************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mmp14.phase.inp mmp14.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mmp14.phase.out_freqs : haplotype frequency estimates mmp14.phase.out_pairs : most likely haplotype pairs for each individual mmp14.phase.out_recom : estimates of recombination parameters mmp14.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 37 Positions of loci: 183 345 1578 1592 1977 4132 5229 5808 5944 6060 6079 6081 6168 6414 6972 6973 7409 8137 8483 8523 8647 8792 8798 8804 8852 9111 11265 11843 11972 13130 13157 13199 13403 13451 13759 14114 14370 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mmp14.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCTGTCCCGCC 2 CCCDGACGCCGGTGTITCTTACAAT 1.000000 2 GCTGTCCCGCG 4 CTCDGACGTGGGTGCIGCCTATGCT 1.000000 3 GCTGTCCCGCG 4 CTCDGACGTGGGTGTITCCTACAAT 2.000000 4 GCTGTCCCACC 4 GCCDGAGGCCGGTACITCCTACAAT 2.000000 5 GCTGTCCCACC 4 GCTIGACGCCGGTATITCTTACAAT 1.000000 6 GCTGTCCCACC 4 GCTIGACGCCGGTGCITCTTACAAT 1.000000 7 GCTGTCCCACC 4 GCTIGACGCCGGTGCITCTTACGCT 1.000000 8 GCTGTCCGGCC 4 CCCDGACGCCGGTACITCTTACGCT 1.000000 9 GCTGTCCGGCC 4 CCCDGGCGCGGGTGTITGTTATAAT 1.000000 10 GCTGTGCCGCC 4 CCCDGACGCCTCCACITCCGATGAT 1.000000 11 GCTGTGCCGCG 4 CTCDGACGTGGGTGTITCTTACGAT 1.000000 12 GCTGTGCCGCG 4 CTCDGAGGCCGGTATITCCTACGAT 1.000000 13 GCTGTGCGGCC 4 CCCDGACGCCTCTACITCCGATGAT 1.000000 14 GCTGTGCGGCC 4 CCCDGACGCCTCCACITCCGATGAT 2.000000 15 GCTGTGCGGCC 4 CCCDGACGCCTCCACITCTTACGCT 2.000000 16 GCTGTGCGGCC 4 CCCDGAGGCCGGTACITCCGATGCT 1.000000 17 GCTTTCCCGCC 4 CCCDGACGCCGGTACIGCCTCTAAC 1.000000 18 GCTTTCCCGCC 4 CCCDGAGGCCGGTACITCCTACAAT 1.000000 19 GCTTTCCCGCC 4 CCCDGAGGCCGGTACITCCGATGAT 2.000000 20 GCTTTCCCGCC 4 CCCDGAGGCCGGTACITGCGATGAT 1.000000 21 GCTTTCCCGCC 4 CCCDGAGGCCGGTACIGCTGCTGAT 1.000000 22 GCTTTCCCGCC 4 CCCDAGCGCCTCCACITCTTACAAT 3.000000 23 GCTTTCCCGCC 4 CCCDAGCGCCTCCACITCTTATAAT 1.000000 24 GCTTTCCCGCC 4 CCCDAGCGCCTCCACITGCTACAAC 1.000000 25 GCTTTCCCGCC 4 CCCDAGCGTGGGTGTITCTTACAAT 1.000000 26 GCTTTCCCGCC 4 CTCDGACGCGGGTGTITCTTACACT 1.000000 27 GCTTTCCCGCG 4 CTCDGACGCGGGTGTITGTTATAAT 1.000000 28 GCTTTCCCGCG 4 CTCDGACGTCTCCACITCCTACGAT 1.000000 29 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITCCTACGAT 1.000000 30 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITCCTCTAAT 6.000000 31 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITCTTACAAC 2.000000 32 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITCTTACAAT 26.000000 33 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITCTTACGCT 7.000000 34 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITCTTCCAAT 2.000000 35 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITGCTACAAC 2.000000 36 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITGCTACAAT 1.000000 37 GCTTTCCCGCG 4 CTCDGACGTGGGTGCITGCGATGAT 1.000000 38 GCTTTCCCGCG 4 CTCDGACGTGGGTGCIGCCTATAAT 1.000000 39 GCTTTCCCGCG 4 CTCDGACGTGGGTGCDTCCTACAAT 1.000000 40 GCTTTCCCGCG 4 CTCDGACGTGGGTGCDTCCTCTAAT 1.000000 41 GCTTTCCCGCG 4 CTCDGACGTGGGTGCDTCTTACAAT 1.000000 42 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCCTACGAT 1.000000 43 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCCTCTAAT 2.000000 44 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTACAAC 1.000000 45 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTACAAT 4.000000 46 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTACACT 1.000000 47 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTACGCT 1.000000 48 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTATAAC 1.000000 49 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTCCAAC 1.000000 50 GCTTTCCCGCG 4 CTCDGACGTGGGTGTITCTTCCAAT 1.000000 51 GCTTTCCCGCG 4 CTCDGACGTGGGTGTIGCCTATGCT 1.000000 52 GCTTTCCCGCG 4 CTCDGACACCGGTATDTCCTCTAAT 1.000000 53 GCTTTCCCGCG 4 CTCDGGCGCCTCCACITCTTACAAT 1.000000 54 GCTTTCCCACC 4 GCCDGAGGCCGGTATITCCTACGAT 1.000000 55 GCTTTCCGGTC 2 CCTIGACGCCGGTACITCTTACGAT 2.000000 56 GCTTTCCGGTC 2 CCTIGACGCCGGTACITCTTATGAT 1.000000 57 GCCGTCCCGCC 3 CCCDGGCGCCGGTACIGCTTATGCT 1.000000 58 GCCGTCCCGCC 4 CCCDGACGCCGGTACITCTTACAAT 1.000000 59 GCCGTCCCGCC 4 CCCDGACGCGGGTGTITGTTATGAT 1.000000 60 GCCGTCCCGCC 4 CCCDGACACCGGTACIGCCTATAAT 2.000000 61 GCCGTCCCGCC 4 CCCDGACACCGGTATITCTTACGAT 1.000000 62 GCCGTCCCGCC 4 CCCDGACACCGGTATDTCCTCTAAT 2.000000 63 GCCGTCCCGCC 4 CCCDGGCGCCGGTACITCTTCCAAT 2.000000 64 GCCGTCCCGCC 4 CCCDGGCGCCGGCACITCTTCCAAT 1.000000 65 GCCGTCCCGCC 4 CCCDGGCGCGGGTGTITGTTATAAT 1.000000 66 GCCGTCCCGCC 4 CCCDAGCGCCTCCACITCCTCTAAT 1.000000 67 GCCGTCCCGCC 4 CCCDAGCGCCTCCACITCTTACAAT 4.000000 68 GCCGTCCCGCC 4 CCCDAGCGCCTCCACIGCCTACAAT 1.000000 69 GCCGTCCCGCC 4 CCCDAGCGCCTCCACIGCCTATAAT 1.000000 70 GCCGTCCCGCC 4 CCCDAGCGCCTCCACDTCCTACAAT 1.000000 71 GCCGTCCCGCC 4 CCCDAGCGCCTCCACDTCCTCTAAT 1.000000 72 GCCGTCCCGCC 4 CCCDAGCGCCTCCATITCCTCTAAT 2.000000 73 GCCGTCCCGCC 4 CCCDAGCGCCTCCATITCTTACAAT 2.000000 74 GCCGTCCCGCC 4 CCCDAGCGCCTCCATITCTTACGCT 1.000000 75 GCCGTCCCGCC 4 CCCDAGCGCCTCCATIGCCTACAAT 2.000000 76 GCCGTCCCGCC 4 CCCDAGCGCCTCCATDTCCTACAAC 1.000000 77 GCCGTCCCGCG 4 CTCDGACGTGGGTGCITCTTACAAT 1.000000 78 GCCGTCCCGCG 4 CTCDGACGTGGGTGCDTCCTCTAAT 1.000000 79 GCCGTGTGGTC 2 CCTIGACGCCGGTACIGCCTCTAAC 1.000000 