = A A = = C = = = C = ? C = = = = = = = (A) = C = G T A C = C C = = G C = = T = = = T = ? T = = = = = = = (G) = 0 E106 = = G T ? = = = = = = = A ? = T C A T = = ? = ? = = = = = = (A) ? = = A C ? = = = = = = = C ? = C T G G = = ? = ? = = = = = = (G) ? 0 E107 = ? = ? ? = = = ? ? ? = = = ? ? = = = = = = = = = = = = = = = = = ? = ? ? = = = ? ? ? = = = ? ? = = = = = = = = = = = = = = = = 0 E108 G = A ? C T = T = = ? A A = G C ? ? = = ? ? = A ? ? G = I = = ? C = G ? A C = C = = ? G C = T T ? ? = = ? ? = G ? ? A = D = = ? 0 E109 ? = = ? = T = T T = = A = T = = C A T C = ? C = = (G) (A) = = = (G) ? ? = = ? = C = C C = = G = C = = T G G T = ? T = = (C) (G) = = = (A) ? 0 E110 = = ? = = = = = C = G = = = G = ? ? = T C = = = = = = = = = = = = = ? = = = = = T = A = = = T = ? ? = C T = = = = = = = = = = = 0 E111 = = G T A = = = = = = = C T = T ? ? T = = ? = G = = = = = = G = = = A C C = = = = = = = A C = C ? ? G = = ? = A = = = = = = A = 0 E112 = = ? ? ? = G = = = = = = = = = ? ? = = = ? = A = = = = = = = = = = ? ? ? = A = = = = = = = = = ? ? = = = ? = G = = = = = = = = 0 E113 = ? = = = = = = = = = = C T = = = = = = ? C = = = C = C = = G = = ? = = = = = = = = = = A C = = = = = = ? T = = = G = T = = A = 0 E114 = ? ? C C = = = = = = = ? = = C T G G = = ? = = G C = = D C = A = ? ? T A = = = = = = = ? = = T C A T = = ? = = A G = = I A = G 0 E115 = C = ? ? = = = = = = = ? T = = T G = = = ? = G G C = = D C G ? = T = ? ? = = = = = = = ? C = = C A = = = ? = A A G = = I A A ? 0 E116 G = A ? ? T = T = = G A A = G C T = = = ? C = (A) = C = ? = = = = C = G ? ? C = C = = A G C = T T C = = = ? T = (G) = G = ? = = = = 0 E117 = = = = = = = = = = = ? ? = = = ? ? ? = = = = = = = = = = = = A = = = = = = = = = = = ? ? = = = ? ? ? = = = = = = = = = = = = G 0 E118 G = = = = T = T = = G A = T G = ? ? T = C ? = G = C = C = = G = C = = = = C = C = = A G = C T = ? ? G = T ? = A = G = T = = A = 0 E119 G = ? ? ? T ? ? ? = ? A A = G C ? ? = = C C ? ? = ? = = D = = ? C = ? ? ? C ? ? ? = ? G C = T T ? ? = = T T ? ? = ? = = I = = ? 0 E120 = = = = = = = = = = = = = = = = = = ? = C = = G = = A C = = = G = = = = = = = = = = = = = = = = = = ? = T = = A = = G T = = = A 0 E121 = ? ? C C = = = = = = = C = = C ? ? G = = = = = = (G) = (T) = = A = = ? ? T A = = = = = = = A = = T ? ? T = = = = = = (C) = (C) = = G = 0 E122 = = = ? = = = = C = G = = = G = T = = T = ? ? ? = G A = = = A = = = = ? = = = = T = A = = = T = C = = C = ? ? ? = C G = = = G = 0 H101 = = = ? = = G = C = G = = = G = T = = T C = T = = C = = D = G = = = = ? = = A = T = A = = = T = C = = C T = C = = G = = I = A = 0 H102 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H103 = = = = A = G = = = A = = = T ? = = = = T ? = = = = = = = = = ? = = = = C = A = = = G = = = G ? = = = = C ? = = = = = = = = = ? 0 H104 = = = ? ? = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0 H105 = = = ? = = ? ? C = G = = = G = T = = T C = T = = ? = = D = G ? = = = ? = = ? ? T = A = = = T = C = = C T = C = = ? = = I = A ? 