************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mmp1x.phase.inp mmp1x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mmp1x.phase.out_freqs : haplotype frequency estimates mmp1x.phase.out_pairs : most likely haplotype pairs for each individual mmp1x.phase.out_recom : estimates of recombination parameters mmp1x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 41 Positions of loci: 341 1013 1108 1192 1428 1525 1607 1627 1955 2135 2815 3774 3875 4182 4280 4521 4673 4794 5153 5168 5567 6246 7129 7334 7355 7361 8372 9025 9081 9173 9243 9562 9739 9758 9879 9964 10431 11200 11201 11654 12032 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mmp1x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 DTATATTCCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 2.000000 2 DTATATTCTGGGTAGGACAAGGAATDACCCTAACTCTTCTA 1.000000 3 DTATATCTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 4 DTATGATCCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 1.000000 5 DTATGATTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 2.000000 6 DTATGATTCAGGCCGGACAAGGAATDAGTTTAACTCCTCCG 3.000000 7 DTATGATTCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 1.000000 8 DTATGATTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 3.000000 9 DTATGATTCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 5.000000 10 DTATGACTCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 1.000000 11 DTATGTTCCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 1.000000 12 DTATGTTTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 13 DTATGTTTCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 2.000000 14 DTATGTTTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 5.000000 15 DTATGTTTCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 1.000000 16 DTATGTCTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 4.000000 17 DTAGAATTCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 1.000000 18 DTAGAACTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 3.000000 19 DTGTAATTCAGGCCGGACAAAAAATDACCCTAACCCCTCCG 2.000000 20 DTGTAACTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 21 DTGTATTCCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 2.000000 22 DTGTATTTCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 2.000000 23 DTGTGATCCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 1.000000 24 DTGTGATTCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 2.000000 25 DTGTGATTCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 1.000000 26 DTGGATTCCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 1.000000 27 DCGTAATCCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 1.000000 28 DCGTAATTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 29 DCGTAATTCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 30 DCGTAATTCGGGCCTGACAAGGAAAIACCCCAGCTCCTCCG 1.000000 31 DCGTAATTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 32 DCGTAATTCGGGCCTGACAAGGAATDACCCCAGCTCCTCCG 1.000000 33 DCGTATTCCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 34 DCGTATTCCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 10.000000 35 DCGTATTTTGGGCCGGACAAAACGTDACCCTAACCCCTCCG 1.000000 36 ITATGATCCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 1.000000 37 ITAGAATCCGGGCCGAATTAAGAATDACCCTAACTCCTCCG 1.000000 38 ITGTAATCCAGGCCGGACAAGGAATDAGTTTAACTCCTCCG 2.000000 39 ITGTAATCCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 2.000000 40 ITGTAATTCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 2.000000 41 ITGTAATTCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 3.000000 42 ITGTAATTCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 1.000000 43 ITGTAACTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 3.000000 44 ITGTATTCCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 45 ITGTATTCCAGGCCGGACAAGGAATDAGTTTAACTCCTCCG 3.000000 46 ITGTATTCCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 47 ITGTATTCCGGACCGGACAGGGAGTDACCTTAGCTCCTCCG 1.000000 48 ITGTATTTCAGGCCGGACAAGAAATDACCCTAACTCCTCCG 1.000000 49 ITGTATTTCAGGCCGGACAAGACGTDACCCTCACCCCTCCG 2.000000 50 ITGTATTTCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 1.000000 51 ITGTATTTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 52 ITGTGATCCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 53 ITGTGATTCAGGCCGGACAAAAAATDACCCTAACCCCTCCG 2.000000 54 ITGTGACTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 2.000000 55 ITGGAATCCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 6.000000 56 ITGGAATCCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 57 ITGGAATCCGGGTAGGACAAGGAATDACCCTAACTCTTCTA 1.000000 58 ITGGAATTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 2.000000 59 ITGGAATTCAGGCCGGACAAGGAATDAGTTTAACTCCTCCG 1.000000 60 ITGGAATTCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 2.000000 61 ITGGAATTCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 9.000000 62 ITGGAATTCGAGCCGGGCTAAGAATDGCCCTAACTCCGACG 1.000000 63 ITGGAATTTGGGTAGGACAAGGAATDACCCTAACTCTTCTA 1.000000 64 ITGGAACCCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 65 ITGGAACTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 3.000000 66 ITGGAACTCAGGCCGGACAAAACGTDACCCTAACCCCTCCG 1.000000 67 ITGGAACTCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 2.000000 68 ITGGAACTCGGGCCGGACAAAAAAAIACCCCAGCTTCTCCG 1.000000 69 ITGGAACTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 12.000000 70 ITGGATTCCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 2.000000 71 ITGGATTCCGGGCCGGACAAGACGTDACCCTCACCCCTCCG 3.000000 72 ITGGATTCCGGGCCGAATTAAGAATDACCCTAACTCCTCCG 1.000000 73 ITGGATTCCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 74 ITGGATTCTGGGTAGGACAAGGAATDACCCTAACTCTTCTA 7.000000 75 ITGGATTTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 76 ITGGATTTCAGGCCGAATTAAGAATDACCCTAACTCCTCCG 2.000000 77 ITGGATTTCGGACCGGACAGGGAGTDACCTTAATTCCTCCG 9.000000 78 ITGGATTTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 1.000000 79 ITGGATTTTGGGTAGGACAAGGAATDACCCTAACTCTTCTA 2.000000 80 ITGGATCTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 81 ITGGATCTCGGGCCTGACAAGGAAAIACCCCAGCTTCTCCG 3.000000 82 ITGGATCTTGGGTAGGACAAGGAATDACCCTAACTCTTCTA 2.000000 83 ITGGGATTCAGACCGGACAGGGAGTDACCTTAATTCCTCCG 1.000000 84 ICGTATTCCGGGCCGGACAAGACGADACCCTCACCCCTCCG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (14,55) P002: (34,41) P003: (9,30) P004: (40,42) P005: (3,69) P006: (14,74) P007: (74,76) P008: (13,33) P009: (14,81) P010: (18,20) P011: (24,35) P012: (8,55) P013: (13,49) P014: (16,58) P015: (1,57) P016: (61,65) P017: (36,61) P018: (25,39) P019: (77,80) P020: (9,60) P021: (43,68) P022: (77,77) P023: (70,77) P024: (54,69) P025: (54,67) P026: (34,69) P027: (46,70) P028: (2,74) P029: (23,48) P030: (5,77) P031: (81,82) P032: (34,69) P033: (74,79) P034: (61,11) P035: (50,65) P036: (10,38) P037: (4,83) P038: (34,41) P039: (9,76) P040: (6,74) P041: (52,74) P042: (32,58) P043: (14,73) P044: (1,14) P045: (44,61) P046: (22,28) P047: (64,37) P048: (6,43) P049: (45,59) P050: (31,55) P051: (18,75) P052: (6,72) P053: (39,40) P054: (17,79) P055: (63,69) P056: (19,21) P057: (34,53) P058: (15,16) P059: (41,51) P060: (9,66) P061: (34,34) P062: (43,45) P063: (61,77) P064: (29,53) P065: (21,69) P066: (69,69) P067: (56,84) P068: (49,61) P069: (61,69) P070: (55,65) P071: (27,38) P072: (22,69) P073: (8,71) P074: (45,71) P075: (55,77) P076: (61,71) P077: (16,77) P078: (8,9) P079: (78,26) P080: (24,34) P081: (74,81) P082: (5,69) P083: (61,16) P084: (18,67) P085: (60,82) P086: (12,55) P087: (7,34) P088: (19,62) P089: (34,47) P090: (69,77) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 D T A T G (T) T T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G [G] A (A) T C C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P002 D (C) G T A (T) T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G [I] (T) G T A (A) T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P003 D (T) (A) T (G) A T T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G D (C) (G) T (A) A T T C G G G C C T G A C A A G G A A A I A C C C C A G C T C C T C C G 0 P004 I T G T A A T T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G I T G T A A T T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G 0 P005 D T A T A (T) C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A (A) C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P006 D T A T G T T T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A T T C T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P007 I T G G A T T (C) T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A I T G G A T T (T) C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P008 D (T) (A) T (G) T T (T) C (A) G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G D (C) (G) T (A) T T (C) C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P009 D T A T G T (T) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A T (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P010 D T A G A A C T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G D T G T A A C T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P011 D (T) G T (G) (A) T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G D (C) G T (A) (T) T T T G G G C C G G A C A A A A C G T D A C C C T A A C C C C T C C G 0 P012 (D) T (A) (T) (G) A T (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G (I) T (G) (G) (A) A T (C) C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P013 (D) T (A) T (G) T T T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G (I) T (G) T (A) T T T C A G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P014 (D) T (A) (T) (G) (T) (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G (I) T (G) (G) (A) (A) (T) T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P015 (D) T (A) (T) A (T) T C C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G (I) T (G) (G) A (A) T C C (G) G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P016 I T G G A A (T) T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A A (C) T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P017 I T (A) (T) (G) A T (C) C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G I T (G) (G) (A) A T (T) C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P018 (D) T G T (G) A T (T) C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T G T (A) A T (C) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P019 I T G G A T (T) T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A T (C) T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P020 (D) T (A) (T) (G) A T T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T (G) (G) (A) A T T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P021 I T G (T) A A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G (G) A A C T C G G G C C G G A C A A A A A A A I A C C C C A G C T T C T C C G 0 P022 I T G G A T T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A T T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P023 I T G G A T T (C) C (A) G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G I T G G A T T (T) C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P024 [I] T G T G A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P025 I T G (T) (G) A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G (G) (A) A C T C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P026 D C G T A (T) T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G I T G G A (A) C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P027 I T G (T) A T T C C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G (G) A T T C C (A) G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P028 D T A T A T T C T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A I T G G A T T C T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P029 (D) T G T (G) (A) T (C) C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T G T (A) (T) T (T) C A G G C C G G A C A A G A A A T D A C C C T A A C T C C T C C G 0 P030 D T A T G (A) T T C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A (T) T T C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P031 I T G G A T C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A T C T T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P032 D C G T A (T) T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G I T G G A (A) C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P033 I T G G A T T C T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A I T G G A T T T T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P034 (I) T (G) (G) (A) (A) T (T) C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G (D) T (A) (T) (G) (T) T (C) C (A) G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P035 I T G (T) A (T) (T) T C (G) G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G I T G (G) A (A) (C) T C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P036 (D) T (A) T (G) A (C) (T) C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T (G) T (A) A (T) (C) C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G 0 P037 (D) T (A) (T) G A T (C) C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G (I) T (G) (G) G A T (T) C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P038 (D) (C) G T A (T) T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G (I) (T) G T A (A) T T C [G] G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P039 (D) T (A) (T) (G) (A) T T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T (G) (G) (A) (T) T T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P040 D T A T G A T (T) C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G I T G G A T T (C) T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P041 I T G (T) (G) A T C C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G (G) (A) T T C T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P042 (D) (C) G (T) A A T T C (G) G G C C T G A C A A G G A A T D A C C C C A G C T C C T C C G (I) (T) G (G) A A T T C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P043 D T A T G T T T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A T T C C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P044 D T A T (A) T T (C) C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G D T A T (G) T T (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P045 I T G (T) A (T) T C C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G (G) A (A) T T C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P046 D (T) G T A (T) T T C (G) G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G D (C) G T A (A) T T C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P047 I T (G) G A A (C) C C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T (A) G A A (T) C C G G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P048 D T (A) T (G) A (T) T C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G [I] T (G) T (A) A (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P049 I T G (T) A (T) T C C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G I T G (G) A (A) T T C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G 0 P050 (D) (C) G (T) A A T (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G (I) (T) G (G) A A T (C) C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P051 D T A G A A C T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A T T T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P052 (D) T (A) (T) (G) (A) T (T) C (A) G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G (I) T (G) (G) (A) (T) T (C) C (G) G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P053 [I] T G T A A T (C) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G T A A T (T) C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G 0 P054 (D) T (A) G A (A) T T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G (I) T (G) G A (T) T T T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P055 I T G G A A (T) T [T] G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A I T G G A A (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P056 [D] T G T A (A) T (T) C A G G C C G G A C A A A A A A T D A C C C T A A C C C C T C C G [D] T G T A (T) T (C) C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G 0 P057 (D) (C) G T (A) T T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G (I) (T) G T (G) A T T C A G G C C G G A C A A A A A A T D A C C C T A A C C C C T C C G 0 P058 D T A T G T (T) T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G D T A T G T (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P059 I T G T A (A) T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G T A (T) T T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P060 (D) T (A) (T) (G) A (T) T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T (G) (G) (A) A (C) T C A G G C C G G A C A A A A C G T D A C C C T A A C C C C T C C G 0 P061 D C