80 GATGCCCCGCC 4 CCCDAGCGCCTCCACITCTTACAAT 1.000000 81 GATGCCCCGCC 4 GCCDGAGGCCGGTACITCTTACAAT 1.000000 82 GATGCCCCGCC 4 GCCDGAGGCCGGTACITCTTACGAT 1.000000 83 GATGCCCCACC 4 GCCDGAGGCCGGTATITCTTACAAT 1.000000 84 GATGCCCCACC 4 GCCDGAGGCCGGTATITCTTACGCT 1.000000 85 GATGCCTGGTC 2 CCTIGACGCCGGTACITCTTACGCT 2.000000 86 GATGCCTGGTC 2 CCTIGACGCCGGTACITGCTACAAC 6.000000 87 GATGCCTGGTC 2 CCTIGACGCCGGTACDTCCTACAAT 1.000000 88 GATGCCTGGTC 2 CCTIGACGCCGGTATITCCTACGAT 3.000000 89 GATGCCTGGTC 2 CCTIGACGCCGGTATITCTTACAAT 1.000000 90 GATGCCTGGTC 2 CCTIGACGCCGGTATITCTTATGAT 2.000000 91 GATGCCTGGTC 2 CCTIGACGCCGGTATITGTTCCGAT 1.000000 92 GATGCCTGGTC 2 CCTIGACGCCGGTGTITCTTACAAC 2.000000 93 GATGCCTGGTC 2 CCTIGACGCCGGTGTITCTTACAAT 2.000000 94 GATGCCTGGTC 2 CCTIGACGCCTCCATITGTTATAAT 1.000000 95 GATGCCTGGTC 2 CCTIGGCGCCTCCATITCTTACGCT 1.000000 96 CCCGTCCCGCC 2 CCCDGACACCGGTACITCTTACGCT 3.000000 97 CCCGTCCCGCC 4 CCCDGACACCGGTACITCCTATAAT 1.000000 98 CCCGTCCCGCC 4 CCCDGACACCGGTATITCCTACAAT 3.000000 99 CCCGTCCCGCC 4 CCCDGACACCGGTATITCTTACGCT 1.000000 100 CCCGTCCCGCC 4 CCCDGAGGCCGGTATITCTTACGAT 2.000000 101 CCCGTCCCGCC 4 CCCDGAGGCCGCCACITCCTACAAC 1.000000 102 CCCGTCCCACC 4 GCCDGAGGCCGGTATITCCTACGAT 2.000000 103 CCCGTCCCACC 4 GCCDGAGGCCGGTATITCTTACGCT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (33,86) P002: (22,73) P003: (55,89) P004: (9,15) P005: (76,86) P006: (15,51) P007: (49,102) P008: (32,36) P009: (4,90) P010: (62,103) P011: (16,57) P012: (31,95) P013: (5,31) P014: (64,72) P015: (67,83) P016: (32,34) P017: (53,82) P018: (13,63) P019: (46,98) P020: (32,86) P021: (18,81) P022: (22,61) P023: (35,86) P024: (32,32) P025: (69,75) P026: (28,30) P027: (68,97) P028: (32,32) P029: (60,65) P030: (41,86) P031: (6,7) P032: (79,87) P033: (29,74) P034: (30,30) P035: (32,32) P036: (23,77) P037: (25,32) P038: (8,14) P039: (3,44) P040: (26,96) P041: (20,102) P042: (10,37) P043: (32,96) P044: (32,67) P045: (32,93) P046: (38,48) P047: (45,45) P048: (3,84) P049: (32,92) P050: (17,21) P051: (32,92) P052: (40,71) P053: (33,85) P054: (32,35) P055: (32,88) P056: (33,56) P057: (55,91) P058: (88,98) P059: (19,58) P060: (24,96) P061: (22,60) P062: (2,4) P063: (12,86) P064: (14,59) P065: (45,100) P066: (32,33) P067: (30,32) P068: (32,32) P069: (43,43) P070: (32,34) P071: (30,66) P072: (73,99) P073: (30,88) P074: (42,93) P075: (67,75) P076: (45,50) P077: (33,72) P078: (52,80) P079: (32,94) P080: (32,101) P081: (70,98) P082: (11,90) P083: (33,39) P084: (62,85) P085: (33,78) P086: (47,54) P087: (63,100) P088: (19,67) P089: (1,27) P090: (32,32) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C G C T G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T G C T A [C] A A C 0 P002 G C T T T C C C G C C 4 C C C D A G C G C C T C C A (C) I T C T T A [C] A A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A (T) I T C T T A C A A T 0 P003 G C T T T C C G G T C 2 C C T I G A C G C C G G T A (C) I T C T T A C [G] A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A (T) I T C T T A C [A] A T 0 P004 G C T G T C C G G C C 4 C C C D G G C G C [G] G G T [G] T I T G T T A T A A T G C T G T G C G G C C 4 C C C D G A C G C C [T] [C] [C] A C I T C T T A C G C T 0 P005 G C C G T C C C G C C 4 C C C D A G C G C C T C C A T D T C C T [A] [C] A A C G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T G C T A [C] A A C 0 P006 G C T G T G C G G C C 4 C C C D G A C G C C T C C A (C) I (T) C (T) T A (C) G C T G C T [T] T C C C G C G 4 C T C D G A C G T G G G T G (T) I (G) C (C) T A (T) G C T 0 P007 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C (T) T (C) C (A) A (C) C C C G T C C C A C C 4 G C C D G A G G C C G G T A T I T C (C) T (A) C (G) A (T) 0 P008 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T G C T A [C] [A] A T 0 P009 G C T G T C C C A C C 4 G C C D G A G G C C G G T A C I T C (C) T A (C) A A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A T I T C (T) T A (T) G A T 0 P010 (G) C C G T C C C (G) C C 4 (C) C C D G A (C) (A) C C G G T A T D T C C T C T (A) (A) T (C) C C G T C C C (A) C C 4 (G) C C D G A (G) (G) C C G G T A T I T C T T A C (G) (C) T 0 P011 G C T G T G C G G C C (4) C C C D G A G G C C G G T A C I (T) C (C) (G) A T G C T G C C G T C C C G C C (3) C C C D G G C G C C G G T A C I (G) C (T) (T) A T G C T 0 P012 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C T T A C (A) (A) (C) G A T G C C T G G T C 2 C C T I G G C G C C T C C A (T) I T C T T A C (G) (C) (T) 0 P013 G C T G T C C C A C C 4 G C T I G A C G C C G G T A (T) I T C T T A C [A] A (T) G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C T T A C A A (C) 0 P014 G C C G T C C C G C C 4 C C C D G G C G C C G G C A (C) I T C (T) T C [C] A A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A (T) I T C (C) T C [T] A A T 0 P015 G C C G T C C C G C C 4 C C C D A G C G C C T C C A (C) I T C T T A C [A] A T G A T G C C C C A C C 4 G C C D G A G G C C G G T A (T) I T C T T A C [A] [A] T 0 P016 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T C C A A T 0 P017 G C T T T C C C G C G 4 C T C D G G C G C C T C C A C I T C T T A C (A) A T G A T G C C C C G C C 4 G C C D G A G G C C G G T A C I T C T T A C (G) A T 0 P018 G C T G