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 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 G T T C A G A t G A C C A C T T C A C C G A C A G G C G C C G A C G T G T T G G T T G T (1) 2: C T C T C T G A G A C T 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 A A T C A D C C G C T C A G A t G A C C A A T T A A C C G A C A A G C G C C G A C A C G T T A G C T G T (1) 3: C T C C C T G A A T T C G T C A A C T T G T A G A G G T C C C G A C C G C T G C A G C T G C C T G G C T D A T G T A G T T C G T G C C C C G A C C C G D A C G T C A G G T I T C D D A C A T A T G C G T T G G T T A D T C G T T C A G A t G 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 C G T T G G T G G C (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 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 C A G T T G T (1) 5: 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 I C C G T T C A G A t G A C C A C T T A A C C G A C A G G C G C C G A C G C G T T A G C T G T (2) 6: T G T C T T A G A T T C A C C G G G T T G T A G A G G T C C T 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 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 T C C C G A T C A D C C G C G G G G G t G G C C C A T T C G C T A G C G A G C G C C G A C A C G T T A G C T G T (1) 7: 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 (3) 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 C 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 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 A T T G G T T G T (1) 9: 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 A T T G G T G G C (2) 10: T G T C T T A G A T T C A C C G G G T T G C G A G G A C G T C 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 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 G T T C A G A t G 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 (2) 11: C T C T C T G A G A C T 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 A 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 T C C C G G T C A I C C G T G G G G G t G G C G C A C T C G C T A G C G A A C G C T G A T G T A T T A G T G G C (1) 12: 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 G T T G C T G G C (2) 13: T G T C T T A G A T T C A C T G G G C 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 T 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 C A T C A G T T G T (1) 14: C T C T C T G A G A C T G T C G A C T 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 G G C I T C G t A T A C G T C C C T T A A T C A D C C G C T C A G A t G A C C A C T T A A C C G A C A G G C G C C G A C A C G T T A G C T A T (1) 15: 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 A 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 A C G T C T C C C G G T C A I C C G T G G G G G t G G C G C A T T C G C C G G C A G G C G C C G A C G T A T C A G T T A T (1) 16: C T C T C T G A G A C T 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 A 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 D T T D t A T A C G T C T C C C G G T C A I C C G T G G G G G t G G C C C A C T C G C C G G C A G G C G C C G A T G C G T T A G T G G T (1) 17: C T C C C C G A G A C T G T C A A C T T G T A G A G G T C C C G A C C G C T G C A G C T G C C T G G C T D A T G T A G T T C G T G C C C C G A C C C G D A C G T C A G G T I T T G D A C A T A T G C G T T G G T T A D T C G T T C A G A t G A C C A C T T C A C T A A C G A A C G C T G A C G C G T T G G T T G T (1) 18: T G T T T T G G G T C T A C C G G G T T G T G G A G G T C C T A C C T G C T A C A G T C G T C D G G T C I G T G T A A C T T G T A C C G T G A T C G G D A C A C C A C G C I T T D t A T A T A T C C G C C G G T T A I T C G T G G A G A t G G C C A A C T C G C T A G C G A A C G C T G A T G T G T T G G T T G T (1) 19: C T C C C T A A A A T C G T T G A C T T A C A A G A A C C T C G A A C G T C G A G A C C G C C D G G T T I G T A A A A T C C G C G T G 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 C G T G T C T T G G T C A I C C G T T C G T G t A A 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 G T T G G T G G T (1) 20: T G T C T T A G A T T C A C C G A C 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 D 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 D C C G T T C A G A t G A C C A A C 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 A C (1) 21: T G T C T T A G A T T C A C C 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 C C T A T T C I A T G T A A T T C G 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 G T T C A G A t G A C C A A T T C G C T A G C G A A C G C T G A T G C G T T G G T T G T (1) 22: C T C T C T G A G A C T 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 A 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 T C C C G G T C A I C C G T G G G G G t G G C G C A T C C G C T A G C A G G C G C C G A C G C G T T A C T G G C (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 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 G T T C A G A t G A C C A A T T C A C T G G T A G G G A C C G G C G T G T T G G C T G T (1) 24: 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 T A G T T G C (1) 25: 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 C G 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 A D C C G T T C A G A t G 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 C T G T (1) 27: T G T T T T G G G T C T A C C G G G T T G T G G A G G T C C T A C C T G C T A C A G T C G T C D G G T C I G T G T A A C T T G T A C C G T G A T C G G D A C A C C A C G C I T C G t A T A T A T C C G C C G G T C A I C C G T G G A G A t G G C C A A C T C G C T A G C G A A C G C T G A T G T G T T G G T T G T (1) 28: C T C C C T A A A A T C G T C G A C T T A C A A G A A C C T C G A A C G T C G A G A C C G C C D G G T T I G T A A A A T C C G C G T G C C G A T C G G D A T A C C C G A C D T T G t A C A C G T G T C T T A G T C A D C C G T T C G G G t G A 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 G T T G G T G G T (1) 