G T A T T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G D C G T A T T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P062 I T G T A (A) C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G T A (T) T C C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G 0 P063 I T G G A A T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A T T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P064 D (C) G T (A) A T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G [I] (T) G T (G) A T T C A G G C C G G A C A A A A A A T D A C C C T A A C C C C T C C G 0 P065 (D) T G (T) A (T) (T) (C) C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G (I) T G (G) A (A) (C) (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P066 I T G G A A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P067 I (T) G (G) A (A) T C C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I (C) G (T) A (T) T C C G G G C C G G A C A A G A C G A D A C C C T C A C C C C T C C G 0 P068 I T G (T) A (T) T T C (A) G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G I T G (G) A (A) T T C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P069 I T G G A A T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A A C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P070 I T G G A A T C C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A A C T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P071 (D) (C) G T A A T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G (I) (T) G T A A T C C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G 0 P072 (D) T G (T) A (T) (T) T C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G (I) T G (G) A (A) (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P073 (D) T (A) (T) (G) (A) T (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G (I) T (G) (G) (A) (T) T (C) C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P074 I T G (T) A T T C C A G G C C G G A C A A G G A A T D A G T T T A A C T C C T C C G I T G (G) A T T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P075 I T G [G] A A T [C] C (A) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A [T] T T C (G) G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P076 I T G G A (A) T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A (T) T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P077 (D) T (A) (T) (G) T (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G (I) T (G) (G) (A) T (T) T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P078 D T A T G A T T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G D T A T G A T T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G 0 P079 (I) T G G A T T (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G (D) T G G A T T (C) C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P080 D T G T G A T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G D C G T A T T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P081 I T G G A T (T) (C) T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A I T G G A T (C) (T) C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P082 (D) T (A) (T) (G) A (T) T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G (I) T (G) (G) (A) A (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P083 (I) T (G) (G) (A) (A) (T) T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G (D) T (A) (T) (G) (T) (C) T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G 0 P084 (D) T (A) G A A C T C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G (I) T (G) G A A C T C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P085 I T G G A (A) (T) T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G I T G G A (T) (C) T T G G G T A G G A C A A G G A A T D A C C C T A A C T C T T C T A 0 P086 D T A T G (T) T (T) C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G I T G G A (A) T (C) C A G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C G 0 P087 D T A T G (A) T T C A G G C C G A A T T A A G A A T D A C C C T A A C T C C T C C G D C G T A (T) T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G 0 P088 (D) T G (T) A A T T C A G G C C G G A C A A A A A A T D A C C C T A A C C C C T C C G (I) T G (G) A A T T C G A G C C G G G C T A A G A A T D G C C C T A A C T C C G A C G 0 P089 D (C) G T A T T C C G G G C C G G A C A A G A C G T D A C C C T C A C C C C T C C G [I] (T) G T A T T C C G G A C C G G A C A G G G A G T D A C C T T A G C T C C T C C G 0 P090 I T G G A (A) C T C G G G C C T G A C A A G G A A A I A C C C C A G C T T C T C C G I T G G A (T) T T C G G A C C G G A C A G G G A G T D A C C T T A A T T C C T C C 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 P001 ? = A ? G (T) = T = G = G ? = T = = = = A = = = A A I = = = C C = G C = T = = = = = ? = G ? A (A) = C = A = A ? = G = = = = G = = = G T D = = = T T = A T = C = = = = = 0 P002 ? (C) = = = (T) = C = = = G = = = = = = = A = A C = = = = = = C = ? ? C C = = = = = = ? (T) = = = (A) = T = = = A = = = = = = = G = G A = = = = = = T = ? ? T T = = = = = = 0 P003 = (T) (A) = (G) = = = = = A = = = G = G = T = ? = = = T D G = = = T = A = = = = G A = = = (C) (G) = (A) = = = = = G = = = T = A = A = ? = = = A I A = = = C = G = = = = T C = = 0 P004 = = = = = = = = = A G = = = = A A T = = = = = = = = A = = = = ? ? = = = = T C = = = = = = = = = = = G A = = = = G G C = = = = = = = = G = = = = ? ? = = = = G A = = 0 P005 D = A T = (T) = = = = = = ? = = = = = = = ? = = = = = ? = = = = = = = = = = = = = = I = G G = (A) = = = = = = ? = = = = = = = ? = = = = = ? = = = = = = = = = = = = = = 0 P006 D = A T G = = T C = = = C C T = = = = = = = = = A ? = = = = C = G ? = T C ? ? C G I = G G A = = C T = = = T A G = = = = = = = = = T ? = = = = T = A ? = C T ? ? T A 0 P007 = = = = = = = (C) T G = = T A = G = C A = G = = = = = = = = = = = = = = = T ? ? T A = = = = = = = (T) C A = = C C = A = T T = A = = = = = = = = = = = = = = = C ? ? C G 0 P008 ? (T) (A) = (G) = = (T) = (A) = G = = = A = T T A A = = A = = = = = C = = = C = = = = = = = ? (C) (G) = (A) = = (C) = (G) = A = = = G = C A G G = = G = = = = = T = = = T = = = = = = = 0 P009 D = A T G = (T) = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = G G A = (C) = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P010 = = A G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P011 = (T) = = (G) (A) = = C = = A = = = = = = = G G G A = = = = = = T = = = T T = = = = = = = (C) = = (A) (T) = = T = = G = = = = = = = A A A C = = = = = = C = = = C C = = = = = = 0 P012 (D) = (A) (T) (G) = = (T) = G = G = = T = = = = A = = = A A I ? = = C C = G C = T = = = = = (I) = (G) (G) (A) = = (C) = A = A = = G = = = = G = = = G T D ? = = T T = A T = C = = = = = 0 P013 (D) = (A) = (G) = = = = = = = ? = = A = T T = A G A A = = = = = = = A = = T = = = = = = (I) = (G) = (A) = = = = = = = ? = = G = C A = G A C G = = = = = = = C = = C = = = = = = 0 P014 (D) = (A) (T) (G) (T) (C) = = G = G = = T = = = = A = = = A A I = = = C C = G C = T = = = = = (I) = (G) (G) (A) (A) (T) = = A = A = = G = = = = G = = = G T D = = = T T = A T = C = = = = = 0 P015 (D) = (A) (T) = (T) = = = (A) = A C C = = = = = G = = = G = = = = = T = = = T = = C ? ? C G (I) = (G) (G) = (A) = = = (G) = G T A = = = = = A = = = A = = = = = C = = = C = = T ? ? T A 0 P016 ? = = = = = (T) = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = (C) = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P017 = = (A) (T) (G) = = (C) = = = G = = = = = = = A = A C = = = = = = C = C = C C = = = = = = = = (G) (G) (A) = = (T) = = = A = = = = = = = G = G A = = = = = = T = A = T T = = = = = = 0 P018 (D) = = = (G) = = (T) = = A = = = G = G = T = A = = = T D G = = = T = A = = C = G A = = (I) = = = (A) = = (C) = = G = = = T = A = A = G = = = A I A = = = C = G = = T = T C = = 0 P019 = = = = = = (T) = = G = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = A = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P020 (D) = (A) (T) (G) = = = = G A = = = = ? G ? = = = = = = = = G = = = = = = = = = = G A = = (I) = (G) (G) (A) = = = = A G = = = = ? A ? = = = = = = = = A = = = = = = = = = = T C = = 0 P021 = = = (T) = = = = = = = = ? ? T = = = = = G G = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = ? ? G = = = = = A A = = = = = = = = = = = = = = = = = = = 0 P022 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = 0 P023 = = = = = = = (C) = (A) = G = = = A = T T A A = = A = = = = = C = = = C = = = = = = = = = = = = = = (T) = (G) = A = = = G = C A G G = = G = = = = = T = = = T = = = = = = = 0 P024 ? = = T G = = = = = = = ? = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = ? = = G A = = = = = = = ? = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = 0 P025 = = = (T) (G) = = = = = = = = = T = = = = = = G A A A I = = = = C A G = T T = = = = = = = = (G) (A) = = = = = = = = = G = = = = = = A C G T D = = = = T C A = C C = = = = = 0 P026 D C = T = (T) T C = = = = = = G = = = = = = A C G T D = = = = T C A = C C = = = = = I T = G = (A) C T = = = = = = T = = = = = = G A A A I = = = = C A G = T T = = = = = 0 P027 = = = (T) = = = = = (G) = A = = = G = C A G G = = G = = = = = T = = = T = = = = = = = = = = (G) = = = = = (A) = G = = = A = T T A A = = A = = = = = C = = = C = = = = = = = 0 P028 D = A T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = G G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P029 (D) = = = (G) (A) = (C) = G A = = = = = G = T = A G = = = = ? = = = = = = = = = = G A = = (I) = = = (A) (T) = (T) = A G = = = = = A = A = G A = = = = ? = = = = = = = = = = T C = = 0 P030 D = A T G (A) = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = G G A (T) = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P031 = = = = = = = = C = = = C C T = = = = = = = = = A I = = = = C = G = = T C ? ? C G = = = = = = = = T = = = T A G = = = = = = = = = T D = = = = T = A = = C T ? ? T A 0 P032 ? C = T = (T) T C = = = = = = G = = = ? ? ? A C G T D = = = = T C A = C C = = = = = ? T = G = (A) C T = = = = = = T = = = ? ? ? G A A A I = = = = C A G = T T = = = = = 0 P033 = = = = = = = C = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P034 (I) = (G) (G) (A) (A) = (T) = (G) = ? ? = = G = C A G G = = G = = = = = T = = = T = = = = = = = (D) = (A) (T) (G) (T) = (C) = (A) = ? ? = = A = T T A A = = A = = = = = C = = = C = = = = = = = 0 P035 = = = (T) = (T) (T) = = (G) = ? = = = = = = = A = A C = = = = = = C = C = C C = = = = = = = = = (G) = (A) (C) = = (A) = ? = = = = = = = G = G A = = = = = = T = A = T T = = = = = = 0 P036 (D) = (A) = (G) = (C) (T) = G A = ? = = = G = T = A = = = = = ? C C C = = = = = = = G A = = (I) = (G) = (A) = (T) (C) = A G = ? = = = A = A = G = = = = = ? G T T = = = = = = = T C = = 0 P037 (D) = (A) (T) = = = (C) = G = G ? = = = = = = A = A C = = = = = = C = C = C C = = ? ? = = (I) = (G) (G) = = = (T) = A = A ? = = = = = = G = G A = = = = = = T = A = T T = = ? ? = = 0 P038 (D) (C) = = = (T) = C = ? = G ? = = ? ? ? = A = A C = = = = = = C = C = C C = = ? ? = = (I) (T) = = = (A) = T = ? = A ? = = ? ? ? = G = G A = = = = = = T = A = T T = = ? ? = = 0 P039 (D) = (A) (T) (G) (A) = = = G A = = = = G G C = = = = = = = = G = = = = = = = = = = G A = = (I) = (G) (G) (A) (T) = = = A G = = = = A A T = = = = = = = = A = = = = = = = = = = T