T G C G G C C 4 C C C D G A C G C C T C T A C I T C C G A T G A T G C C G T C C C G C C 4 C C C D G G C G C C G G T A C I T C T T C C A A T 0 P019 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C (T) T A C A (C) T [C] C C G T C C C G C C 4 C C C D G A C A C C G G T A T I T C (C) T A C A (A) T 0 P020 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T G C T A [C] A A C 0 P021 G C T T T C C C G C C 4 C C C D G A G G C C G G T A C I T C [C] [T] A [C] [A] A T G A T G C C C C G C C 4 G C C D G A G G C C G G T A C I T C T T A C [A] A T 0 P022 G C (T) (T) T C C C G C C 4 C C C D A G C G C C T C C A (C) I T C T T A C (A) A T G C (C) (G) T C C C G C C 4 C C C D G A C A C C G G T A (T) I T C T T A C (G) A T 0 P023 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T G C T A [C] A A C G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T G C T A [C] A A C 0 P024 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T 0 P025 G C C G T C C C G C C 4 C C C D A G C G C C T C C A (C) I G C C T A T A A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A (T) I G C C T A C A A T 0 P026 G C T T T C C C G C G 4 C T C D G A C G T C T C C A C I T C C T (A) (C) (G) A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C C T (C) (T) (A) A T 0 P027 G C C G T C C C G C C 4 C C C D A G C G C C T C C A C I (G) C C T A (C) A A T C C C G T C C C G C C 4 C C C D G A C A C C G G T A C I (T) C C T A (T) A A T 0 P028 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C [T] T A C [A] A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C [T] T A C A A T 0 P029 [G] C C G T C C C G C C 4 C C C D G A C A C C G G T A C I G C C T A T A A T G C C G T C C C G C C 4 C C C D G G C G C G G G T G T I T G T T A T A A T 0 P030 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C (D) T C T T A C [A] [A] T G A T G C C T G G T C 2 C C T I G A C G C C G G T A C (I) T G C T A [C] A A C 0 P031 G C T G T C C C A C C 4 G C T I G A C G C C G G T G C I T C T T A C A A T G C T G T C C C A C C 4 G C T I G A C G C C G G T G C I T C T T A C G C T 0 P032 G (C) (C) G (T) (G) T G G T C 2 C C T I G A C G C C G G T A C I G C C T C T [A] A (C) G (A) (T) G (C) (C) T G G T C 2 C C T I G A C G C C G G T A C D T C C T A C A A (T) 0 P033 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C (C) T A C G (A) T G C C G T C C C G C C 4 C C C D A G C G C C T C C A (T) I T C (T) T A C G (C) T 0 P034 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C C T C T A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C C T C T A A T 0 P035 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A [T] 0 P036 G C T T T C C C G C C 4 C C C D A G C G C C T C C A C I T C T T A T A A T G C C G T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T 0 P037 G C T T T C C C G C C 4 C C C D A G C G T G G G T G (T) I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C T T A C A A T 0 P038 G C T G T (C) C G G C C 4 C C C D G A C G C C (G) (G) (T) A C I T C T T A C G C T G C T G T (G) C G G C C 4 C C C D G A C G C C (T) (C) (C) A C I T C C G A T G A T 0 P039 G C T (G) T C C C G C G 4 C T C D G A C G T G G G T G T I T C C T A C [A] A (T) G C T (T) T C C C G C G 4 C T C D G A C G T G G G T G T I T C T T A C A A (C) 0 P040 G C T T T C C C G C C 4 C T C D G A C G C G G G T G T I T C T T A C A C T C C C G T C C C G C C 2 C C C D G A C A C C G G T A C I T C T T A C G C T 0 P041 (G) C (T) (T) T C C C G C C 4 C C C D G A G G C C G G T A C I T (G) C G A T G A T (C) C (C) (G) T C C C A C C 4 G C C D G A G G C C G G T A T I T (C) C T A C G A T 0 P042 G C T G T G C C G C C 4 C C C D G A C G C C T C C A C I T (C) C G A T G A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T (G) C G A T [G] A T 0 P043 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C (A) (A) T C C C G T C C C G C C 2 C C C D G A C A C C G G T A C I T C T T A C (G) (C) T 0 P044 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A C I T C T T A C A A T 0 P045 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C T T A C A A T G A T G C C T G G T C 2 C C T I G A C G C C G G T G (T) I T C T T A C A A T 0 P046 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I G C C T A T A A (T) G C T T T C C C G C G 4 C T C D G A C G T G G G T G (T) I T C T T A T A A (C) 0 P047 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C T T A C A A T 0 P048 G (C) T G (T) C C C G C G 4 C T C D G A C G T G G G T G T I T C (C) T A C (A) (A) T G (A) T G (C) C C C A C C 4 G C C D G A G G C C G G T A T I T C (T) T A C (G) (C) T 0 P049 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A (T) G A T G C C T G G T C 2 C C T I G A C G C C G G T G T I T C T T A C A A (C) 0 P050 G C T T T C C C G C C 4 C C C D G A (C) G C C G G T A C I G C (C) (T) C T (A) A (C) G C T T T C C C G C C 4 C C C D G A (G) G C C G G T A C I G C (T) (G) C T (G) A (T) 0 P051 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A (T) G A T G C C T G G T C 2 C C T I G A C G C C G G T G T I T C T T A C A A (C) 0 P052 G C (T) (T) T C C C G C G 4 C T C D G A C G T G G G T G C D T C C T C T A A T G C (C) (G) T C C C G C C 4 C C C D A G C G C C T C C A C D T C C T C T A A T 0 P053 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C G C T