************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 gata3.phase.inp gata3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST gata3.phase.out_freqs : haplotype frequency estimates gata3.phase.out_pairs : most likely haplotype pairs for each individual gata3.phase.out_recom : estimates of recombination parameters gata3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 79 Positions of loci: 258 682 898 1851 2042 2044 2053 2668 3203 3505 3661 4307 4609 4613 4614 4615 5116 5131 5911 6411 6756 7536 7543 7744 7782 8035 8464 8470 8485 8500 8692 9205 9292 9580 10228 10836 10942 10985 11184 11204 11230 11387 12773 12817 12865 12868 13075 13295 13757 13921 14004 14059 14066 14098 14147 14309 14508 14550 14627 15140 15423 15653 15894 16106 16597 16628 16727 16828 17416 17565 17598 18873 18899 19052 19407 19517 19847 20988 21083 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file gata3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGCACCCGCCTGGATTTCCTATCCGCTGACCCAAAGTTCCGDCTTATACCCTCTDDTTDGGCCCTCCICAGACCACCAA 1.000000 2 GGCACCCGCCTGGATTTCCTATCCGCTGGCCCGCGACCACGDGGCACTGTCTAGIDTGIGATTTTCCICAGACCGCCGA 3.000000 3 GGCACCCGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICAGGCCACAAA 18.000000 4 GGCACCCGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCITAGGCCACAAA 2.000000 5 GGCACCCGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDICTDGGCCCTTCICAGACCACCAG 1.000000 6 GGCACCCGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCTCTDDTTDGGCTCTCCICAGGCCACAAA 2.000000 7 GGCACCCGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCTAGIDTGIGATTTTCCICAGACCGCCGA 1.000000 8 GGCACCCGCCTGGATTTCCTATCCGCTGGCCTGCGACCACGDGGCACTCCCGCTDDTTDGGCTCTCCICAGGCCACAAA 1.000000 9 GGCACCCGCCTGGATTTCCTATCCGCCCGTACGCGACCACGDGGCACTGTCTAGIDTGIGATTTTCCICAGACCGCCAA 1.000000 10 GGCACCCGCCTGGATTTCCTGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 1.000000 11 GGCACCCGCCTAGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCTCTDICTDGGCCCTTCICAGACCACCAG 2.000000 12 GGCACCTGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICAGGCCACAAA 1.000000 13 GGCGCCCATTTGATGATCATGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 4.000000 14 GGCGCCCATTTGATGATCATGTACGCTGGCCCGCGACCACGDGGCACTGTCTCGIDTGIGATTTTCCICAGACCGCCGA 1.000000 15 GGCGCCCATTTGATGATCATGTCCGCTGACCCAAAGTTCCCDCTTATACCCGCTDDTTDGGCTCCCCICTGACCATCAA 1.000000 16 GGCGCCCATTTGATGATCATGTCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCITAGGCCACAAA 1.000000 17 GGCGCCCGCCTGGATTTCACGTAAAGCCGTACGCGACCACGDGGCACTCCCGCTDDTTDGGCTCTCCICAGGCCACAAA 1.000000 18 GGCGCCCGCCTGGATTTCACGTAAAGCCGTACGCGACCACGDGGCACTGTCTAGIDTGIGATTTTCCICAGACCGCCGA 6.000000 19 GGCGCCCGCCTGGATTTCACGTAAAGCCGTACGCGACCACGDGGCACTGTCTAGIDTGIGATTTTCTICAGACCGCCGA 2.000000 20 GGCGCCCGCCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICAGGCCACAAA 1.000000 21 GGCGCCCGCCTGGATTCCACGTCCGCTGGCCCGCGACCATGDGGCACTGCCGCTDDTTDGGCTCCCCICTGACCATCAA 1.000000 22 GGCGCCCGCCTGGATTCCACGTCCGCTGGCCCGCGACCATGDGGCACTGCCTCTDICTDGGCCCTTCICAGACCACCAG 1.000000 23 GGTGTCCGCCTGGATTCCACGTCCGCTGGCCCGCGACCACGDGGCACTGTCTAGIDTGIGATTTTCCICAGACCGCCGA 1.000000 24 GGTGTCCGCCTGGATTCCACGTCCGCTGGCCCGCGACCATGDGGCACTGCCTCTDICTDGGCCCTTCICAGACCACCAG 2.000000 25 GACACCCGCCTAGATTTCCTATCCGCTGGCCTGCAGCCACCDCTTATACCCGCTDDTTDGGCTCTCCICAGGCCACAAA 1.000000 26 GACGCCCACCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICAGGCCACAAA 3.000000 27 GACGCCCATTTGATGATCATGCAAAGCCGTCCGCGGCCACGIGTCACAGCCGCTDDTTDGGCTCTTCICAGACCACCAG 1.000000 28 GACGCCCATTTGATGATCATGTCCGCTGACCCGCGGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICTGACCATCAA 2.000000 29 GACGCCCATTCGATGATCATGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 6.000000 30 GACGCCCATTCGATGATCATGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCGCCGA 1.000000 31 GACGCCCATTCGATGATCATGTCCGCTGGCCCGAAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICAGACCATCAA 1.000000 32 GACGCCCATTCGATGATCACGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 1.000000 33 GACGCCCATTCGATGATTATGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 