C = = 0 P040 ? = A T G A = (T) C A = = C C = = = = = = = = = = = = ? G T T = = = = = = C ? ? C G ? = G G A T = (C) T G = = T A = = = = = = = = = = = = ? C C C = = = = = = T ? ? T A 0 P041 = = = (T) (G) A = = C A = A C C = = = = = G = = = G = = = = = T = = = T = = C ? ? C G = = = (G) (A) T = = T G = G T A = = = = = A = = = A = = = = = C = = = C = = T ? ? T A 0 P042 (D) (C) = (T) = = = = = (G) = G = = T = = = = A = = = A = = = = = C C = G C = = = = = = = (I) (T) = (G) = = = = = (A) = A = = G = = = = G = = = G = = = = = T T = A T = = = = = = = 0 P043 D = A T G = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = G G A = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P044 = = = = (A) = = (C) = A = ? = = G = = = = G = = = G T D = = = T T = A T = C = = = = = = = = = (G) = = (T) = G = ? = = T = = = = A = = = A A I = = = C C = G C = T = = = = = 0 P045 = = = (T) = (T) = C = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = (A) = T = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P046 = (T) = = = (T) = = = (G) = G ? = = = = = = A = A C = = = = = = C = C = C C = = = = = = = (C) = = = (A) = = = (A) = A ? = = = = = = G = G A = = = = = = T = A = T T = = = = = = 0 P047 = = (G) = = = (C) = = = = = = = T G = C A = G = = = A I = = = = C = G = = T = = = = = = = (A) = = = (T) = = = = = = = G A = T T = A = = = T D = = = = T = A = = C = = = = = 0 P048 ? = (A) = (G) = (T) = = A = = = = G = = = = = = = = = T D ? G T T T = A = = C = = = = = ? = (G) = (A) = (C) = = G = = = = T = = = = = = = = = A I ? C C C C = G = = T = = = = = 0 P049 = = = (T) = (T) = C = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = (G) = (A) = T = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = 0 P050 (D) (C) = (T) = = = (T) = G = G = = T = = = = A = = = A A I = = = C C = G C = T = = = = = (I) (T) = (G) = = = (C) = A = A = = G = = = = G = = = G T D = = = T T = A T = C = = = = = 0 P051 D = A = = A C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = G = = T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P052 (D) = (A) (T) (G) (A) = (T) = (A) = = = = = G = C A = G = = = = = ? G T T = ? = = = = = = = = = (I) = (G) (G) (A) (T) = (C) = (G) = = = = = A = T T = A = = = = = ? C C C = ? = = = = = = = = = 0 P053 ? = = = = = = (C) = G = = = = T G = C A = G = = = A I = = = = C = G = = T = = = = = ? = = = = = = (T) = A = = = = G A = T T = A = = = T D = = = = T = A = = C = = = = = 0 P054 (D) = (A) = = (A) = = C A = = C C = A = T T = A = = = = = = = = = = ? = = = = C ? ? C G (I) = (G) = = (T) = = T G = = T A = G = C A = G = = = = = = = = = = ? = = = = T ? ? T A 0 P055 = = = = = = (T) = ? ? ? = T A G = = = = = = = = = T D = = = = T = A = = C T ? ? T A = = = = = = (C) = ? ? ? = C C T = = = = = = = = = A I = = = = C = G = = T C ? ? C G 0 P056 ? = = = = (A) = (T) = A G = = = = = A = A = = A = = = = ? ? ? ? ? ? = = C = = T C = = ? = = = = (T) = (C) = G A = = = = = G = T = = G = = = = ? ? ? ? ? ? = = T = = G A = = 0 P057 (D) (C) = = (A) T = C = G = = = = = = = = = = G = C G = = = = = = = C = = = = = = = = = (I) (T) = = (G) A = T = A = = = = = = = = = = A = A A = = = = = = = A = = = = = = = = = 0 P058 = = = = = = (T) = = = A = = = G = G = T = A = = = T D G = = = T = A = = C = G A = = = = = = = = (C) = = = G = = = T = A = A = G = = = A I A = = = C = G = = T = T C = = 0 P059 = = = = = (A) = = = = = A = = G = = = = G = = = G T D = = = T T = A T = C = = = = = = = = = = (T) = = = = = G = = T = = = = A = = = A A I = = = C C = G C = T = = = = = 0 P060 (D) = (A) (T) (G) = (T) = = G A = = = = = G = T = = G A A = = G = = = = = = = T = = G A = = (I) = (G) (G) (A) = (C) = = A G = = = = = A = A = = A C G = = A = = = = = = = C = = T C = = 0 P061 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P062 = = = = = (A) C T = G = = = = T = = = = = = = = = A I ? C C C C = G = = T = ? ? = = = = = = = (T) T C = A = = = = G = = = = = = = = = T D ? G T T T = A = = C = ? ? = = 0 P063 = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P064 ? (C) = = (A) = = = = G = A = = = = = = = G G G = G = = = = = T = = = T T = = = = = = ? (T) = = (G) = = = = A = G = = = = = = = A A A = A = = = = = C = = = C C = = = = = = 0 P065 (D) = = (T) = (T) (T) (C) = = ? = = = G = G = T = A = = = T ? G = = = T = A = = C = G A = = (I) = = (G) = (A) (C) (T) = = ? = = = T = A = A = G = = = A ? A = = = C = G = = T = T C = = 0 P066 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P067 = (T) = (G) = (A) = = = = = = = = T = = = = = = G A A = ? = = = = C A G = T T = = = = = = (C) = (T) = (T) = = = = = = = = G = = = = = = A C G = ? = = = = T C A = C C = = = = = 0 P068 = = = (T) = (T) = = = (A) = G = = = = = = = A = A C = = = = = = C = C = C C = = = = = = = = = (G) = (A) = = = (G) = A = = = = = = = G = G A = = = = = = T = A = T T = = = = = = 0 P069 = = = = = = T = = = = A = = G = = = = G = = = G T D = = = T T = A T = C = = = = = = = = = = = C = = = = G = = T = = = = A = = = A A I = = = C C = G C = T = = = = = 0 P070 = = = = = = T C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P071 (D) (C) = = = = = = = G = = = = = = = = = = = A C G = = ? C C C = C = = C = = ? ? = = (I) (T) = = = = = = = A = = = = = = = = = = = G A A = = ? G T T = A = = T = = ? ? = = 0 P072 (D) = = (T) = (T) (T) = = = = = = = G = = = = = = A C G T D = = = = T C A = C C = = = = = (I) = = (G) = (A) (C) = = = = = = = T = = = = = = G A A A I = = = = C A G = T T = = = = = 0 P073 (D) = (A) (T) (G) (A) = (T) = = = = = = T = = = = = = G A A A I = = = = C A G = T T = = = = = (I) = (G) (G) (A) (T) = (C) = = = = = = G = = = = = = A C G T D = = = = T C A = C C = = = = = 0 P074 = = = (T) = = = = = A = = = = = = = = = = = G A A = = ? G T T = A = = T = = = = = = = = = (G) = = = = = G = = = = = = = = = = = A C G = = ? C C C = C = = C = = = = = = 0 P075 = ? ? ? ? ? ? ? = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P076 = = = = = (A) = T = = = A = = = = = = = G = G A = = = = = = T = A = T T = = = = = = = = = = = (T) = C = = = G = = = = = = = A = A C = = = = = = C = C = C C = = = = = = 0 P077 (D) = (A) (T) (G) = (C) = = = = G = = T = = = = A = = = A A I = = = C C = G ? = T = = = = = (I) = (G) (G) (A) = (T) = = = = A = = G = = = = G = = = G T D = = = T T = A ? = C = = = = = 0 P078 = = = = = = = = = = G = = = T = A = A = G = ? = A I A = = = C = G = = T = T C = = = = = = = = = = = = A = = = G = G = T = A = ? = T D G = = = T = A = = C = G A = = 0 P079 (I) = = = = = = (T) = = = = = = T = = = = = = G A A A I = = = = C A G = T T = = = = = (D) = = = = = = (C) = = = = = = G = = = = = = A C G T D = = = = T C A = C C = = = = = 0 P080 = T = = G A = T = = = A = = = = = = = G = G A = = = = = = T = A = ? T = = = = = = = C = = A T = C = = = G = = = = = = = A = A C = = = = = = C = C = ? C = = = = = = 0 P081 ? = = = = = (T) (C) T = = = T A G = = = = = = = = = T D = = = = T = A = = C T ? ? T A ? = = = = = (C) (T) C = = = C C T = = = = = = = = = A I = = = = C = G = = T C ? ? C G 0 P082 (D) = (A) (T) (G) = (T) = = A = A = = G = = = = G = = = G T ? = = = T T = A T = C = = = = = (I) = (G) (G) (A) = (C) = = G = G = = T = = = = A = = = A A ? = = = C C = G C = T = = = = = 0 P083 (I) = (G) (G) (A) (A) (T) = = = = A = = G = = = = G = = = G T ? = = = T T = A T = C = = = = = (D) = (A) (T) (G) (T) (C) = = = = G = = T = = = = A = = = A A ? = = = C C = G C = T = = = = = 0 P084 (D) = (A) = = = = = = A = A = = = = = = = G = G A = = = = = = T = A = T T = = = = = = (I) = (G) = = = = = = G = G = = = = = = = A = A C = = = = = = C = C = C C = = = = = = 0 P085 = = = = = (A) (T) = C A = = C C = A = T T = A = = = = = = = = = = = = = = = C ? ? C G = = = = = (T) (C) = T G = = T A = G = C A = G = = = = = = = = = = = = = = = T ? ? T A 0 P086 D = A T G (T) = (T) = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = I = G G A (A) = (C) = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P087 = T A = G (A) = T = A = = = = = A = T T = A G A A = = = = = = = A = = T = = = = = = = C G = A (T) = C = G = = = = = G = C A = G A C G = = = = = = = C = = C = = = = = = 0 P088 (D) = = (T) = = = = = A G = = = = = A = A = = A = = = = A = = = = = = = C = = T C = = (I) = = (G) = = = = = G A = = = = = G = T = = G = = = = G = = = = = = = T = = G A = = 0 P089 ? (C) = = = = = = = = ? G = = = = = = = A = A C = = = ? = = C = C A = C = = = = = = ? (T) = = = = = = = = ? A = = = = = = = G = G A = = = ? = = T = A G = T = = = = = = 0 P090 ? = = = = (A) C = = = = G = = T = = = = A = = = A A ? = = = C C = G C = T = = = = = ? = = = = (T) T = = = = A = = G = = = = G = = = G T ? = = = T T = A T = C = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS ? = 0.93 ? 0.93 0.75 = 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 = = = = = ? 0.87 = = = 0.83 = 0.95 = = = 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = ? ? 1.00 1.00 = = = = = = = 0.71 0.71 = 0.71 = = = = = 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 = = 0.92 = 0.92 0.93 = 0.63 = = = = = = ? = = = = = = = ? = = = = = ? = = = = = = = = = = = = = = 0.96 = 0.96 0.96 0.96 = = 0.96 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = 1.00 ? = = = = 1.00 = 1.00 ? = 1.00 1.00 ? ? 1.00 1.00 = = = = = = = 0.76 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = 1.00 ? ? 1.00 1.00 ? 0.70 0.70 = 0.70 = = 0.66 = 0.77 = 1.00 = = = 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 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.91 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.69 = = 0.72 0.79 = = 0.95 = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = = = = = = 1.00 = = = 1.00 1.00 = = = = = = 0.70 = 0.70 0.70 0.70 = = 0.71 = 0.98 = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 ? = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = 0.86 = 0.89 = 0.89 = = = = = = = ? = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = 0.50 = 0.50 0.51 0.51 0.60 0.56 = = 1.00 = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = 0.54 = 0.54 0.54 = 0.51 = = = 0.89 = 1.00 1.00 1.00 = = = = = 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = = 1.00 ? ? 1.00 1.00 ? = = = = = 0.86 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.65 0.60 0.64 = = 0.82 = = = 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = = = 0.73 = = = 0.78 = = 0.61 = = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = 0.66 = = 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.66 = 0.65 0.68 0.68 = = = = 1.00 1.00 = = = = ? 1.00 ? = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = = = = = 0.53 = = = = = = = = ? ? 1.00 = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.73 = 0.74 = 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = 1.00 = = = 1.00 = = = = = = = ? = = 0.93 1.00 = = = = = = = ? = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = 0.70 0.71 = = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = 0.96 0.97 = 0.97 = 0.89 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 = = = = = = = = 0.73 = = = = = 0.53 = 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = 1.00 = = = 1.00 = = = = = = = 1.00 = 1.00 0.96 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.80 = = = 0.67 0.71 = 0.68 = 0.97 1.00 = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = ? = = = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 0.54 = = = 0.80 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = 0.90 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 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 = 0.51 0.51 0.51 0.67 = 0.57 = 0.56 = ? ? = = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = 1.00 = = = 1.00 = = = = = = = = = = 0.74 = 0.63 0.68 = = 0.60 = ? = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = = = 0.73 = 0.72 = 0.74 = 0.70 0.79 = 1.00 1.00 = ? = = = 1.00 = 1.00 = 1.00 = = = = = ? 