G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T C T T A C G C T 0 P054 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T G C T A [C] A A C 0 P055 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C (T) T A C (A) A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A (T) I T C (C) T A C (G) A T 0 P056 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A (C) G (C) T G C T T T C C G G T C 2 C C T I G A C G C C G G T A C I T C T T A (T) G (A) T 0 P057 G C T T T C C G G T C 2 C C T I G A C G C C G G T A (C) I T (C) T T (A) C G A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A (T) I T (G) T T (C) C G A T 0 P058 G A T G C C T G G T C 2 C C T I G A C G C C G G T A T I T C C T A C G A T C C C G T C C C G C C 4 C C C D G A C A C C G G T A T I T C C T A C A A T 0 P059 G C (T) (T) T C C C G C C 4 C C C D G A (G) G C C G G T A C I T C C [G] A [T] [G] A T G C (C) (G) T C C C G C C 4 C C C D G A (C) G C C G G T A C I T C T T A C [A] A T 0 P060 G C T T T C C C G C C 4 C C C D A G C G C C T C C A C I T (G) (C) T A [C] A A [C] C C C G T C C C G C C 2 C C C D G A C A C C G G T A C I T (C) (T) T A C [G] [C] [T] 0 P061 G C (T) (T) T C C C G C C 4 C C C D A G C G C C T C C A C I (T) C (T) T A [C] A A T G C (C) (G) T C C C G C C 4 C C C D G A C A C C G G T A C I (G) C (C) T A [T] A A T 0 P062 G C T G T C C C G C G 4 C T C D G A C G T G G G T G C I (G) C C T A [T] (G) (C) T G C T G T C C C A C C 4 G C C D G A G G C C G G T A C I (T) C C T A [C] (A) (A) T 0 P063 G C T G T G C C G C G 4 C T C D G A G G C C G G T A T I T C C T A C [G] A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T G C T A [C] A A C 0 P064 G C T G T G C (G) G C C 4 C C C D G A C G C C T C C A C I T C C G A T G A T G C C G T C C (C) G C C 4 C C C D G A C G C G G G T G T I T G T T A T G A T 0 P065 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C T T A C [A] [A] T C C C G T C C C G C C 4 C C C D G A G G C C G G T A T I T C T T A C [G] A T 0 P066 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C G C T 0 P067 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C C T C T A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T 0 P068 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T 0 P069 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C C T C T A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C C T C T A A T 0 P070 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T C C A A T 0 P071 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C C T C T A A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A C I T C C T C T A A T 0 P072 G C C G T C C C G C C 4 C C C D A G C G C C T C C A T I T C T T A C (A) (A) T C C C G T C C C G C C 4 C C C D G A C A C C G G T A T I T C T T A C (G) (C) T 0 P073 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C C T (C) (T) (A) A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A (T) I T C C T (A) (C) (G) A T 0 P074 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C (C) T A C (G) A T G A T G C C T G G T C 2 C C T I G A C G C C G G T G T I T C (T) T A C (A) A T 0 P075 G C C G T C C C G C C 4 C C C D A G C G C C T C C A (C) I T C T T A C A A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A (T) I G C C T A C A A T 0 P076 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C T T C C A A T 0 P077 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T C (T) T (A) (C) (G) (C) T G C C G T C C C G C C 4 C C C D A G C G C C T C C A (T) I T C (C) T (C) (T) (A) (A) T 0 P078 G (C) T (T) [T] C C C G C (G) 4 C (T) C D G A C A C C G G T A (T) (D) T C (C) T (C) (T) A A T G (A) T (G) [C] C C C G C (C) 4 C (C) C D A G C G C C T C C A (C) (I) T C (T) T (A) (C) A A T 0 P079 G C T T T C C C G C G 4 C T C D G A C G T G G G T G (C) I T (C) T T A C A A T G A T G C C T G G T C 2 C C T I G A C G C C T C C A (T) I T (G) T T A [T] A A T 0 P080 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C [T] T A C A A T C C C G T C C C G C C 4 C C C D G A G G C C G C C A C I T [C] [C] T A [C] A A C 0 P081 G C [C] G T C C C G C C 4 C C C D A G C G C C T C C A (C) D T C C T A C A A T C C C G T C C C G C C 4 C C C D G A C A C C G G T A (T) I T C C T A C A A T 0 P082 G C T G T G C C G C G 4 C T C D G A C G T G G G T G T I T C T T A (C) G A T G A T G C C T G G T C 2 C C T I G A C G C C G G T A T I T C T T A (T) G A T 0 P083 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C (I) T C (T) T A C G C T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C (D) T C (C) T A C A A T 0 P084 G C C G T C C C G C C 4 C C C D G A C A C C G G T A T D T C C T C T (A) (A) T G A T G C C T G G T C 2 C C T I G A C G C C G G T A C I T C T T A C (G) (C) T 0 P085 G C (T) (T) T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C (G) (C) T G C (C) (G) T C C C G C G 4 C T C D G A C G T G G G T G C D T C C T C T (A) (A) T 0 P086 G C T T T C C C G C G 4 C T C D G A C G T G G G T G T I T C (T) T A C G (C) T G C T T T C C C A C C 4 G C C D G A G G C C G G T A T I T C (C) T A C G (A) T 0 P087 G C C G T C C C G C C 4 C C C D G G C G C C G G T A C I T C T T [C] C A A T C C C G T C C C G C C 4 C C C D G A G G C C G G T A T I T C [T] T A C G A T 0 P088 G C T T T C C C G C C 4 C C C D G A G G C C G G T