3.000000 34 GACGCCCGCCTGGATTTCATGCAAAGCCGTCCGCGGCCACGIGTCACAGCCGCTDDTTDGGCCCTCCICAGACCACCAA 1.000000 35 GACGCCCGCCTGGATTTCATGTCCGCTGGCCCAAAGTTCCCDGGCACTGTCTAGIDTGIGATTTTCCICAGACCGCCGA 1.000000 36 GACGCCCGCCTGGATTTCATGTCCGCTGGCCCGAAGTTCCGDCTTATACCCTCTDDTTDGGCCCTTCICAGACCACCAG 1.000000 37 GACGCCTACCTGGATTTCCTATCCGCTGGCCTGCAGTTCCCDCTTATACCCGCTDDTTDGGCTCTCCICAGGCCACAAA 1.000000 38 GACGCTCATTCGATGATCACGCAAAGCCGTCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 1.000000 39 GACGCTCGCCTGGATTTCATGTCCGCTGGCCCGCGGCCACGICTTATACCCGCTDDTTDGGCTCTCCICAGACCATCAA 1.000000 40 TGCGCCCATTTGATGATCATGCAAGCTGACCCGCGGCCACGIGTCATACCCTCTDICTDGGCCCTTCICAGACCACCAG 1.000000 41 TGCGCCCATTTGATGATCATGTCCGCTGACCCGCGGTTCCCDCTTATACCCGCTDDTTDGGCTCCCCICTGACCATCAA 3.000000 42 TGCGCCCATTTGATGATCATGTCCGCTGACCCGCGGTTCCCDCTTATACCCGCTDDTTDGGCTCCCCDCTGACCATCAA 1.000000 43 TGCGCCCATTTGATGATCATGTCCGCTGACCCGCGGTTCCGDCTTATACCCTCTIDTTDAGTTTTCTDCAAACTATCAA 1.000000 44 TGCGCCCGCCTGGATTTCACGTAAAGCCGTACGCGACCACGDGGCACTGTCTAGIDTGIGATTTTCCICAGACCACCAA 1.000000 45 TGCGCTCATTTGATGATCATGCAAAGCCGTCCGCGGCCACGIGTCACAGCTTCTIICTDGGCCCTTCICAGACCACCAA 1.000000 46 TGCGCTCATTTGATGATCATGTCCGCTGACCCGCGGTTCCGDGTTGCAGCTTCTIDTTDAGTTTTCTDCAGACTACCAG 1.000000 47 TGCGCTCATTTGATGATCATGTCCGCTGACCCGCGGTTCCGDGTTGCAGCTTCTIDTTDAGTTTTCTDCAAATTATCAA 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,16) D002: (38,39) D003: (22,29) D004: (8,13) D005: (15,43) D006: (24,46) D007: (13,45) D008: (21,40) D009: (28,29) D010: (41,41) D011: (3,18) D012: (14,29) D013: (5,13) D014: (3,26) D015: (34,35) D016: (28,44) D033: (2,29) D034: (47,47) D035: (2,13) D036: (24,36) D037: (3,31) D038: (23,27) D039: (41,47) D040: (42,47) E001: (3,29) E002: (18,29) E003: (7,26) E004: (3,3) E005: (11,32) E006: (3,4) E007: (6,18) E008: (2,18) E009: (10,26) E010: (3,18) E011: (9,25) E012: (3,3) E013: (3,18) E014: (3,33) E015: (20,30) E016: (3,19) E017: (3,6) E018: (11,33) E019: (12,37) E020: (3,3) E021: (4,33) E022: (3,3) E023: (17,19) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G G C (A) C C C (G) (C) (C) T G (G) (A) (T) (T) T C (C) T A T C C G C T G A C C C A A A G T T C C G D C T T A T A C C C T C T D D T T D G G C C C T C C I C A G A C C A C C A A G G C (G) C C C (A) (T) (T) T G (A) (T) (G) (A) T C (A) T G T [C] C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I T A G G C C A C A A A 0 D002 G A C G C T C A T T C G A T G A T C A (C) G C A A A G C C G T C C G C G G C C A C G I (G) T (C) A T A C C C (T) C T D (I) (C) T D G G C (C) C T (T) C I C A G A C C A (C) C A (G) G A C G C T C G C C T G G A T T T C A (T) G T C C G C T G G C C C G C G G C C A C G I (C) T (T) A T A C C C (G) C T D (D) (T) T D G G C (T) C T (C) C I C A G A C C A (T) C A (A) 0 D003 G G C G C C C G C C T G G A T T C C A C G T C C G C T G G C C C G C G A C C A T G D G G C A C T G C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G G A C G C C C A T T C G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D004 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C G A C C A C G D G G C A C T C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C A T T T G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D005 (G) G C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C A A A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C C C C I C T G A C C A T C A A (T) G C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C G D C T T A T A C C C T C T I D T T D A G T T T T C T D C A A A C T A [T] C A A 0 D006 G G T G T C C G C C T G G A T T C C A C G T C C G C T G G C C C G C G A C C A T G D G G C A C T G C C T C T D I C T D G G C C C T T C I C A G A C (C) A C C A G T G C G C T C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C G D G T T G C A G C T T C T I D T T D A G T T T T C T D C A G A C (T) A C C A G 0 D007 (G) G C G C (C) C A T T T G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A (G) (T) G C G C (T) C A T T T G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A C A G C T T C T I I C T D G G C C C T T C I C A G A C C A C C