1.00 1.00 1.00 = = = = = = = 1.00 1.00 = = 0.53 = 0.57 0.51 = = = 0.55 = 0.95 = 1.00 ? = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = ? ? = = 0.84 0.84 = = = 0.85 = 0.94 = ? = 1.00 ? = = ? ? ? = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = ? ? = = 0.66 = 0.66 0.66 0.66 0.83 = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = = ? = 0.94 0.94 0.94 0.97 = 0.87 1.00 1.00 = = 1.00 1.00 = = = = = = = = = = = = ? 1.00 1.00 1.00 = = = = = = 1.00 ? ? 1.00 1.00 = = = 0.54 0.68 0.91 = = 1.00 1.00 = 1.00 1.00 1.00 = = = = = 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = = 1.00 ? ? 1.00 1.00 0.67 0.67 = 0.67 = = = = = 0.84 = 1.00 = = 0.95 = = = = 1.00 = = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 = = = = = = = 1.00 = 1.00 1.00 1.00 = = 0.95 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.80 = = 0.81 = 0.97 = ? = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = = 0.52 = 0.63 = 0.95 = 0.86 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.84 = = = 0.79 = = = 0.63 = 1.00 ? = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = = = = = 0.53 = = = 0.70 = = = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 = = = = = ? = 0.81 = 0.81 = 0.85 = = 1.00 = = = = 1.00 = = = = = = = = = 1.00 1.00 ? 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 = = = = = = = = 0.88 = 0.70 = 0.97 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = 0.52 0.53 = 0.52 = = = 0.50 = 0.94 = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = 0.96 = 0.96 = = 0.99 0.94 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.70 = 0.70 0.70 0.70 0.75 = 0.70 = 0.80 = = = = = 1.00 = 1.00 1.00 = 1.00 = = = = = ? 1.00 1.00 1.00 = ? = = = = = = = = = ? = = = = = = 0.84 = 0.99 = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 = = = = = 0.64 = 0.64 = = 0.67 = = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = ? = = = = 1.00 ? ? 1.00 1.00 = = = = = = 0.83 = ? ? ? = 1.00 1.00 1.00 = = = = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 1.00 ? ? 1.00 1.00 ? = = = = 0.77 = 0.80 = 1.00 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = = = ? ? ? ? ? ? = = 1.00 = = 1.00 1.00 = = 0.78 0.84 = = 0.87 0.98 = 0.99 = 1.00 = = = = = = = = = = 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = = = = = = = = = = = = = 0.56 = = = 1.00 = = = 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 = = = = = 0.82 = 0.82 0.84 0.84 = 0.74 = = 0.96 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.70 0.91 0.96 = 1.00 = = = = 1.00 = = = = = = = = = 1.00 1.00 ? 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 = ? ? = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0.65 = = 0.66 = = = = 1.00 = 1.00 = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = 1.00 1.00 = = = = = = 0.73 = = 0.84 = 0.78 0.87 0.85 = = ? = = = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 ? 1.00 = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.87 = 0.85 = 0.71 = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 = ? = = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = 0.83 = 0.80 = = = 0.72 = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.81 0.84 = = = = = = = 0.99 = = = = = = = = = = = 1.00 1.00 1.00 = = ? 1.00 1.00 1.00 = 1.00 = = 1.00 = = ? ? = = 0.77 = = 0.72 = 0.70 0.85 = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = 0.79 = 0.79 0.79 0.79 0.53 = 0.84 = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = 0.81 = = = = = 1.00 = = = = = = = = = = = 1.00 1.00 1.00 = = ? 1.00 1.00 1.00 = 1.00 = = 1.00 = = = = = = = ? ? ? ? ? ? ? = 0.88 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.65 = 0.94 = = = 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = = = 0.66 = 0.65 0.65 0.65 = 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 = 1.00 = 1.00 = 1.00 = ? = 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = 0.52 = = = = = = 0.67 = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = 0.92 = = 0.93 0.94 = 0.97 = = = 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = ? 1.00 = = = = = = ? = = = = = 0.83 0.83 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 1.00 ? ? 1.00 1.00 0.60 = 0.60 0.57 0.58 = 0.62 = = 0.99 = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 ? = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = 0.56 = 0.56 0.56 0.56 0.50 0.73 = = = = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 ? = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = 0.89 = 0.89 = = = = = = 0.98 = 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = = 0.71 0.80 = 1.00 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 0.96 0.61 = 0.85 = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.94 0.94 = 0.93 0.65 = 0.94 = 0.99 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = 0.69 = = 0.73 = = = = = 1.00 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = ? 0.81 = = = = = = = = ? 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = ? = = 1.00 = 1.00 1.00 = 1.00 = = = = = = ? = = = = 0.67 0.95 = = = = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 ? = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = END PHASEPROBS