List of haplotypes found in best reconstruction, with frequencies in parentheses. 1: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T T G T (2) 2: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t G C A T A T G C G T T A G T C A D C C G T T C A G A t G A C C A A T C C G C T A G C G A A C G C T G A C G T G T T A G C G G T (1) 3: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T C T G T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T C G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G T (1) 4: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G T A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G C (1) 5: C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C G T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G T T A G C G A A C G C T G A C G C A T C A G T T G C (1) 6: C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G T T A G C G A A C G C T G A C G C A T C A G T T G C (1) 7: C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G C T A G C G A A C G C T G A C G T G T T G G T T G T (1) 8: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I C T G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T G G T (1) 9: T G T C T T A G A T T C G T C G A C T T A T A G A G G T C C C G A C C G C T G C A G C C G C C D G G T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C C G G C I T C G t A C A T A C G C G T T G G T C A D C C G T T C A G A t G A C C A A T T C A C C G A T A A A C G C T G A C G T G T T G G T T G C (1) 10: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C G C T A G C G G G C G C C G A C G T G T T G G T G G T (2) 11: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G C (4) 12: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T (4) 13: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C A C C G A T A A A C G C T G A C G T G T T G G T G G T (2) 14: C T T C C T A A G T T T A T C G A G C T G T G A G G G C C C C G C A T G C T G A A G C C G T C D G G T C I G T G A A A C C C G C A C G G T G A T C G G A A C A C C A C G C I T T D t A T A C A T G C C C T G G T C A I T C G T T C G T G t A A C C A C T T C A C T G G C G A G G G C T G A C G C G T T A G T T G T (1) 15: T G C C T C G G A A C C G C T G G C T T G C A G A A A T C T T A A C T A T C A C G G T C G C C D G G T T I G T A T A A T T T G T G T C C C G A T C G G D A C A C C C G A C I T T D t A C A T G T C T G T C G G T T A I C C G T G G A G A t G G C G C A T T C G C C A A C A G A C G C C G A C G T G T C G G T G G T (1) 16: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G T G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T (1) 17: C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G C T A G C G A A C G C T G A C G C A T C A G T T G C (1) 18: T G T C T T A G A T T C G T C G A C T T A T A G A G G T C C C G A C C G C T G C A G C C G C C D G G T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C C G G C I T C G t A C A T A C G C G T C G G T C A D C C G T T C A G A t G A C C A A T T C A C C G A T A A A C G C T G A C G C G T T G G T T G T (1) 19: T G C C T C G G A A C C G C T G G C T T G C A G A A A T C T T A A C T A T C A C G G T C G C C D G G T T I G T A T A A T T T G T G T C C C G A T C G G D A C A C C C G A C I T T D t A C A T G T C T G T C G G T T A I C C G T G G A G A t G G C G C A T T C G C T A G C G A A C G C T G A C G T A T C G G T G G C (1) 20: C T T C C T A A G T T T A T C G A G C T G T G A G G G C C C C G C A T G C T G A A G C C G T C D G G T C I G T G A A A C C C G C A C G G T G A T C G G A A C A C C A C G C I T T D t A T A C A T G C C C T G G T C A I T C G T T C G T G t A A C C A A T T C G T T A G C G A G G G C T G A C G C G T T A G T T G C (1) 21: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C G G G t G A T C A C T T C A C C G A T A G G C G C C G A C G C G T T G C T T G C (2) 22: C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G A G A t G G C G C A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G T (1) 23: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C C C A C I T T G t A T A C G T C T C C C G G T C A I C T G T G C G T G D G A T G C A T C C G C T A G C A G G C A T C C G C G T G C T G G T G G T (1) 24: T G T C T T A G A T T C G T C G A C T T A T A G A G G T C C C G A C C G C T G C A G C C G C C D G G T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C