A (A) 0 D008 G G C G C C C G C C T G G A T T C C A C G T C C G C T G G C C C G C G A C C A T G D G G C A C T G C C G C T D D T T D G G C T C C C C I C T G A C C A T C A A T G C G C C C A T T T G A T G A T C A T G C A A G C T G A C C C G C G G [C] [C] [A] C [G] [I] G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D009 G A C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C T G A C C A T C A A G A C G C C C A T T C G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D010 T G C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C C D C T T A T A C C C G C T D D T T D G G C T C C C C I C T G A C C A T C A A T G C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C C D C T T A T A C C C G C T D D T T D G G C T C C C C I C T G A C C A T C A A 0 D011 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A 0 D012 G (G) C G C C C A T T (T) G A T G A T C A T G T A C G C T G G C C C G C G A C C A C G D G G C A C T G T C T C G I D T G I G A T T T T C C I C A G A C C G C C G A G (A) C G C C C A T T (C) G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D013 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D I C T D G G C C C T T C I C A G A C C A C C A G G G C G C C C A T T T G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D014 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G A C G C C C A C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 D015 G A C G C C C G C C T G G A T T T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A C A G C C G C T D D T T D G G C C C T C C I C A G A C C A C C A A G A C G C C C G C C T G G A T T T C A T G T C C G C T G G C C C A A A G T T C C C D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A 0 D016 (G) A C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C T G A C C A T C A A (T) G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C A C C A A 0 D033 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A G A C G C C C A T T C G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D034 T G C G C T C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C G D G T T G C A G C T T C T I D T T D A G T T T T C T D C A A A T T A [T] C A A T G C G C T C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C G D G T T G C A G C T T C T I D T T D A G T T T T C T D C A A A T T A [T] C A A 0 D035 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A G G C G C C C A T T T G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 D036 G G T G T C C G C C T G G A T T C C A C G T C C G C T G G C C C G C G A C C A T G D G G C A C T G C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G G A C G C C C G C C T G G A T T T C A T G T C C G C T G G C C C G A A G T T C C G D C T T A T A C C C T C T D D T T D G G C C C T T C I C A G A C C A C C A G 0 D037 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G (G) C C A (C) (A) A A G A C G C C C A T T C G A T G A T C A T G T C C G C T G G C C C G A A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G (A) C C A (T) (C) A A 0 D038 G G T G T C C G C C T G G A T T C C A C G T C C G C T G G C C C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A G A C G C C C A T T T G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A C A G C [C] G C T D D T T D G G C T C T T C I C A G A C C A C C A G 0 D039 T G C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C C D C T T A T A C C C G C T D D T T D G G C T C C C C I C T G A C C A T C A A T G C G C T C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C G D G T T G C A G C T T C T I D T T D A G T T T T C T D C A A A T T A [T] C A A 0 D040 T G C G C C C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C C D C T T A T A C C C G C T D D T T D G G C T C C C C D C T G A C C A T C A A T G C G C T C A T T T G A T G A T C A T G T C C G C T G A C C C G C G G T T C C G D G T T G C A G C T T C T I D T T D A G T T T T C T D C A A A T T A [T] C A A 0 E001 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G A C G C C C A T T C G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 E002 