A C I T C (C) (G) A [T] [G] A T G C C G T C C C G C C 4 C C C D A G C G C C T C C A C I T C (T) (T) A C [A] A T 0 P089 G C T (G) T C C C G C (C) (2) C (C) C D G A C G C (C) G G T G [T] I T (C) T T A C A A T G C T (T) T C C C G C (G) (4) C (T) C D G A C G C (G) G G T G T I T (G) T T A [T] A A T 0 P090 G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T G C T T T C C C G C G 4 C T C D G A C G T G G G T G C I T C T T A C A A T END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 P001 = ? = ? T = ? C = C G 4 = T C D = = = = T G = = = G ? = = C T = ? ? G C T = ? = ? C = ? G = T C 2 = C T I = = = = C C = = = A ? = = G C = ? ? A A C 0 P002 = = T ? = = = = = = = = = = ? ? ? ? = = = = = = = = (C) = = = = = ? ? = = = = = C ? = = = = = = = = = = ? ? ? ? = = = = = = = = (T) = = = = = ? ? = = = 0 P003 = C = ? T = C = = = = = = = = = = = = = = = = = = = (C) = = = = = = ? ? ? = = A = ? C = T = = = = = = = = = = = = = = = = = = = (T) = = = = = = ? ? ? = 0 P004 = = = = = C ? = = = = = = ? = = = G ? ? ? ? ? ? ? ? T = = G = = = T A A = = = = = = G ? = = = = = = ? = = = A ? ? ? ? ? ? ? ? C = = C = = = C G C = 0 P005 = ? C = T = C C = C = 4 = ? C D A ? = = = = T C C = T D = C = = ? ? ? ? = = ? T = C = T G = T = 2 = ? T I G ? = = = = G G T = C I = G = = ? ? ? ? = 0 P006 = = = ? = G = G = = C = ? ? = = = = = = C C T C C A (C) = (T) = (T) = = (C) = = = = = = ? = C = C = = G = ? ? = = = = = = T G G G T G (T) = (G) = (C) = = (T) = = = 0 P007 G = T ? = = = = G = G = C T = = = = C = T G = = = G = = = = (T) = (C) = (A) = (C) C = C ? = = = = A = C = G C = = = = G = C C = = = A = = = = (C) = (A) = (G) = (T) 0 P008 = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = C T = ? ? ? ? = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = G C = ? ? ? ? = 0 P009 = C = = T = C C A C = 4 G = C D = = G = = = = = = = C = = = (C) = = (C) A = ? = A = = C = T G G T = 2 C = T I = = C = = = = = = = T = = = (T) = = (T) G = ? 0 P010 (G) = = = = = = = (G) = = = (C) = = = = ? (C) (A) = = = = = = = D = = C = C T (A) (A) = (C) = = = = = = = (A) = = = (G) = = = = ? (G) (G) = = = = = = = I = = T = A C (G) (C) = 0 P011 = = T = = G ? G = = = (4) = = = = = A G = = = = = = = = = (T) = (C) (G) = = = = = = = C = = C ? C = = = (3) = = = = = G C = = = = = = = = = (G) = (T) (T) = = = = = 0 P012 = C = T T = C C = C G 4 = T C D = A = = T G G G T G (C) = = = = = = = (A) (A) (C) = A = G C = T G = T C 2 = C T I = G = = C C T C C A (T) = = = = = = = (G) (C) (T) 0 P013 = = = G = = = = A = C = G C T I = = = = C C = = = A (T) = = = = = ? ? ? ? (T) = = = T = = = = G = G = C T C D = = = = T G = = = G (C) = = = = = ? ? ? ? (C) 0 P014 = = = = = = = = = = = = = = = = G = = = = = G G = = (C) = = = (T) = = ? = = = = = = = = = = = = = = = = = = = A = = = = = T C = = (T) = = = (C) = = ? = = = 0 P015 = C C = T = = = G = = = C = = = A ? C = = = T C C = (C) = = = = = = ? ? ? = = A T = C = = = A = = = G = = = G ? G = = = G G T = (T) = = = = = = ? ? ? = 0 P016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = 0 P017 = C = T T = = = = = G = C T = = = G C = = = T C C = = = = = = = = = (A) = = = A = G C = = = = = C = G C = = = A G = = = G G T = = = = = = = = = (G) = = 0 P018 = = T = = G = G = = = = = = = = = A = = = = T C = = = = = = C G A ? ? ? = = = C = = C = C = = = = = = = = = G = = = = G G = = = = = = T T C ? ? ? = 0 P019 ? ? T T = = = ? = = G = = T = = ? = = G T G = = = G = = = = (T) = = = = (C) = ? ? C G = = = ? = = C = = C = = ? = = A C C = = = A = = = = (C) = = = = (A) = 0 P020 = C = T T = C ? ? C G 4 = T C D = = = = T G = = = ? = = = C T = ? ? ? ? T = A = G C = T ? ? T C 2 = C T I = = = = C C = = = ? = = = G C = ? ? ? ? C 0 P021 = C = T T = = = = = = = C = = = = = = = = = = = = ? = = = ? ? ? ? ? ? ? = = A = G C = = = = = = = G = = = = = = = = = = = = ? = = = ? ? ? ? ? ? ? = 0 P022 = = (T) (T) = = = = = = = = = = = = ? ? = G = = T C C = (C) = = = = = = = (A) = = = = (C) (G) = = = = = = = = = = = = ? ? = A = = G G T = (T) = = = = = = = (G) = = 0 P023 = C = T T = ? C = C G 4 = T C D = = = = T G = = = G = = = = = = ? ? = = = = A = G C = ? G = T C 2 = C T I = = = = C C = = = A = = = = = = ? ? = = = 0 P024 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P025 = = = = = = = = = = = = = = = = = ? = = = = = = = = (C) = = = = = = T = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = (T) = = = = = = C = = = 0 P026 = = = = = = = ? ? = = = = = = = = ? = = = C T C C A = = = = = = (A) (C) (G) = = = = = = = = = ? ? = = = = = = = = ? = = = G G G T G = = = = = = (C) (T) (A) = = 0 P027 G = = = = = = = = = = = = = = = A G = G = = T C C = = = (G) = = = = (C) = = = C = = = = = = = = = = = = = = = G A = A = = G G T = = = (T) = = = = (T) = = = 0 P028 = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = 0 P029 ? ? = = = = = = = = = = = = = = = A = A = C = = = A C = G C C = = = = = = ? ? = = = = = = = = = = = = = = = G = G = G = = = G T = T G T = = = = = = 0 P030 = C = T T = C C = C G 4 = T C D = = = = T G = = = G = (D) = C T = ? ? ? ? T = A = G C = T G = T C 2 = C T I = = = = C C = = = A = (I) = G C = ? ? ? ? C 0 P031 = = = = = = = = = = = = = = = = = ? = = = = = ? = = = ? = = = = ? ? A A = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = ? = = = = ? ? G