C G G C I T C G t A C A T A C G C G T C G G T C A D C C G T T C A G A t G A C C A A T T C A C C G A C A A A C G C T G A C G C A T C A G T T G C (1) 25: C T C C C C G A G A C T G T C G A C C T G T A G A G G T C C C G A C T A C T G C A G C C G C C D G G T C I G T G T A A T T C G T G C C C C G A T C G G D A C A C C C C A C I T T D t A T A C G T C C C C T G G T C A I C C G T G G G G G t G G C G C C T T C A C C G A C G G G C G C C G A C G C G T C A G T T G T (1) 26: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C G D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T (1) 27: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T G C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C G D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T C A G T T G T (1) 28: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C C C A C I T T G t A T A C G T C T C C C G G T C A I C T G T G C G G G D G A T G C A T C C G C T A G C A G G C A T C C G C G T G C T G G T G G T (1) 29: T G T C T T A G A T T C A C T G G G T T G C G A A G A C C T T G C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I C T D t A C A T A T G C G T T G G T T A I T C G T T G A T A t A G C C A A T T C G C T A G C G A A G G C T G A C G C G T T G G T T G T (1) 30: C T C C C T G A G A C T A T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T T A T T T I A C G A A A T C C G C A T G C C A G T T G G A C C G T C C C A C I C T G t A T A C G T C T C C C G G T C G I C C G T T G G G G t G G C G C A T T C G T T A G T G A A C G C T G A C G C G T C A G T T G T (2) 31: T G T C T T A G A T T C G C T G G G T T G C G A G A A C C T T G C A T G T C A A G G T C A C C D A T T C D G T G T G A C T T C T G C C G T G A T C G A D A T A C C A G G C I T C D t A C A T A T G C G T T A G T C A D C C A T G C A G A t G A T C A C T T C A C C G A C A G G C G C C G A C G T A T T G G T T G T (1) 32: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T G C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C G C T A G C G G G C G C C G A C G T G T T G G T G G T (1) 33: T G T C T T A G A T T C G C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C D A T T C D G T G T G A C T T C T G C C G T G A T C G A D A T A C C A G G C I T C D t A C A T A T G C G T T A G T C A D C C A T G C A G A t G A T C A C T T C A C C G A C A G G C G C C G A C G T A T T G G T T G T (1) 34: T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C C C A C I C T G t A T A C G T C T C C C G G T C A I C T G T G C G G G D G A T G C A T C C G T T A G C A G G C A T C C G C G C A C T A G T T G T (1) 35: T G T C T T A G A T T C A C T G G G T T G C G A A A A C C T T G C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I C T D t A C A T A T G C G T T G G T T A I T C G T T G A T A t A G C C A A T T C G C T A G C G A A G G C T G A C G C G T T G G T T G T (1) Summary of best reconstruction (numbers refer to the list of haplotypes given above) E001: (1,2) E002: (3,4) E003: (5,6) E004: (7,8) E005: (9,10) E006: (11,11) E007: (1,12) E008: (10,13) E009: (12,12) E010: (11,11) E011: (14,15) E012: (16,12) E013: (17,18) E014: (19,20) E015: (21,22) E016: (23,21) E017: (24,25) E018: (26,27) E019: (28,29) E020: (30,31) E021: (32,13) E022: (30,33) E023: (34,35) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: E001 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t (A) C A T A T G C G T T (G) G T (T) A (I) (T) C G T T C A (T) A t (A) A C C A A T (T) C G C T A G C G A A C G C T G A C G T G T T (G) G (T) (T) G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t (G) C A T A T G C G T T (A) G T (C) A (D) (C) C G T T C A (G) A t (G) A C C A A T (C) C G C T A G C G A A C G C T G A C G T G T T (A) G (C) (G) G T E002 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T (C) T (G) T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T (C) G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G (T) T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T (G) T (A) T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T (T) G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G (C) E003 C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C G T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G T T A G C G A A C G C T G A C G C A T C A G T T G C C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G T T A G C G