G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A G A C G C C C A T T C G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 E003 G (G) C (A) C C C (G) C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C T A G I D T G I G A T T T T C C I C A G A C C G C C G A G (A) C (G) C C C (A) C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E004 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E005 G G C A C C C G C C T A G A T T T C C (T) A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G G A C G C C C A T T C G A T G A T C A (C) G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 E006 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I T A G G C C A C A A A 0 E007 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C T C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A 0 E008 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A 0 E009 G (G) C (A) C C C (G) C C T G G A T T T C C T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G G (A) C (G) C C C (A) C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E010 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A 0 E011 G (G) C A C C C G C C T (G) G A T T T C C T A T C C G C (C) (C) G (T) (A) (C) G C (G) (A) C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C A A G (A) C A C C C G C C T (A) G A T T T C C T A T C C G C (T) (G) G (C) (C) (T) G C (A) (G) C C A C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E012 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E013 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C C I C A G A C C G C C G A 0 E014 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G A C G C C C A T T C G A T G A T T A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 E015 G [G] C G C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G A C G C C C A T T C G A T G A T C A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C [G] C C G A 0 E016 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T A G I D T G I G A T T T T C T I C A G A C C G C C G A 0 E017 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C T C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E018 G G C A C C C G C C T A G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G G A C G C C C A T T C G A T G A T T A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 E019 G G C A C C T G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G A C G C C T A C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E020 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E021 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I T A G G C C A C A A A G A C G C C C A T T C G A T G A T T A T G C A A A G C C G T C C G C G G C C A C G I G T C A T A C C C T C T D I C T D G G C C C T T C I C A G A C C A C C A G 0 E022 G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C A C C C G C C T G G A T T T C C T A T C C G C T G G C C T G C A G T T C C C D C T T A T A C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A 0 E023 G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T C C C G C T D D T T D G G C T C T C C I C A G G C C A C A A A G G C G C C C G C C T G G A T T T C A C G T A A A G C C G T A C G C G A C C A C G D G G C A C T G T C T [A] G I D T G I G A T T T T C T I C A G A C C G C C G A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 D001 = = = (A) = = = (G) (C) (C) = = (G) (A) (T) (T) = = (C) = A ? ? ? = = = = A = = C A A = ? = = = = G = = = = = = = = = = T = = = = = = = = = = C ? = = = = C = = ? ? ? = = C = = = = = (G) = = = (A) (T) (T) = = (A) (T) (G) (A) = = (A) = G ? ? ? = = = = G = = T G C = ? = = = = C = = = = = = = = = = G = = = = = = = = = = T ? = = = = T = = ? ? ? = = A = = 0 D002 = = = = = = = A T T C = A T G A = = = (C) = C A A A G C C = T = = = = = = = = = = = = (G) = (C) = = = = = = (T) = = = (I) (C) = = = = = (C) = = (T) = = = = = = = = = (C) = = (G) = = = = = = = G C C T = G A T T = = = (T) = T C C G C T G = C = = = = = = = = = = = = (C) = (T) = = = = = = (G) = = = (D) (T) = = = = = (T) = = (C) = = = = = = = = = (T) = = (A) 0 D003 = G = = = = = G C C T = G A