C = 0 P032 = (C) (C) = (T) (G) = = = = = = = = = = = ? = = = = = = = = = I G = = = C ? ? ? (C) = (A) (T) = (C) (C) = = = = = = = = = = = ? = = = = = = = = = D T = = = A ? ? ? (T) 0 P033 = = T T = = = = = = G = = T = = G A = = T G G G T G (C) = = = (C) = = = = (A) = = = C G = = = = = = C = = C = = A G = = C C T C C A (T) = = = (T) = = = = (C) = 0 P034 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = 0 P035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 P036 = = T T = = ? ? = = C = = C = = A G = = C C T C C ? = = = = = = = T = = = = = C G = = ? ? = = G = = T = = G A = = T G G G T ? = = = = = = = C = = = 0 P037 = = = = = = = = = = C = = C = = A G = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = G = = T = = G A = = = = = = = = (C) = = = = = = = = = = 0 P038 = = = = = (C) = = = = = = = = = = = = = = = = (G) (G) (T) = = = = = T T = C = C = = = = = = (G) = = = = = = = = = = = = = = = = (T) (C) (C) = = = = = C G = T = A = 0 P039 = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = C = ? ? ? ? (T) = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = T = ? ? ? ? (C) 0 P040 G = T T = = = = = = = 4 = T = = = = ? ? = G = = = G T = = = = = = = A = = C = C G = = = = = = = 2 = C = = = = ? ? = C = = = A C = = = = = = = G = = 0 P041 (G) = (T) (T) = = = = G = = = C = = = = = = = = = = = = = C = = (G) = G = T = = = (C) = (C) (G) = = = = A = = = G = = = = = = = = = = = = = T = = (C) = T = C = = = 0 P042 = = = G = G = = = = C = = C = = = = = = C C T C C A = = = (C) = = ? ? ? ? = = = = T = C = = = = G = = T = = = = = = T G G G T G = = = (G) = = ? ? ? ? = 0 P043 G = T T = = ? = = = G 4 = T = = = = = G T G = = = G = = = = = = = ? (A) (A) = C = C G = = ? = = = C 2 = C = = = = = A C C = = = A = = = = = = = ? (G) (C) = 0 P044 = = T T = = = = = = G = = T = = G A = = T G G G T ? = = = = = = = = = = = = = C G = = = = = = C = = C = = A G = = C C T C C ? = = = = = = = = = = = 0 P045 = C = T T = C C = C G 4 = T C D = ? = = T G = = = = (C) = = = = = = = = = = = A = G C = T G = T C 2 = C T I = ? = = C C = = = = (T) = = = = = = = = = = 0 P046 = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = G = C = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = T = T = = = = = (C) 0 P047 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = 0 P048 = (C) = = (T) = ? = G = G = C T ? ? = = C = T G = = = G = = = = (C) = = = (A) (A) = = (A) = = (C) = ? = A = C = G C ? ? = = G = C C = = = A = = = = (T) = = = (G) (C) = 0 P049 = C = T T = C C = C G 4 = T C D = = = = T G = = = = C = = = = = = = ? ? (T) = A = G C = T G = T C 2 = C T I = = = = C C = = = = T = = = = = = = ? ? (C) 0 P050 = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = (C) (T) = = (A) = (C) = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = (T) (G) = = (G) = (T) 0 P051 = C = T T = C C = C G 4 = T C D = = = = T G = = = = C = = = = = = ? ? ? (T) = A = G C = T G = T C 2 = C T I = = = = C C = = = = T = = = = = = ? ? ? (C) 0 P052 = = (T) (T) = = ? = = = G = = T = = G A = = T G G G T G = = = = = = = = = = = = = (C) (G) = = ? = = = C = = C = = A G = = C C T C C A = = = = = = = = = = = 0 P053 = C = T T = C C = C G 4 = ? C D = = = = T G = = = ? = = = = = ? = ? = = = = A = G C = T G = T C 2 = ? T I = = = = C C = = = ? = = = = = ? = ? = = = 0 P054 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = ? ? ? ? T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = ? ? ? ? C 0 P055 = C = T T = ? C = C G 4 = T C D = = = = T G = = = G (C) = = = (T) = = = (A) = = = A = G C = ? G = T C 2 = C T I = = = = C C = = = A (T) = = = (C) = = = (G) = = 0 P056 = = = = ? = = C = C G 4 = T C D = = = = T G = = = G = = = = = = = (C) = (C) = = = = = ? = = G = T C 2 = C T I = = = = C C = = = A = = = = = = = (T) = (A) = 0 P057 = C = T T = C = = = = = = = = = = = = = = = = = = = (C) = = (C) = = (A) = = = = = A = G C = T = = = = = = = = = = = = = = = = = = = (T) = = (G) = = (C) = = = = 0 P058 G A T = C = T G = T = 2 = = T I = = = G = = = = = = = = = = = = = ? G = = C C C = T = C C = C = 4 = = C D = = = A = = = = = = = = = = = = = ? A = = 0 P059 = = (T) (T) = = = ? ? = = = = = = = = = (G) = = = = = = = = ? ? = C ? ? ? ? ? = = = (C) (G) = = = ? ? = = = = = = = = = (C) = = = = = = = = ? ? = T ? ? ? ? ? = 0 P060 G = T ? = = = = = = = 4 = = = = A G = G = = T C C = = = = (G) (C) = ? ? ? ? ? C = C ? = = = = = = = 2 = = = = G A = A = = G G T = = = = (C) (T) = ? ? ? ? ? 0 P061 = = (T) (T) = = = = = = = = = = = = A G = G = = T C C = = = (T) = (T) = = ? ? ? = = = (C) (G) = = = = = = = = = = = = G A = A = = G G T = = = (G) = (C) = = ? ? ? = 0 P062 = = = = = = = = G = G = C T = = = = C = T G = = = G = = (G) = = = = ? (G) (C) = = = = = = = = = A = C = G C = = = = G = C C = = = A = = (T) = = = = ? (A) (A) = 0 P063 = C = = T G C ? = C G 4 = T C D = = G = = = = = = = T = = C = = ? ? ? ? T = A = = C C T ? = T C 2 = C T I = = C = = = = = = = C = = G = = ? ? ? ? C 0 P064 = = T = = G ? (G) = = = = = = ? ? = = = = = C T C C A C = = C C G = = = = = = = C = = C ? (C) = = = = = = ? ? = = = = = G G G T G T = = G T T = = = = = 0 P065 G = T T = = = = = = G = = T = = = = C = T G = = = G = = = = = = = = ? ? = C = C G = = = = = = C = = C = = = = G = C C = = = A = = = = = = = = ? ? = 0 P066 = = = = = = = = = = = = = = = = = ? = = = = = ? = = ? = = = = = = = A A = = = = = = = = = = = = = = = = = = ? = = = = = ? = = ? = = = = = = = G C = 0 P067 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = A C = = = 0 P068 = = = = = = = = = = = = = ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = = = = = = = = = = = = = = = 0 P069 = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? = = = = = = = = = = = = = 0 P070 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C ? = = = 0 P071 = = T T = = = = = = G = = T = = G A = = T G G G T G = = = = = = = ? = = = = = C G = = = = = = C = = C = = A G = = C C T C C A = = = = = = = ? = = = 0 P072 G = = = = = = = = = = = = = = = ? G = G = = T C C = = = = = = = = = (A) (A) = C = = = = = = = = = = = = = = = ? A = A = = G G T = = = = = = = = = (G) (C) = 0 P073 = C = T T = C C = C G 4 = T C D ? = = = T G = = = G (C) = = = = = (C) (T) (A) = = = A = G C = T G = T C 2 = C T I ? = = = C C = = = A (T) = = = = = (A) (C) (G) = = 0 P074 = C = T T = C ? ? C G 4 = T C D = = = = T G = = = = = = = = (C) = = = (G) = = = A = G C = T ? ? T C 2 = C T I = = = = C C = = = = = = = = (T) = = = (A) = = 0 P075 = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = T = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = G = C = = = = = = 0 P076 = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = C = = = = 0 P077 = = T T = = = = = = G = = T = = G ? = = T G G G T G (C) = = = (T) = (A) (C) (G) (C) = = = C G = = = = = = C = = C = = A ? = = C C T C C A (T) = = = (C) = (C) (T) (A) (A) = 0 P078 = (C) = (T) ? = = ? = = (G) = = (T) = = G A = A = = G G T = (T) (D) = = (C) = (C) (T) = = = = (A) = (G) ? = = ? = = (C) = = (C) = = A G = G = = T C C = (C) (I) = = (T) = (A) (C) = = = 0 P079 = C = T T = C C = C G 4 = T C D = = = = T G G G T G (C) = = (C) = = = ? = = = = A = G C = T G = T C 2 = C T I = = = = C C T C C A (T) = = (G) = = = ? = = = 0 P080 G = T T = = = = = = G = = T = = = = C = T G = G T G = = = ? ? ? ? ? ? ? T C = C G = = = = = = C = = C = = = = G = C C = C C A = = = ? ? ? ? ? ? ? C 0 P081 G = ? ? ? = = = = = = = = = = = ? ? = G = = T C C = (C) D = = = = = = = = = C = ? ? ? = = = = = = = = = = = ? ? = A = = G G T = (T) I = = = = = = = = = 0 P082 = C = = T G C C = C G 4 = T C D = = = = T G = = = G = = = = = = = (C) = = ? = A = = C C T G = T C 2 = C T I = = = = C C = = = A = = = = = = = (T) = = ? 0 P083 = = = = = ? = = = = = = = = = = = ? = = = = = = = = = (I) = = (T) = = = G C = = = = = = ? = = = = = = = = = = = ? = = = = = = = = = (D) = = (C) = = = A A = 0 P084 = C C = T = C C = C = 4 = = C D = = = A = = = = = = T D = = C = C T (A) (A) ? = A T = C = T G = T = 2 = = T I = = = G = = = = = = C I = = T = A C (G) (C) ? 0 P085 = = (T) (T) = = = = = = = = = = = = = = = = = = = = = = = I = = T = A ? (G) (C) = = = (C) (G) = = = = = = = = = = = = = = = = = = = = = = = D = = C = C ? (A) (A) = 0 P086 = = = = = = = = G = G = C T = = = = C = T G = = = G = = = = (T) = = = = (C) = = = = = = = = = A = C = G C = = = = G = C C = = = A = = = = (C) = = = = (A) = 0 P087 G = = = = = = = = = = = = = = = = G C = = = = = = = C = = ? ? ? ? ? A = = C = = = = = = = = = = = = = = = = A G = = = = = = = T = = ? ? ? ? ? G = = 0 P088 = = T T = = = = = = = = = = = = G A G = = = G G T = = = = = (C) (G) = ? ? ? = = = C G = = = = = = = = = = = = A G C = = = T C C = = = = = (T) (T) = ? ? ? = 0 P089 ? ? = (G) = = = = = = (C) (2) = (C) = = = = = = = (C) = = = = ? = = (C) = = = ? = = = ? ? = (T) = = = = = = (G) (4) = (T) = = = = = = = (G) = = = = ? = = (G) = = = ? = = = 0 P090 = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 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 ? = = 0.91 0.91 = ? ? 0.91 0.91 0.91 = = 1.00 ? = = = = = = = = = = ? ? ? ? = = = = = = = = 0.73 = = = = = ? ? = = = = 1.00 = ? 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = 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 = ? ? = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 0.65 = 0.53 = 0.59 = = 0.53 = = = 0.98 = 0.98 ? = = = = 1.00 = 1.00 = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 0.73 = 0.68 = 0.70 = 0.69 = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = 1.00 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 = = = 0.72 = = 0.55 0.92 = ? 0.87 = = = = = = = 0.89 = = = 0.89 = = = = ? 0.89 0.89 = = = = = = = 1.00 = = 0.99 = 0.99 0.99 0.58 0.58 = = = 0.98 = = 0.98 ? 0.98 = = = 0.51 = = = = = 0.99 0.99 = = = = = = = = = 0.69 = 0.58 0.70 = = = = = = 0.97 = 0.97 0.97 = 0.97 0.97 = 0.97 0.97 0.97 = 0.97 0.97 0.97 = 0.93 = = 0.93 0.93 0.93 0.93 0.93 0.93 0.60 = = = = = = = 0.51 0.51 0.52 = = = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 0.67 = = = = = ? ? ? ? 0.56 = = = = = = = = = = = = = = = = 0.98 = = = = = 0.98 0.98 = = 0.88 = = = 0.88 = = ? = = = = 0.99 0.99 = 0.99 = = = 1.00 = = = 1.00 = = = 1.00 ? 1.00 = = = 1.00 1.00 1.00 = 0.85 = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = 0.59 = = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 = = = = = = 1.00 1.00 1.00 ? ? ? = ? ? 1.00 1.00 = = = ? = = 1.00 = = 1.00 = = ? = = 1.00 1.00 1.00 = = = 1.00 = = = = 0.84 = = = = 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 = = = ? = = = 0.93 0.93 = ? ? ? ? 