A A C G C T G A C G C A T C A G T T G C E004 C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G (G) G (G) t G G C G C (A) T T C (G) C (T) (A) (G) (C) (G) (A) (A) C G C (T) G A C G T G T T G G T (T) G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I C T G t A C A T A T G C G T T G G T T A I T C G T T C (A) T (A) t A A C C A (C) T T C (A) C (C) (G) (A) (T) (A) (G) (G) C G C (C) G A C G T G T T G G T (G) G T E005 T G T C T T A G A T T C G T C G A C T T A T A G A G G T C C C G A C C G C T G C A G C C G C C D G G T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C C G G C I T C G t A C A T A C G C G T T G G T C A D C C G T T C A G A t G A C C A A T T C A C C G A (T) (A) A A C G C T G A C G T G T T G G T T G (C) T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C G C T A G (C) (G) G G C G C C G A C G T G T T G G T G G (T) E006 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G C T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G C E007 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T T G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T E008 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C (G) C (T) (A) (G) (C) (G) G G C G C C G A C G T G T T G G T G G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C (A) C (C) (G) (A) (T) (A) A A C G C T G A C G T G T T G G T G G T E009 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T E010 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G C T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C G C T A G C G A A C G C T G A C G T G T T G G T G G C E011 (C) (T) (T) C C (T) (A) A (G) T T T A T C G A (G) C T G T G A (G) G G (C) C C C G C A T (G) (C) (T) (G) A (A) G C C G (T) C D G G T (C) I G T (G) (A) A A (C) C (C) G C A (C) (G) (G) (T) G A T C G G [(A)] A C A C C (A) C G C I T T D t A (T) A C A T G [(C)] (C) [(C)] (T) G G T (C) A I (T) C G T T C (G) (T) G t A A C (C) A (C) T T C (A) C (T) (G) (G) C (G) (A) [(G)] [(G)] G C (T) G A C G C G T T A G T (T) G T (T) (G) (C) C T (C) (G) G (A) A C C G C T G G (C) T T G C A G (A) A A (T) C T T A A C T (A) (T) (C) (A) C (G) G T C G (C) C D G G T (T) I G T (A) (T) A A (T) T (T) G T G (T) (C) (C) (C) G A T C G G [(D)] A C A C C (C) G A C I T T D t A (C) A T G T C [(T)] (G) [(T)] (C) G G T (T) A I (C) C G T G G (A) (G) A t G G C (G) C (A) T T C (G) C (C) (A) (A) C (A) (G) [(A)] [(C)] G C (C) G A C G T G T C G G T (G) G T E012 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G T G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T T G G T T G T E013 C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C [A] T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G G G G t G G C G C A T T C G C T A G C G A A C G C T G A C G C A T C A G T T G (C) T G T C T T A G A T T C G T C G A C T T A T A G A G G T C C C G A C C G C T G C A G C C G C C D G G T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C C G G C I T C G t A C A T A C G C G T C G G T C A D C C G T T C A G A t G A C C A A T T C A C C G A [T] [A] A A C G C T G A C G C G T T G G T T G (T) E014 (T) (G) (C) C T (C) (G) G (A) A C C G C T G G (C) T T G C A G (A) A A (T) C T T A A C T (A) (T) (C) (A) C (G) G T C G (C) C D G G T (T) I G T (A) (T) A A (T) T (T) G T G (T) (C) (C) (C) G A T C G G [(D)] A C A C C (C) G A C I T T D t A (C) A T G T C [(T)] (G) [(T)] (C) G G T (T) A I (C) C G T G G (A) (G) A t G G C (G) C A T T C G (C) T A G C G A [(A)] [(C)] G C T G A C G T (A) T C G G T (G) G C (C) (T) (T) C C (T) (A) A (G) T T T A T C G A (G) C T G T G A (G) G G (C) C C C G C A T (G) (C) (T) (G) A (A) G C C G (T) C D G G T (C) I G T (G) (A) A A (C) C (C) G C A (C) (G) (G) (T) G A T C G G [(A)] A C A C C (A) C G C I T T D t A (T) A C A T G [(C)] (C) [(C)] (T) G G T (C) A I (T) C G T T C (G) (T) G t A A C (C) A A T T C G (T) T A G C G A [(G)] [(G)] G C T G A C G C (G) T T A G T (T) G C E015 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G [G] C I T C G t A C A T A T G [C] G [T] [T] A G T C A D C C A T T C (G) G (G) t G A T C A (C) T T C A C C G A T A (G) (G) C [G] C (C) G A C G (C) G T T G (C) T (T) G (C) C T C C C T G A G A C T G T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T D A T T T D A C G A G A C C T G C A T G G T A G T T G A A C C G T C C C A C I C T D t A T G C G T C T C C C G G C C A I C C G T G G (A) G (A) t