T T C = = C = T C C G C T G = C = = = = = A = = = T = D = G = = C T G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = A T T C = A T G A T = = T = C A A A G C C = T = = = = = G = = = C = I = T = = T A C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D004 = = = A = = = G C C = = G A T T = = C = A T C C G C T G = C = T = = = A = = = = = D = G = = C T = = = G = = = D T = = = = = T = = C = = = = = G = = = = A = A = = = G = = = A T T = = A T G A = = A = G C A A A G C C = T = C = = = G = = = = = I = T = = T A = = = T = = = I C = = = = = C = = T = = = = = A = = = = C = G 0 D005 (G) = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = A A A = = = = = C = ? ? ? ? = = = = = G = = D = = = = G = C = C C = C I = T G = = C ? ? = = = (T) = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = G C G = = = = = G = ? ? ? ? = = = = = T = = I = = = = A = T = T T = T D = A A = = T ? ? = = = 0 D006 G = T = T C = G C C = = G A T T C = = C = = = = = = = = G = = = = = = A C C A T = = = G C A = T = = C = = = D I C = = G = C C C = T C I = = = = = (C) ? ? = = = T = C = C T = A T T = = A T G A T = = T = = = = = = = = A = = = = = = G T T C C = = = T T G = A = = T = = = I D T = = A = T T T = C T D = = = = = (T) ? ? = = = 0 D007 (G) = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C = C = = = D = = = = = = = = = = = = = = = = = = = = = = = (G) (T) = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = G = T = = = I = = = = = = = = = = = = = = = = = = = = = = = (A) 0 D008 G = = = = = = G C C = = G A T T C = = C = T C C = = = = G = = = = = = A ? ? ? ? ? ? = ? = = C T G = = G = = = D T = = = = = T = C C = = = T = = = = = T = = A T = = = = = = A T T = = A T G A T = = T = C A A = = = = A = = = = = = G ? ? ? ? ? ? = ? = = T A C = = T = = = I C = = = = = C = T T = = = A = = = = = C = = G 0 D009 = = = = = = = = = = T = = = = = = = = = = T C C G C T G A C = ? = = = = T T C = C D C = T = = = = = = G = = = D T = = = = = T = = C = = = T = = = = = T = = A = = = = = = = = = = C = = = = = = = = = = C A A A G C C G T = ? = = = = C C A = G I G = C = = = = = = T = = = I C = = = = = C = = T = = = A = = = = = C = = G 0 D010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D011 = = = A = = = = = = = = = = = = = = C T A = C C G C T G = C C T = = A G T T C = C = C T T = T A C C = G C T D = = T D = G C = C = = = = = = = G = = A = A ? ? = = = G = = = = = = = = = = = = = = A C G = A A A G C C = T A C = = G A C C A = G = G G C = C T G T = T A G I = = G I = A T = T = = = = = = = A = = G = C ? ? 0 D012 = (G) = = = = = = = = (T) = = = = = ? ? = = = T = C G C T G = C = = = = = A ? ? ? ? ? ? = G = = C T G T = = = G I D ? ? I = A ? T T = C = = = = = = = = G = = G A = (A) = = = = = = = = (C) = = = = = ? ? = = = C = A A G C C = T = = = = = G ? ? ? ? ? ? = T = = T A C C = = = T D I ? ? D = G ? C C = T = = = = = = = = A = = A G 0 D013 = = = A = = = G C C = = G A T T = = C = A T C C G C T G = C = T = = A = T T C = C D C = T = ? ? = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = A T T = = A T G A = = A = G C A A A G C C = T = C = = G = C C A = G I G = C = ? ? = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D014 = G = A = = = G = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = A = G = = = A = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = 0 D015 = = = = = = = = = = = = = = = = = = = = = C A A A G C C = T = = G C G = C C A = G I = T = = = A = C = G C T D = = T D = G C C C = = = = = = = = = = A = = A = = = = = = = = = = = = = = = = = = = = = = T C C G C T G = C = = A A A = T T C = C D = G = = = T = T = T A G I = = G I = A T T T = = = = = = = = = = G = = G = 0 D016 (G) A = = = = = A T T = = A T G A = = = T = = C ? G C T G A C C ? = = = G T T C = C = C T T = T A C ? ? ? ? ? ? = = T D = G C = C = = = = = T = = = = = T = = = (T) G = = = = = G C C = = G A T T = = = C = = A ? A G C C G T A ? = = = A C C A = G = G G C = C T G ? ? ? ? ? ? = = G I = A T = T = = = = = A = = = = = C = = = 0 D033 = G = A = = = G C C T = G A T T = = C = A T C C G C T G = C = = = = = A = = = = = D ? ? ? ? C T G T = = A G I D ? ? I = A T T T = C = = = = = = = = G = = G A = A = G = = = A T T C = A T G A = = A = G C A A A G C C = T = = = = = G = = = = = I ? ? ? ? T A C C = = C T D I ? ? D = G C C C = T = = = = = = = = A = = A G 0 D034 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = 0 D035 = = = A = = = G C C = = G A T T = = C = A T C C G C T G = C = = = = = A ? ? ? ? ? ? = G = = C T G T = = A G I D ? ? I = A T T T = C = = = = = = = = G = = G A = = = G = = = A T T = = A T G A = = A = G C A A A G C C = T = = = = = G ? ? ? ? ? ? = T = = T A C C = = C T D I ? ? D = G C C C = T = = = = = = = = A = = A G 0 D036 = G T = T = = = = = = = = = = = C = = C = = = = = = = = = = = = = C G A C C A T = = G G C = C T G = = = = = = I C = = = = = = = = = = = = = = = = = = = = = = = A C = C = = = = = = = = = = = T = = T = = = = = = = = = = = = = A A G T T C C = = C T T = T A C = = = = = = D T = = = = = = = = = = = = = = = = = = = = = = 0 D037 = G = A = = = G C C T = G A T T = = C = A = = = = = = = = = = T = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = (C) (A) = = = A = G = = = A T T C = A T G A = = A = G = = = = = = = = = = C = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = (T) (C) = = 0 D038 ? G T = T = = G C C = = G A T T C = = C = T C C G C T G = C = = = = = A = = = = = D = G = = = T = ? ? ? ? ? ? = = G I = A T = T = C = = = = = = = = G = = G A ? A C = C = = A T T = = A T G A T = = T = C A A A G C C = T = = = = = G = = = = = I = T = = = A = ? ? ? ? ? ? = = T D = G C = C = T = = = = = = = = A = = A G 0 D039 = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? C = = A T = C = C G = = D = = = = G = C = C C = C I = T G = C C ? ? = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? G = = G C = G = T T = = I = = = = A = T = T T = T D = A A = T T ? ? = = = 0 D040 = = = = = C = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = C = C = = A T = C ? ? ? ? ? ? = = = = G = C = C C = C = = T G = C C ? ? = = = = = = = = T = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = G = G = = G C = G ? ? ? ? ? ? = = = = A = T = T T = T = = A A = T T ? ? = = = 0 E001 = G = A = = = G C C T = G A T T = = C = A T C C G C T G = C = T = = A = T T C = C D C = T = = = = = = G = = = D T = = = = = T = = C = = = = = G = = = = A = A = A = G = = = A T T C = A T G A = = A = G C A A A G C C = T = C = = G = C C A = G I G = C = = = = = = T = = = I C = = = = = C = = T = = = = = A = = = = C = G 0 E002 ? G = = = = = G C C T = G A T T = = = C = T = = = = = = = = A = = = = A = = = = = D = G = = C T G T = = A G I D ? ? I = A T T T = C = = = = = = = = G = = G A ? A = = = = = A T T C = A T G A = = = T = C = = = = = = = = C = = = = G = = = = = I = T = = T A C C = = C T D I ? ? D = G C C C = T = = = = = = = = A = = A G 0 E003 = (G) = (A) = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A G I = = G I = A T = T = = = = = = = A = = G = C G = = (A) = (G) = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C T D = = T D = G C = C = = = = = = = G = = A = A A = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 = ? = A = = = G C C T A G A T T = = C (T) ? T C C G C T G = C = T = = A = T T C = C D C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = G = = = A T T C G A T G A = = A (C) ? C A A A G C C = T = C = = G = C C A = G I G = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 E007 ? = = A = = = = = = = = = = = = = = C T A = C C G C T G = C C T = = A G ? ? ? ? ? ? ? ? ? ? T A C C = = C T D = = T D = G C = C = = = = = = = G = = A = A A = ? = = G = = = = = = = = = = = = = = A C G = A A A G C C = T A C = = G A ? ? ? ? ? ? ? ? ? ? C T G T = = A G I = = G I = A T = T = = = = = = = A = = G = C G = 0 E008 = = = A ? ? ? = = = = = = = = = = = C T A = C C G C T G = C C = = = = = = = = = = = ? ? ? ? = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = G ? ? ? = = = = = = = = = = = A C G = A A A G C C = T A = = = = = = = = = = = ? ? ? ? = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = (G) = (A) ? ? ? (G) = = = = = = = = = = = = G C A A A G C C = T = C = = G = C C A = G I G = C = = = = = = T = = = I C = = = = = C = = T = = = = = A = = = = C = G = (A) = (G) ? ? ? (A) = = = = = = = = = = = = A T C C G C T G = C = T = = A = T T C = C D C = T = = = = = = G = = = D T = = = = = T = = C = = = = = G = = = = A = A 0 E010 = = = ? ? ? ? = = = = = = = = = = = C T A = C C G C T G = C C T = = A G T T C = C = C T T = T A C C = G C T D = = T D = G C = C = = = = = = = G = = A = A A = = = = ? ? ? ? = = = = = = = = = = = A C G = A A A G C C = T A C = = G A C C A = G = G G C = C T G T = T A G I = = G I = A T = T = = = = = = = A = = G = C G = 0 E011 = (G) = = = = = = = = = (G) = = = = = = = = = = = = = = (C) (C) = (T) (A) (C) = = (G) (A) = = = = G = G G C = C T G T = T A G I = = G I = A T = T = = = = = = = ? ? ? G = C = = = (A) = = = = = = = = = (A) = = = = = = = = = = = = = = (T) (G) = (C) (C) (T) = = (A) (G) = = = = C = C T T = T A C C = G C T D = = T D = G C = C = = = = = = = ? ? ? A = A = = 0 E012 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = A = = = = = = = = = = = = = = C T A = C C G C T G = C C T = = A G T T C = C = C T T = T A C C = G C T D = = T D = G C = C = = = = = = = G = = ? ? A ? ? = = = G = = = = = = = = = = = = = = A C G = A A A G C C = T A C = = G A C C A = G = G G C = C T G T = T A G I = = G I = A T = T = = = = = = = A = = ? ? C ? ? 0 E014 = G = ? = = = G C C T = G A T T = C C = A T C C G C T G = C = T = = A = T T C = C D ? ? ? ? = = = = = G = = = D T = = = = = T = = C = = = = = G = = = = A = A = A = ? = = = A T T C = A T G A = T A = G C A A A G C C = T = C = = G = C C A = G I ? ? ? ? = = = = = T = = = I C = = = = = C = = T = = = = = A = = = = C = G 0 E015 ? ? ? = = = = G C C T = G A T T = = C = A T C C G C T G = C = ? = = A = T T C = C D C = T = = = = = = G = = = D T = = = = = T = = C = = = = = G = = ? ? A A = ? ? ? = = = = A T T C = A T G A = = A = G C A A A G C C = T = ? = = G = C C A = G I G = C = = = = = = T = = = I C = = = = = C = = T = = = = = A = = ? ? C G = 0 E016 ? ? ? ? ? ? ? = = = = = = = = = = = C T A = C C G C T G = C C T = = A G T T C = C = ? ? ? ? T A C ? ? ? ? ? ? = = T D = G C = C = = C = = = = G = = A = A A = ? ? ? ? ? ? ? = = = = = = = = = = = A C G = A A A G C C = T A C = = G A C C A = G = ? ? ? ? C T G ? ? ? ? ? ? = = G I = A T = T = = T = = = = A = = G = C G = 0 E017 = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = ? = = 0 E018 = G = A = = = G C C T A G A T T = C C = A T C C G C T G = C = T = = A = T T C = C D C = T = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = A = G = = = A T T C G A T G A = T A = G C A A A G C C = T = C = = G = C C A = G I G = C = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 E019 = G = A = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? = = = = A = G = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? = = = 0 E020 = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = 0 E021 = G = A ? ? ? G C C T = G A T T = C C = A T C C G C T G = C = T = = A = T T C = C D C = T = = = = = = G = = = D T = = = = = T = = C = = T = = G = = = = A = A = A = G ? ? ? A T T C = A T G A = T A = G C A A A G C C = T = C = = G = C C A = G I G = C = = = = = = T = = = I C = = = = = C = = T = = C = = A = = = = C = G 0 E022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E023 = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = C ? ? ? ? ? ? = = T D = G C = C = = C = = = = G = = A = A A = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = G ? ? ? ? ? ? = = G I = A T = T = = T = = = = A = = G = C G = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = 0.89 = = = 0.89 0.89 0.89 = = 0.89 0.89 0.89 0.89 = = 0.89 = 1.00 ? ? ? = = = = 1.00 = = 1.00 1.00 1.00 = ? = = = = 1.00 = = = = = = = = = = 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 = 0.99 0.99 0.99 0.99 0.99 0.99 0.99 = 0.99 = = = = = = = = = = = = 0.53 = 0.53 = = = = = = 0.53 = = = 0.53 0.53 = = = = = 0.53 = = 0.53 = = = = = = = = = 0.53 = = 0.53 = 0.99 = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 0.87 = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = = = 1.00 = ? ? ? ? = = = = = 1.00 = = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 ? ? = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = 0.55 ? ? = = = 0.69 = = = = 0.69 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 0.51 1.00 = = = = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = = = = = 1.00 ? ? ? ? ? ? = ? = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = = 1.00 = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = ? = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = 1.00 = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = 1.00 = 1.00 ? ? = 0.62 = = = = = = = = 0.63 = = = = = ? ? = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 ? ? ? ? ? ? = 1.00 = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 ? ? 1.00 = 1.00 ? 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 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 = = 0.90 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = 1.00 = 0.99 = 0.99 0.99 0.99 0.99 = = 0.99 0.99 = 0.99 0.99 0.99 0.99 = = = = = = = = = = 0.98 = = 0.98 = 0.74 0.97 = = = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 ? ? ? ? ? ? = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = 1.00 ? ? ? ? 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 ? ? 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 ? ? ? ? ? ? = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 ? ? 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = 1.00 0.99 = 0.99 = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 = = = 0.58 0.58 = = ? 0.97 1.00 = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = 1.00 = 1.00 = = = 1.00 = ? ? ? ? ? ? = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 ? ? = = = = = = = = 1.00 = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 ? ? ? ? ? ? = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 ? ? = = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 ? 1.00 = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = = = = = = 1.00 = = = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 ? ? 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = 0.56 = 0.56 = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 1.00 = = = 1.00 1.00 1.00 1.00 0.97 1.00 1.00 1.00 1.00 = = 1.00 0.58 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = ? = = 0.99 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 ? ? ? ? ? ? ? ? ? ? 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 ? ? ? = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = ? ? ? ? = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 0.57 = 0.57 ? ? ? 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 = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 = = = ? ? ? ? = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 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 = = = = = = = = = 0.52 = = = = = = = = = = = = = = 0.82 0.82 = 0.82 0.82 0.82 = = 0.82 0.82 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = ? ? ? 1.00 = 1.00 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = ? ? 1.00 ? ? = 1.00 = ? = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 0.99 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 ? ? ? ? = = = = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 ? ? ? = = = = 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 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = 1.00 = = ? ? 1.00 1.00 = ? ? ? ? ? ? ? = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? ? ? ? 1.00 1.00 1.00 ? ? ? ? ? ? = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 = = 1.00 = 1.00 1.00 = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0.99 = 1.00 = = = 1.00 1.00 1.00 1.00 0.93 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = 1.00 = 1.00 ? ? ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 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 = = 1.00 = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 1.00 ? ? ? ? ? ? = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 = = 1.00 = 1.00 1.00 = END PHASEPROBS