0.93 = 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = = = = = = = = = = ? = = = ? ? ? ? ? ? ? = = = 0.53 0.53 = = = = = = = = = = = = ? ? = 1.00 = = 1.00 1.00 1.00 = 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 = = = 1.00 = = = = = = ? ? = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0.70 = = = = = = 1.00 = = = = = = = = = = ? ? = = = = = = = = ? = = = 1.00 1.00 1.00 1.00 1.00 = = = = = = 0.60 0.60 0.57 = = 0.93 = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 0.52 = = = = 0.55 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = ? ? = = = = = = = = = = = = = = = 0.96 = 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 = = = 1.00 = 0.83 = 0.98 1.00 = ? ? ? ? 1.00 = = = = = = = = = = = = = = = = = ? = = = = = ? = = = ? = = = = ? ? 1.00 1.00 = = 0.61 0.61 = 0.61 0.63 = = = = = = = = = = = ? = = = = = = = = = 0.99 0.99 = = = 0.99 ? ? ? 0.72 = = 0.99 0.99 = = = = = = 1.00 = = 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 0.55 = = = 0.53 = = = = 0.52 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 1.00 1.00 = = ? ? = = 1.00 = = 1.00 = = 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 = = = = = = = = = = = = = = = 0.77 = = = = = = = = = = = = = = = = 0.83 0.83 0.83 = = = = = 0.99 0.99 = 0.99 = 1.00 = = = = 0.84 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = ? ? ? ? 0.82 0.99 = 0.99 0.99 = = = = = = = 1.00 = 1.00 = = = = ? ? = 0.99 = = = 0.99 1.00 = = = = = = = 1.00 = = 0.79 = 0.79 0.79 = = = = 0.90 = = = 0.90 = = = = = = = = = = = = = 0.94 = = 0.69 = 0.91 = 0.91 = = = = = = 0.94 = 0.94 = = = = 1.00 = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 0.86 = = ? ? ? ? = 1.00 = 1.00 1.00 = = ? = = = 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = = = 1.00 = = = = = = = ? 0.83 0.82 = = = 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 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = ? = = 1.00 1.00 = = = = 0.90 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.63 = 1.00 = 1.00 = = = = = 0.79 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = 0.90 = = 0.90 = ? = 1.00 = 1.00 = 1.00 1.00 ? ? = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 0.82 = = = 0.59 0.60 = = 1.00 = 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 = = = = = = = ? ? 0.83 = = = = = = = = = = = = = = = = = = 0.77 = = = = = = = = = = = 0.77 0.82 = = 0.72 = 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 = = = = 0.96 = = = = = = ? ? ? 0.80 = = 0.77 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 = 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 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 0.84 = = = 0.82 = = = 0.83 = = = = = = ? = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 = = = = = = = 0.55 = 0.62 = = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = 0.62 = = 0.60 = = 0.52 = = = = 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 = = = ? ? = = = = = = = = = 0.77 = = = = = = = = ? ? = 0.92 ? ? ? ? ? = 1.00 = 1.00 ? = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = 0.83 0.83 = ? ? ? ? ? = = 0.61 0.61 = = = = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 0.78 = 0.78 = = ? ? ? = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = 0.82 = = = = ? 0.72 0.72 = = 1.00 = = 1.00 1.00 1.00 ? = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = = = = = 0.93 = = 0.93 = = ? ? ? ? 0.93 = = 0.96 = = 0.95 ? 0.89 = = = = = = ? ? = = = = = 1.00 1.00 1.00 1.00 1.00 0.94 = = 0.97 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = 0.99 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 = = = = = = = ? = = = 0.98 = = = = = = = = = = = = = = = ? 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = 0.55 0.57 = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 ? = = = 1.00 1.00 = = = 1.00 0.85 = = = = = 0.87 0.87 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 = = = = = = = = 0.76 = = = 0.73 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.66 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = = 1.00 ? = = 1.00 1.00 1.00 1.00 1.00 1.00 0.64 = = = 0.52 = 0.52 0.52 0.54 0.54 = = 0.69 = 0.69 ? = = ? = = 0.89 = = 0.89 = = 0.95 0.95 = 0.95 = = 0.95 0.95 0.95 = 0.85 0.66 = = 0.66 = 0.66 0.66 = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 0.85 = = 0.85 = = = ? = = = 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 = 0.79 0.92 = = = = = = = = = = 0.99 = = 0.99 0.92 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 = = = = = = = 0.60 = = ? = = = = = ? = = = = = = = = = = = ? = = = = = = = = = 0.69 = = 0.73 = = = 0.99 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = = 0.94 0.90 = = 0.90 = 0.90 0.90 0.51 0.51 ? = = 0.61 0.61 = = = = = = = = = = = = = = = = = = = = = = = 0.92 = = 0.99 = 0.99 ? 0.85 0.85 = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 0.55 = = = = 0.55 = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 0.95 = = ? ? ? ? ? 0.95 = = = = 0.99 0.99 = = = = = = = = = = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = = = = 0.77 0.77 = ? ? ? = ? ? = 0.63 = = = = = = 0.69 0.69 = 0.69 = = = = = = = 0.86 = = = = ? = = 0.86 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = END PHASEPROBS