G G C G C (A) T T C G C T A G [C] G (A) (A) C G C (T) G A C G (T) G T T G (G) T (G) G (T) E016 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C C (C) (A) C I T T [G] t A T A C G T C [(T)] C (C) (C) G G T C A I C T G T G C G [T] G D [G] [A] [T] [G] [C] A T C C G C T A G C A G G C [(A)] T C C G C G (T) G C T G G T (G) G (T) T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A (G) (G) C I T C G t A C A T A T G [(C)] G (T) (T) A G T C A D C C A T T C G G G t G A T C A C T T C A C C G A T A G G C [(G)] C C G A C G (C) G T T G C T (T) G (C) E017 (T) (G) (T) C (T) (T) (A) (G) (A) (T) (T) (C) G T C G A C (T) T (A) T A G A G G T C C C G A C (C) (G) C T G C A G C C G C C D G G T C I G T G T A A T T C (C) T G C C C C G A T C G G D A (T) A C C C (G) (G) C I T (C) (G) t A (C) A (T) (A) (C) (G) C (G) (T) (C) G G T C A (D) C C G T (T) (C) (A) G (A) t G (A) C (C) (A) (A) T T C A C C G A C (A) (A) (A) C G C (T) G A C G C (A) T C A G T T G (C) (C) (T) (C) C (C) (C) (G) (A) (G) (A) (C) (T) G T C G A C (C) T (G) T A G A G G T C C C G A C (T) (A) C T G C A G C C G C C D G G T C I G T G T A A T T C (G) T [G] C C C [C] G A T C G G D A (C) A C C C (C) (A) C I T (T) (D) t A (T) A (C) (G) (T) (C) [C] (C) (C) (T) G G T C A (I) C C G T (G) (G) (G) G (G) t G (G) C (G) (C) (C) T T C A C C G A C (G) (G) (G) [C] G C (C) G A C G C (G) T C A G T T G (T) E018 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T (A) C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G [C] G T T A G T C G D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T (T) (G) G T T G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T (G) C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G [C] G T T A G T C G D C C A T T C A G A t G A T C A C T T C A C C G A T A G G C G C C G A C G T G T (C) (A) G T T G T E019 T G T C T T A G A T T C A C T G G G T T G C G A (G) (A) A C C T T (A) C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C C [C] [(A)] C I (T) T (G) t A T A C G T C [(T)] [C] [(C)] (C) G G T C A I C T G T G (C) G [(G)] G D [(G)] [(A)] [(T)] [(G)] [(C)] A T C C G C T A G C A G G (C) (A) T C C G C G (T) G C T G G T (G) G T T G T C T T A G A T T C A C T G G G T T G C G A (A) (G) A C C T T (G) C A T G T C A A G G T C G T C [D] G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A [G] [(G)] C I (C) T (D) t A C A T A T G [(C)] [G] [(T)] (T) G G T T A I T C G T T (G) [A] [(T)] A t [(A)] [(G)] [(C)] [(C)] [(A)] A T T C G C T A G C G A A (G) (G) C T G A C G (C) G T T G G T (T) G T E020 C T C C C T G A G A C T A T C G A C T C G T A A A G G T G C C (A) A C C G C T G A A G C C G C T T A T T T (I) A C G (A) (A) A (T) (C) (C) G C A T G (C) C A G T T G G [(A)] (C) C G T C C C A C I C T [(G)] t A T A C G T C (T) (C) (C) C G G T C G I C C G T T G G G G t G G C G C A T T C G T T A G T G A A C G C T G A C G C G T C A G T T G T T G T C T T A G A T T C G C T G G G T T G C G A G A A C C T T (G) C A T G T C A A G G T C A C C D A T T C (D) G T G (T) (G) A (C) (T) (T) C T G C C (G) T G A T C G A [(D)] (A) T A C C A G G C I T C [(D)] t A C A T A T G (C) (G) (T) T A G T C A D C C A T G C A G A t G A T C A C T T C A C C G A C A G G C G C C G A C G T A T T G G T T G T E021 T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T (G) C A T G T C A A G G T C A C C T A T T C I G T G T A A T T C C T G C C C C G A T C G G D A T A C C A G G C I T C G t A C A T A T G C G T T A G T C A D C C A T T C A G A t G A T C A C T T C (G) C (T) (A) (G) (C) (G) G G C G C C G A C G T G T T G G T G G T T G T C T T A G A T T C A C T G G G T T G C G A G A A C C T T (A) C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A G G C I T C G t A C A T A T G C G T T G G T T A I T C G T T C A T A t A A C C A A T T C (A) C (C) (G) (A) (T) (A) A A C G C T G A C G T G T T G G T G G T E022 C T C C C T G A G A C T A T C G A C T C G T A A A G G T G C C A A C C G C T G A A G C C G C T T A T T T (I) A C G (A) (A) A (T) (C) (C) G C A T G (C) C A G T T G G [(A)] (C) C G T C C C A C I C T [(G)] t A T A C G T C (T) (C) (C) C G G T C G I C C G T T G G G G t G G C G C A T T C G T T A G T G A A C G C T G A C G C G T C A G T T G T T G T C T T A G A T T C G C T G G G T T G C G A G A A C C T T A C A T G T C A A G G T C A C C D A T T C (D) G T G (T) (G) A (C) (T) (T) C T G C C (G) T G A T C G A [(D)] (A) T