0 H106 G = = = = T = T = = ? A = T G = ? ? T = C C = G G = A = D = G G C = = = = C = C = = ? G = C T = ? ? G = T T = A A = G = I = A A 0 H107 = = ? = = = = = ? ? ? = = ? G = T = = T C ? = = = G = = I = A G = = ? = = = = = ? ? ? = = ? T = C = = C T ? = = = C = = D = G A 0 H108 G = = = = T = T = = ? A = T G = = A T = ? C = = = = (A) (C) = = = (G) C = = = = C = C = = ? G = C T = = G G = ? T = = = = (G) (T) = = = (A) 0 H109 = = = = A = = = = = ? = = = T = = = = = T = = G G = = T D = = = = = = = C = = = = = ? = = = G = = = = = C = = A A = = C I = = = 0 H110 = = = = A = G = C = = = = = = = T = = = = ? = (G) (G) = = = = = = = = = = = C = A = T = = = = = = = C = = = = ? = (A) (A) = = = = = = = 0 H111 = = = = = = (G) = = = = = = = = = = = = = = ? = = = = A C = = = G = = = = = = (A) = = = = = = = = = = = = = = ? = = = = G T = = = A 0 H112 G = ? = = T G T = = ? A = T G = = = ? = ? C = = = C A C = = = G C = ? = = C A C = = ? G = C T = = = ? = ? T = = = G G T = = = A 0 H113 = ? = ? ? = G = C = = = = = = = T = = T = = T G G C = = D = G = = ? = ? ? = A = T = = = = = = = C = = C = = C A A G = = I = A = 0 H114 G = = = = = G = = T = = = = = = = = = T = ? = = G C = = D = G = C = = = = = A = = C = = = = = = = = = C = ? = = A G = = I = A = 0 H115 G = ? ? = T G T = = = A A = = C T = ? = = C = = G ? = = = = = G C = ? ? = C A C = = = G C = = T C = ? = = T = = A ? = = = = = A 0 H116 = = = = A = = = = = A = = = T = = = = = T ? C = = G = T = = A = = = = = C = = = = = G = = = G = = = = = C ? T = = C = C = = G = 0 H117 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 H118 G = = = = T = ? = = G A = T G = = A T = C C = G ? ? A C = = G G C = = = = C = ? = = A G = C T = = G G = T T = A ? ? G T = = A A 0 H119 G = = = = T = T T = = A = T = = C A T C = C C = = G A = = = (A) G C = = = = C = C C = = G = C = = T G G T = T T = = C G = = = (G) A 0 H120 = = = = = = = = = = = = = = = = = = = = = = C A A G = = I = A = = = = = = = = = = = = = = = = = = = = = = = T G G C = = D = G = 0 H121 = = = = = = = = C = G = = = G = T = = T C ? T = = C = C = = G = = = = = = = = = T = A = = = T = C = = C T ? C = = G = T = = A = 0 H122 = C = = = = = = = = = = C T = = = = = = = ? = G G = A = D C G = = T = = = = = = = = = = A C = = = = = = = ? = A A = G = I A A = 0 X101 = = = ? = = = = = = = = = = = = = = = = = ? = A A = = C I = = = = = = ? = = = = = = = = = = = = = = = = = ? = G G = = T D = = = 0 X102 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = 0 X103 = ? = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = 0 X104 = = = = A = = = = = A = = = T = = = = = = = = = = = = = = = = = = = = = C = = = = = G = = = G = = = = = = = = = = = = = = = = = 0 X105 = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = 0 X106 = = = = A = G = = = A = = = T = ? ? = = T = = ? G = = T D = = = = = = = C = A = = = G = = = G = ? ? = = C = = ? A = = C I = = = 0 X107 = ? = ? ? = = = = = A = = = T = = = = = T ? = G G = = T D = = = = ? = ? ? = = = = = G = = = G = = = = = C ? = A A = = C I = = = 0 X108 = = = = = = = = = = G = = = G = ? ? = = ? = = A A = = C = = = = = = = = = = = = = = A = = = T = ? ? = = ? = = G G = = T = = = = 0 X109 = = = = ? = = = = = = = = = = = ? ? = = = ? = = = = = = = = = ? = = = = ? = = = = = = = = = = = ? ? = = = ? = = = = = = = = = ? 0 X110 = ? = = = = (G) = = = = = = = = = = = = T C ? T = = = = = = = = = = ? = = = = (A) = = = = = = = = = = = = C T ? C = = = = = = = = = 0 X111 = = = = A = G = C = = = = = = = T = = T ? = T = = = = (C) = = (G) = = = = = C = A = T = = = = = = = C = = C ? = C = = = = (T) = = (A) = 0 X112 = ? = = = = = = = = = = = = = = ? ? = = = ? = A = = = = = = = = = ? = = = = = = = = = = = = = = ? ? = = = ? = G = = = = = = = = 0 X113 = = = = = = G = C = G = = = G = T = = = = ? = = = (C) = (C) = = (G) = = = = = = = A = T = A = = = T = C = = = = ? = = = (G) = (T) = = (A) = 0 X114 = = ? ? ? = = = = = A = = ? T ? ? ? = = T ? = ? G = = T D = = = = = ? ? ? = = = = = G = = ? G ? ? ? = = C ? = ? A = = C I = = = 0 X115 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 X116 = = = = = = (G) = = = = = = = = = ? ? = (T) (C) = = A A = = C I = = = = = = = = = (A) = = = = = = = = = ? ? = (C) (T) = = G G = = T D = = = 0 X117 = = = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = 0 X118 = = = = = = = = ? ? = = = ? = = ? ? ? = = = ? = = = = = D = ? = = = = = = = = = ? ? = = = ? = = ? ? ? = = = ? = = = = = I = ? = 0 X119 = = = = A = G = C = ? = ? = = = T = = T = ? T G G = = T D = = = = = = = C = A = T = ? = ? = = = C = = C = ? C A A = = C I = = = 0 X120 = = = = = = G = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = ? = = = = = = = = = = 0 X121 = = ? = A = G = = = A = = = T = = = = = T = = G G = = T D = = = = = ? = C = A = = = G = = = G = = = = = C = = A A = = C I = = = 0 X122 = = = = A = = = = = A = = = T = ? ? = = T ? = G G = = = = = = = = = = = C = = = = = G = = = G = ? ? = = C ? = A A = = = = = = = 0 X123 = = = = = = (G) = = = = = = = = = = = = = = = = = = C = C = = G = = = = = = = (A) = = = = = = = = = = = = = = = = = = G = T = = A = 0 X124 = = = = A = = = = = A = = = T = ? ? = = T ? = G G = = T D = = = = = = = C = = = = = G = = = G = ? ? = = C ? = A A = = C I = = = 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 = = = = = = = = = 0.95 = = 0.85 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 = = 0.68 0.68 = 0.64 = = 0.64 = = = = 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = = ? = = = = 1.00 ? = = = 1.00 1.00 = = 0.63 = = 0.99 0.99 = ? = = = = 1.00 = 1.00 = = = 1.00 = ? ? = 1.00 = ? 1.00 = = 1.00 1.00 = = = = 0.87 = = 1.00 = 1.00 = = = = 1.00 = ? = = = ? 1.00 1.00 1.00 1.00 = ? = = = 1.00 = = 1.00 1.00 = 0.94 = ? = = = = = = = = = = 0.95 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 = 1.00 = = 1.00 1.00 = = ? ? ? = = = = = = = 1.00 1.00 = = 1.00 1.00 1.00 = = ? = 1.00 = 0.89 = = = = = 0.53 1.00 1.00 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 0.52 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = 0.98 ? ? ? ? = = = 1.00 = ? = = = 1.00 = 1.00 = ? 1.00 ? = 1.00 = 0.88 0.88 = = 0.88 0.88 = = = ? = ? = ? ? ? 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 0.91 = ? 0.91 = = = = 1.00 ? = 1.00 = = = 1.00 1.00 = = = = = = = = = 1.00 = 1.00 = = = 0.96 = = ? = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = 1.00 ? ? = = = 1.00 1.00 = = = = = = 1.00 = = = = ? ? ? = = 1.00 = = = = = = 1.00 0.90 ? ? = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = = = 0.98 = = = = 0.81 0.71 = = = ? ? 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 = = 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 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 = = = 0.79 0.79 = = 1.00 = = ? ? ? 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = = 1.00 1.00 = = = = = = 1.00 = ? ? 1.00 = 1.00 1.00 = = 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 0.92 = = = ? = = = 0.92 = = 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 = = = 0.97 = = 0.97 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 = = 0.99 0.99 = 0.99 = = 0.96 = 0.96 = = 0.96 = = ? = ? ? = = = 1.00 = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 ? ? = = 1.00 = 1.00 = = 1.00 0.76 = = ? ? ? = 0.67 = = = = = = = = = = = = = = 1.00 = 0.56 = = 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 = = = = = = = 0.79 = = = 1.00 1.00 ? = = = = = = = 1.00 ? = 0.98 0.98 0.98 0.98 = = ? = ? = = = = = = 0.72 ? = ? = ? ? = = = ? ? ? = = = ? ? = = = = = = = = = = = = = = = = 1.00 = 1.00 ? 