A C C A G G C I T C [(D)] t A C A T A T G (C) (G) (T) T A G T C A D C C A T G C A G A t G A T C A C T T C A C C G A C A G G C G C C G A C G T A T T G G T T G T E023 T G T C T T A G A T T C A C T G G G T T G C G A (G) A A C C T T (A) C A T G T C A A G G T C G T C D G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C C [C] [(A)] C I C T (G) t A T A C G T C [(T)] [C] [(C)] (C) G G T C A I C T G T G (C) [G] [(G)] G D [(G)] [(A)] [(T)] [(G)] [(C)] A T C C G (T) T A G C A G G (C) (A) T C C G C G C (A) C T (A) G T T G T T G T C T T A G A T T C A C T G G G T T G C G A (A) A A C C T T (G) C A T G T C A A G G T C G T C [D] G G T T I G T A A A A C C T G C A T G G T G A T C G G D A C A C C A [G] [(G)] C I C T (D) t A C A T A T G [(C)] [G] [(T)] (T) G G T T A I T C G T T (G) [A] [(T)] A t [(A)] [(G)] [(C)] [(C)] [(A)] A T T C G (C) T A G C G A A (G) (G) C T G A C G C (G) T T (G) G T T G T Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = E001 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = (A) = = = = = = = = = = (G) = = (T) = (I) (T) = = = = = = (T) = = (A) = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = (G) = (T) (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = (G) = = = = = = = = = = (A) = = (C) = (D) (C) = = = = = = (G) = = (G) = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = (A) = (C) (G) = = E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? (C) = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? (G) = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = E004 C T C = C = G A G A C T G T C = A C = C = T A = A G G T G C C = A C C = C T G = A = C = = C T = A T = = D A C G = G = = = = = = = = = = = A G = T = A ? C = G T = C C A = ? = = D = = T G C G = C T C C C = = C C = = C = = = G G (G) G (G) = G G = G C (A) = = = (G) = (T) (A) (G) (C) (G) (A) (A) = = = (T) = = = = = = = = = = = (T) = = T G T = T = A G A T T C A C T = G G = T = C G = G A A C C T T = C A T = T C A = G = T = = T C = G G = = I G T A = A = = = = = = = = = = = G A = C = G ? A = A C = A G G = ? = = G = = C A T A = G C G T T = = T T = = T = = = T C (A) T (A) = A A = C A (C) = = = (A) = (C) (G) (A) (T) (A) (G) (G) = = = (C) = = = = = = = = = = = (G) = = E005 = = = = = = = = = = = = G T C = A C = = A T A G A G G T = C C G A C C = C T G C A = C = G = = D G G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = C = = = = = G = = = = = = = G = = = = = = = = = C = = A = = = A = C G A (T) (A) A A = = = T = = = = = = = = = = = T = (C) = = = = = = = = = = = = A C T = G G = = G C G A G A A C = T T A C A T = T C A A G = T = A = = T A T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = T = = = = = A = = = = = = = A = = = = = = = = = T = = C = = = G = T A G (C) (G) G G = = = C = = = = = = = = = = = G = (T) E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = E007 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = G T = D G G = T = = = A A = = C C T G C A T G G T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = G = = T = I T = G = = = = T = = A = C = = A = = = G = T A G C G A A = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = A C = T A T = C = = = G T = = T T C C T G C C C C = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = A = = C = D C = A = = = = G = = G = T = = C = = = A = C G A T A G G = = = C = = = = = = = = = = = = = = E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C = T A T = C = = = G T = = T T C C T G C C C C = = = = = ? = = T = = = = = = = = = = = = = = = = = = = = = = = A = = C = D C = A = = = = G = = G = T = = C = = = (G) = (T) (A) (G) (C) (G) G G = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = D G G = T = = = A A = = C C T G C A T G G T = = = = = ? = = C = = = = = = = = = = = = = = = = = = = = = = = G = = T = I T = G = = = = T = = A = C = = A = = = (A) = (C) (G) (A) (T) (A) A A = = = T = = = = = = = = = = = = = = E009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = ? = = = = = = = = = = E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = E011 (C) (T) (T) = C (T) (A) A (G) T T T A T C = A (G) C = = T G A (G) G G (C) = C C G C A = (G) (C) (T) (G) A (A) = C = = (T) = = = = = (C) = = = (G) (A) = = (C) C (C) = C A (C) (G) (G) (T) = = = = = = ? = = = = = (A) C G = = = = ? = = (T) = C A = G ? (C) ? (T) = = = (C) = = (T) = = = T C (G) (T) G = A A = (C) A (C) = = = (A) = (T) (G) (G) = (G) (A) ? ? = = (T) = = = = C = = T A = = (T) = = (T) (G) (C) = T (C) (G) G (A) A C C G C T = G (C) T = = C A G (A) A A (T) = T T A A C = (A) (T) (C) (A) C (G) = T = = (C) = = = = = (T) = = = (A) (T) = = (T) T (T) = T G (T) (C) (C) (C) = = = = = = ? = = = = = (C) G A = = = = ? = = (C) = T G = C ? (G) ? (C) = = = (T) = = (C) = = = G G (A) (G) A = G G = (G) C (A) = = = (G) = (C) (A) (A) = (A) (G) ? ? = = (C) = = = = T = = C G = = (G) = = E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = E013 C T C = C = G A G A C T = = = = = = = C G = = A = = = = G = = A = = = = = = = A = = = = = = T = A T = T D A C = A G = C C T G C ? ? G G T A G = T = A A C ? ? T = = C A = = C T D = = T G C G T C ? C C = = = C = = I = = = = G G G = G = = G = G C = = = = G = T A G ? ? = = = ? = = = = = = = A = C A = = = = (C) T G T = T = A G A T T C = = = = = = = T A = = G = = = = C = = G = = = = = = = C = = = = = = C = G G = C I G T = T A = T T C C T ? ? C C C G A = C = G D A ? ? C = = G G = = T C G = = C A T A C G ? G T = = = T = = D = = = = T C A = A = = A = C A = = = = A = C G A ? ? = = = ? = = = = = = = G = T G = = = = (T) E014 (T) (G) (C) = T (C) (G) G (A) A C C G C T = G (C) T = = C A G (A) A A (T) = T T A A C = (A) (T) (C) (A) C (G) = T = = (C) = = = = = (T) ? = = (A) ? ? = ? T ? = T G (T) (C) (C) (C) = = = = = = ? = = = = = (C) G A = = = = = = = (C) = T G = C ? (G) ? ? = = = (T) = = (C) = = = G G (A) (G) A = G G = (G) C = = = = = (C) = = = = = = ? ? ? = = = = = ? T (A) = C G = ? (G) = = (C) (T) (T) = C (T) (A) A (G) T T T A T C = A (G) C = = T G A (G) G G (C) = C C G C A = (G) (C) (T) (G) A (A) = C = = (T) = = = = = (C) ? = = (G) ? ? = ? C ? = C A (C) (G) (G) (T) = = = = = = ? = = = = = (A) C G = = = = = = = (T) = C A = G ? (C) ? ? = = = (C) = = (T) = = = T C (G) (T) G = A A = (C) A = = = = = (T) = = = = = = ? ? ? = = = = = ? C (G) = T A = ? (T) = = E015 T G T = T = A G A T T ? A C T = G G = T = C G = G A A C C T T = C A T = T C A = G = T = A = C T = = = C I G T = T A = T T C C T G C C C C G A = C = G D ? T A C = A G ? = = T C G = = C A T A = G ? G ? ? A = T = = D = = A = T C (G) = (G) = = A T C A (C) = = = A = C G A ? A (G) (G) ? ? = (C) = = = = (C) = = = = (C) = (T) = (C) C T C = C = G A G A C ? G T C = A C = C = T A = A G G T G C C = A C C = C T G = A = C = G = T D = = = T D A C = A G = C C T G C A T G G T A G = T = A A ? C G T = C C ? = = C T D = = T G C G = C ? C ? ? G = C = = I = = G = G G (A) = (A) = = G C G C (A) = = = G = T A G ? G (A) (A) ? ? = (T) = = = = (T) = = = = (G) = (G) = (T) E016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = D G G = T = = = A A = = C C T G C A T G G T = = = = = = = = C = = = C (C) (A) = = = T ? = = T = C G = C ? C (C) (C) G = = = = I = T G = G = = ? = D ? ? ? ? ? A = C = G = T A G C = = = = ? T = C G = ? (T) = C = = G = (G) = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C = T A T = C = = = G T = = T T C C T G C C C C = = = = = = = = T = = = A (G) (G) = = = C ? = = C = T A = G ? G (T) (T) A = = = = D = C A = T = = ? = t ? ? ? ? ? C = T = A = C G A T = = = = ? C = G A = ? (C) = T = = C = (T) = (C) E017 (T) (G) (T) = (T) (T) (A) (G) (A) (T) (T) (C) = = = = = = (T) = (A) = = = = = = = = = = = = = (C) (G) = = = = = = = = = = = ? = = = = = = = = = = = = = = (C) = ? ? ? ? ? = = = = = = = = (T) = = = = (G) (G) = = = (C) (G) = = (C) = (T) (A) (C) (G) ? (G) (T) (C) = = = = = (D) = = = = (T) (C) (A) = (A) = = (A) = (C) (A) (A) = = = = = = = = = (A) (A) (A) ? = = (T) = = = = = (A) = = = = = = = (C) (C) (T) (C) = (C) (C) (G) (A) (G) (A) (C) (T) = = = = = = (C) = (G) = = = = = = = = = = = = = (T) (A) = = = = = = = = = = = ? = = = = = = = = = = = = = = (G) = ? ? ? ? ? = = = = = = = = (C) = = = = (C) (A) = = = (T) (D) = = (T) = (C) (G) (T) (C) ? (C) (C) (T) = = = = = (I) = = = = (G) (G) (G) = (G) = = (G) = (G) (C) (C) = = = = = = = = = (G) (G) (G) ? = = (C) = = = = = (G) = = = = = = = (T) E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = ? ? = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = = (T) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = ? ? = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = = (C) (A) = = = = = E019 = = = = = = = = = = = = = = = = = = = = = = = = (G) (A) = = = = = (A) = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C ? ? ? = (T) = (G) = = T = C G = C ? ? ? (C) = = = C = = C T = = ? (C) ? ? G D ? ? ? ? ? = = C = = = = = = = A G G (C) (A) T C C G = = (T) = C = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = (A) (G) = = = = = (G) = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A ? ? ? = (C) = (D) = = C = T A = G ? ? ? (T) = = = T = = T C = = ? (G) ? ? A t ? ? ? ? ? = = T = = = = = = = G A A (G) (G) C T G A = = (C) = T = = = = (T) = = E020 C T C = C = G A G A C T A T C = A C = C = T A = A G G T G C C (A) A C C = C T G = A = C = G = T T = = = T (I) A C = (A) (A) = (T) (C) (C) G C A T G (C) C A G = T = G ? (C) C G T = C C A = ? C T ? = = T = C G = C ? ? (C) C G = = = G I = = G = T G G = G = = G C G C A = = = G T T A G T G A A = = = T = = = = C G = C A = = = = = T G T = T = A G A T T C G C T = G G = T = C G = G A A C C T T (G) C A T = T C A = G = T = A = C D = = = C (D) G T = (T) (G) = (C) (T) (T) C T G C C (G) T G A = C = A ? (A) T A C = A G G = ? T C ? = = C = T A = G ? ? (T) T A = = = A D = = A = G C A = A = = A T C A C = = = A C C G A C A G G = = = C = = = = T A = T G = = = = = E021 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = ? = = A C = T A T = C ? = = G T = = T T C C T G C C C C = = = = = = = = T = = = = = = = = = = ? = = = = = = = = ? ? = = A = = C = D C = A = = = = G = = G = T = = C = = = (G) = (T) (A) (G) (C) (G) G G = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = ? = = G T = D G G = T ? = = A A = = C C T G C A T G G T = = = = = = = = C = = = = = = = = = = ? = = = = = = = = ? ? = = G = = T = I T = G = = = = T = = A = C = = A = = = (A) = (C) (G) (A) (T) (A) A A = = = T = = = = = = = = = = = = = = E022 C T C = C = G A G A C T A T C = A C = C = T A = A G G T G C C = A C C = C T G = A = C = G = T T = = = T ? A C = ? ? ? ? ? ? G C A T G ? C A G = T = G ? ? C G T = C C A = = C T ? = = T = C G = C (T) (C) ? C G = = = G I = = G = T G G = G = = G C G C A = = = G T T A G T G A A ? ? = T = = = = C G = C A = = = = = T G T = T = A G A T T C G C T = G G = T = C G = G A A C C T T = C A T = T C A = G = T = A = C D = = = C ? G T = ? ? ? ? ? ? C T G C C ? T G A = C = A ? ? T A C = A G G = = T C ? = = C = T A = G (C) (G) ? T A = = = A D = = A = G C A = A = = A T C A C = = = A C C G A C A G G ? ? = C = = = = T A = T G = = = = = E023 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = (A) = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C ? ? = = = = (G) = = T = C G = C ? ? ? (C) = = = C = = C T = = G ? ? ? ? D ? ? ? ? ? = = C = = (T) = = = = A G G (C) (A) T C C G = = = (A) C = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = (G) = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A ? ? = = = = (D) = = C = T A = G ? ? ? (T) = = = T = = T C = = T ? ? ? ? t ? ? ? ? ? = = T = = (C) = = = = G A A (G) (G) C T G A = = = (G) T = (G) = = = = = Phase probabilities at each site with phase known positions indicated by = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.7 = = = = = = = = = = 0.68 = = 0.7 = 0.69 0.7 = = = = = = 0.69 = = 0.68 = = = = = = 0.69 = = = = = = = = = = = = = = = = = = = = = = 0.68 = 0.7 0.66 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.84 = 0.85 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.7 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.83 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 1 = 1 = 1 1 1 1 1 0.97 1 1 1 = 1 1 = 1 = 1 1 = 0.99 0.94 1 1 1 1 1 = 1 1 1 = 1 1 1 = 1 = 1 = = 1 1 = 1 1 = = 1 1 1 1 = 1 = = = = = = = = = = = 1 1 = 1 = 1 = 0.97 = 1 1 = 1 0.96 0.98 = = = = 0.96 = = 1 1 1 1 = 1 0.94 0.97 0.95 0.99 = = 1 1 = = 1 = = = 0.99 0.99 0.55 1 0.59 = 1 0.98 = 0.97 0.98 0.5 = = = 0.89 = 0.89 0.89 0.9 0.58 0.83 0.6 0.59 = = = 0.59 = = = = = = = = = = = 0.6 = = = = = = = = = = = = = = 1 1 1 = 1 1 = = 1 1 1 1 1 0.99 1 1 = 1 1 0.99 1 0.99 1 = 1 1 1 1 1 = 1 = 1 = = 1 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = 1 = = = = = 1 = = = = = = = 1 = = = = = = = = = 1 = = 0.99 = = = 0.93 = 0.93 0.94 0.95 0.56 0.6 1 1 = = = 1 = = = = = = = = = = = 0.99 = 0.76 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 = 1 1 1 = 1 = = = 1 1 = = 1 1 1 1 0.99 1 1 1 1 1 = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = 0.99 = 0.99 0.99 = 1 = = = = 0.99 = = 0.99 = 1 = = 1 = = = 1 = 1 1 0.99 1 1 1 1 = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 = 1 1 1 = 1 = = = 1 1 = = 1 1 1 0.95 0.95 0.95 1 1 1 1 = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = 1 = = 1 = 1 1 = 1 = = = = 1 = = 1 = 1 = = 1 = = = 0.86 = 0.86 0.87 0.87 0.53 0.58 1 1 = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.81 0.81 0.51 = 1 0.73 0.56 1 0.67 0.98 1 1 1 1 1 = 1 0.52 1 = = 1 1 1 0.69 1 0.94 0.57 = 1 1 1 1 1 = 0.84 0.84 0.85 0.73 1 0.84 = 1 = = 0.64 = = = = = 0.76 = = = 0.84 0.58 = = 0.5 1 0.51 = 1 0.97 0.72 0.69 0.57 0.88 = = = = = = = = = = = = 0.6 1 1 = = = = = = = 0.75 = 1 1 = 1 = 0.62 = 0.51 = = = 0.87 = = 0.84 = = = 1 0.98 0.72 0.85 1 = 0.98 1 = 0.55 1 0.51 = = = 0.5 = 0.51 0.51 0.51 = 0.51 0.53 = = = = 0.52 = = = = 1 = = 1 0.92 = = 0.53 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 1 = 1 = 1 1 1 1 1 0.99 = = = = = = = 1 1 = = 1 = = = = 1 = = 1 = = = = = = = 1 = = = = = = 1 = 1 1 = 1 1 1 1 = 1 1 = 1 1 1 1 1 = = 1 1 1 0.98 0.97 = 1 = 1 1 1 = = 1 = = 1 1 = = 1 1 1 = = 1 1 1 1 1 1 = 1 1 = = = 1 = = 1 = = = = 1 1 1 = 1 = = 1 = 1 1 = = = = 0.98 = 0.97 0.98 0.98 = = = = = = = = = = = = = 0.99 = 0.99 0.99 = = = = 0.72 0.8 0.81 0.51 = 1 0.73 0.56 1 0.67 0.98 1 1 1 1 1 = 1 0.52 1 = = 1 1 1 0.69 1 0.94 0.57 = 1 1 1 1 1 = 0.84 0.84 0.85 0.73 1 0.84 = 1 = = 0.64 = = = = = 0.76 = = = 0.84 = = = = 1 = = 1 0.97 0.72 0.69 0.57 0.88 = = = = = = = = = = = = 0.6 1 1 = = = = = = = 0.75 = 1 1 = 1 = 0.62 = = = = = 0.87 = = 0.84 = = = 1 0.98 0.72 0.85 1 = 0.98 1 = 0.55 1 = = = = = 0.51 = = = = = = = = = = = = = = = 1 0.52 = 1 0.92 = = 0.53 = = 1 1 1 = 1 = 1 1 1 1 1 = 1 1 1 = 1 1 = 1 = 1 1 = 0.99 0.97 1 1 1 1 1 = 1 0.99 1 = 1 1 1 = 1 = 1 = 1 = 1 0.99 = = = 1 1 1 1 = 1 1 = 1 1 1 1 1 1 1 1 1 1 1 1 = 1 = 1 0.98 = 1 1 1 = 1 0.94 = = = 1 1 0.95 = = 1 1 1 1 = 1 = 0.96 = = 1 = 1 = = 1 = = 1 = 0.98 1 0.62 = 0.6 = = 0.98 0.99 0.96 0.98 0.73 = = = 0.93 = 0.93 0.93 0.93 = 0.92 0.84 0.83 = = = 0.84 = = = = 0.82 = = = = 0.86 = 0.56 = 0.89 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 = 0.95 1 1 = 1 = = = 1 1 = = 1 1 1 1 1 1 1 1 1 1 = = = = = = = = 1 = = = 1 0.9 0.65 = = = 1 = = = 1 = 1 1 = 1 = 0.91 0.73 0.56 1 = = = = 1 = 1 1 = 0.96 = = = = 1 = = = = = 0.92 = 1 = 1 = 1 1 1 1 = = = = = 1 = 1 1 = = 0.79 = 1 = = 0.9 = 0.69 = 0.9 0.56 0.57 0.59 = 0.61 0.68 0.72 0.63 0.72 0.61 0.57 0.61 = = = = = = 0.63 = 0.7 = = = = = = = = = = = = = 0.69 0.62 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.71 = = = = = = = = = = = = = = 0.7 = = = = 0.63 0.6 = = = 0.69 0.69 = = 0.68 = 0.62 0.57 0.73 0.57 = 0.51 0.57 0.56 = = = = = 0.69 = = = = 0.59 0.58 0.72 = 0.61 = = 0.54 = 0.6 0.56 0.57 = = = = = = = = = 0.55 0.61 0.6 = = = 0.57 = = = = = 0.5 = = = = = = = 0.57 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.87 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.87 0.87 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.84 0.6 = = = = = 0.82 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = 0.87 = 0.55 = = 1 = 1 1 = 1 = = = 0.56 = = = 1 = = 1 1 = = = 0.83 = = 0.98 1 = = = = = = = 1 = = = = = = = 0.93 0.91 0.92 0.82 0.58 1 0.91 1 1 = = 0.81 = 1 = = = = 0.73 = = 1 1 1 = 1 = 1 1 1 1 1 1 1 1 1 = 1 1 = 1 = 1 1 = 1 1 1 1 0.91 1 1 0.5 1 1 1 = 1 1 1 = 1 = 1 = 1 = 1 1 = = = 1 0.69 1 1 = 0.54 0.54 = 0.58 0.61 0.62 1 1 1 1 1 0.66 1 1 1 = 1 = 1 = 0.86 1 1 1 = 1 1 1 = = 1 1 = = = 1 = 1 1 = 1 = = 0.63 1 1 = = = 1 1 = = 1 = 1 1 1 = 1 = = 1 1 1 1 1 = = = 1 1 1 1 1 1 1 1 1 = = = 1 = = = = 1 1 = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.52 = = = = = = = = = = = = 1 1 = 1 1 1 = 1 = = = 1 1 = = 1 1 1 0.95 0.95 0.95 1 1 1 1 = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = 1 = = 1 = 1 1 = 1 = = = = 1 = = 1 = 1 = = 1 = = = 0.86 = 0.86 0.87 0.87 0.53 0.58 1 1 = = = 1 = = = = = = = = = = = = = = 1 1 1 = 1 = 1 1 1 1 1 1 1 1 1 = 1 1 = 1 = 1 1 = 1 1 1 1 0.91 1 1 = 1 1 1 = 1 1 1 = 1 = 1 = 1 = 1 1 = = = 1 = 1 1 = = = = = = = 1 1 1 1 1 = 1 1 1 = 1 = 1 = = 1 1 1 = 1 1 1 = = 1 1 = = = 1 = 1 1 = 1 0.75 0.64 = 1 1 = = = 1 1 = = 1 = 1 1 1 = 1 = = 1 1 1 1 1 = = = 1 1 1 1 1 1 1 1 1 = = = 1 = = = = 1 1 = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.82 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = 0.55 = = 1 = 1 1 = 1 = = = 0.56 = = = 1 = = 1 1 = = 0.94 = = = = 1 = = = = = = = 1 = = 0.65 = = = = 0.93 0.91 0.92 0.82 0.58 1 0.91 1 1 = = = 0.64 1 = 0.63 = = = = =