1.00 1.00 = 1.00 = = ? 1.00 1.00 = 1.00 1.00 ? ? = = ? ? = 1.00 ? ? 1.00 = 1.00 = = ? ? = = ? = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = ? 1.00 = = 0.71 0.71 = = = 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 = = = ? ? ? = 0.97 = = = = = = = = = ? ? = = = ? = 1.00 = = = = = = = = = ? = = = = = = = = = = 0.97 0.97 = = = = = = ? 0.99 = = = 0.95 = 0.95 = = 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 = = 0.98 0.98 = = = ? = 1.00 1.00 1.00 = = 1.00 1.00 1.00 ? 1.00 = 1.00 ? ? 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = ? 1.00 = 0.80 = 1.00 = ? = = = = = = = = = = = = = = = ? ? = = = ? ? ? = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 = ? ? 1.00 = 1.00 ? = 0.93 = 0.99 = 0.99 = = 0.99 = 1.00 = ? ? ? 1.00 ? ? ? = ? 1.00 1.00 = 1.00 1.00 ? ? = = 1.00 1.00 ? ? = ? = = 0.93 = = ? = = = = = = = = = = = = = = = = = = ? = 0.99 = = 0.94 = = 1.00 1.00 = = = 0.97 = ? ? 1.00 1.00 = = = = = = = 0.90 = = 1.00 ? ? 1.00 = = = = = = 0.90 = 0.90 = = 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 = 0.99 = = 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 = 0.99 = = ? = = 0.94 = 0.94 ? 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 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 = = = = 0.77 0.77 = = = 0.68 = = = = 1.00 = = = = = ? = = = 1.00 = = = = = 1.00 = = 0.99 0.99 = = 0.98 0.98 = = = = = = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = = = = ? = 0.90 0.90 = = = = = = = = = = = = = 0.51 = = = = = = = = = = = = = = ? = = = = 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 = = = = 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 = 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 = = 0.92 0.92 = = = 0.58 0.91 = = = = = = = = = = = = = = = = = = = = = = 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 = = 0.95 = 0.95 = = 0.95 = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = 0.98 = = = 0.99 = = = 0.99 = ? ? = = 0.99 = = ? 1.00 = = 1.00 1.00 = = = = ? = ? ? = = = = = 1.00 = = = 1.00 = = = = = 1.00 ? = 0.99 0.99 = = 0.98 0.98 = = = = = = = = = = = = = 0.99 = = = 0.99 = ? ? = = ? = = 0.98 0.98 = = 0.98 = = = = = = = = ? = = = = = = = = = = = ? ? = = = ? = = = = = = = = = ? = ? = = = = 0.64 = = = = = = = = = = = = 1.00 1.00 ? 1.00 = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = = 1.00 ? = 1.00 = = = = 0.84 = = 0.83 = = ? = = = = = = = = = = = = = = ? ? = = = ? = 1.00 = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = 1.00 = 1.00 = = = = ? = = = 0.71 = 0.71 = = 0.71 = = = ? ? ? = = = = = 0.99 = = ? 0.99 ? ? ? = = 0.99 ? = ? 0.99 = = 0.99 0.99 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0.68 = = = = = = = = = ? ? = 0.84 0.86 = = 1.00 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = = = = = = = = = ? ? = = = ? = = ? ? ? = = = ? = = = = = 1.00 = ? = = = = = 1.00 = 1.00 = 1.00 = ? = ? = = = 1.00 = = 1.00 = ? 1.00 1.00 1.00 = = 0.96 0.96 = = = = = = = = = 1.00 = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? = 1.00 = 0.99 = = = 1.00 = = = 1.00 = = = = = 1.00 = = 0.98 0.98 = = 0.98 0.98 = = = = = = = 1.00 = = = = = 1.00 = = = 1.00 = ? ? = = 1.00 ? = 0.99 0.99 = = = = = = = = = = = = = 0.73 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = 1.00 = = = = = 0.99 = = = = = 0.99 = = = 0.99 = ? ? = = 0.99 ? = 1.00 1.00 = = 0.99 0.99 = = = END PHASEPROBS