29: C T C C C T G A G A T C G T C G A C T T G T A A A G G T C C C A A C C G C T G A A G C T G C C D G T C T D A T G A A G T C C G C A T C C T A A T T G G D C C G T C A C G C I T C D t A C A T G T C C G C T G G T T A I T C G T T C G G G t G G C C C A T T C A C C A G C A G G C G C C G A C G T G T T A G T T G T (1) 30: C T C C C T G A A T C T G T C A A C T C G T A G A G G T G C C G A C C G C T G C A G C C G C T T A G T T D A C G T G A C T T G T G C G G C G G C C C A A A C G T C C G A T I C T G D A T G C A T G T C T C G G C C A D C C G T G G A G A t G A C C A C T T C G C T G A C G A A C G C T G A C G C G T T G C T G A C (1) 31: C T C C C T G A G A T C G T C G A C T T G T A A A G G T C C C A A C C G C T G A A G C T G C C D G T C T D A T G A A G T C C G C A T C C T A A T T G G D C C G T T A C G C I T C D t A C A T G T C C G C T G G T T A I T C G T T C G G G t G G C C C A T T C G C C A G C A G G C G C C G A C G T G T T A G T T G T (1) 32: C T C C C T G A A T C T G T C A A C T C G T A G A G G T G C C G A C C G C T G C A G C C G C T T A G T T D A C G T G A C T T G T G C G G C G G C C C A A A C G T C C G A T I C T G D A T A C A T G T C T C G G C C A D C C G T G G A G A t G A C C A A T T C G C T G G C G A A C G C T G A C G C A T C A G T T G C (1) 33: C T C T C T G A G A C T 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 A 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 T C C C G G T C A I C C G T G G G G G t G G C G C A C T C G C T G G C A G G C G C C G A C G T A T T A G T G G T (1) 34: 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 T C C A C D C T D t A T A C G T C T C C C G G T C A I C C G T G G G G G t G G C G C A T T C G C C A G C A G G C G C C G A C G T A T T A G T G G T (1) 35: 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 C G A A C G C T G A C G C G T C A G C T G T (1) 36: 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 A G G G A T C C G C G C A T T A G T T G C (2) 37: T G T C T T A G A T T C A C C G G G T T G C G A G A G C C T C 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 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 G T T C A G A t G 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 A T T G G T G A T (1) 38: T G T C T T A G A T T C A C C G G G T T G T A G A G G T C C T A 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 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 T C C C G G T 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 G C G C C G A C G T G T T A G T T G T (1) 39: 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 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 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 C T G G T G G C (1) 40: C T C C C T G A G A C T G T C G A 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 C C T A T C T D A T G T A A T T C C T G C C C C 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 A G T C A D C C G T T C A G A t G A C C A A T T C G C C G G C A G G C G C C G A C G C G T C A G C T G T (1) 41: 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 T C C A C D C T D t A T A C G T C T C C C G G T 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 A G G C G C C G A C G T A T T A G T T G T (1) Summary of best reconstruction (numbers refer to the list of haplotypes given above) D001: (1,2) D002: (3,4) D003: (5,6) D004: (7,8) D005: (9,10) D006: (11,12) D007: (13,14) D008: (10,15) D009: (16,17) D010: (18,19) D011: (20,21) D012: (7,7) D013: (22,23) D014: (24,25) D015: (26,9) D016: (27,28) D033: (29,30) D034: (31,32) D035: (33,34) D036: (35,36) D037: (37,38) D038: (12,39) D039: (40,41) D040: (5,36) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: D001 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 G T T C A G A t G A C C A (C) T T C A C C G A C A (G) G C G C C G A C G T [G] T T G G (T) T G T C T C T C T G A G A C T 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 A A T C A D C C G C T C A G A t G A C C A (A) T T A A C C G A C A (A) G C G C C G A C A C G T T A G (C) T G T D002 C T C C C T G A A T T C G T C A A C T T G T A G A G G T C C C G A C C G C T G C A G C T G C C T G G C T D A T G T A G T T C G T G C C C C G A C C C G D A C G T C A G G T I T C [D] D A C A T A T G C G T T G G T T A D T C G T T C A G A t G 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 C 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 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 (C) (A) G T (T) G (T) D003 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 (I) C C G (T) T C A G A t G A C C A C T T A A C C G A C A G G C G C C G A C (G) C G T T A G C T G T T G T C T T A G A T T C A C C G G G T T G T A G A (G) G T C [C] [T] (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 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 T C C [C] G (A) T C A (D) C C G (C) G G G G G t G G C C C A T T C G C T A G C G A G C G C C G A C (A) C G T T A G C T G T D004 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 (C) (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 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 A T T G G [T] T G T D005 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 A T T G G T G G C T G T C T T A G A T T C A C C G G G T T G C G A G (G) A C [G] [T] C 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 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 G T T C A G A t G 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 D006 C T C T C T G A G A C T 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 A 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 T C C C G G T C A I C C G T G G G G G t G G C G C A [C] T C G C T A G C G A A C G C T G A (T) G T (A) T T (A) (G) T G 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 C T A G C G A A C G C T G A (C) G C (G) T T (G) (C) T G G C D007 T G T C T T A G A T T C A C T G G G (C) 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 (T) 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 C A T (C) A G (T) T (G) T C T C T C T G A G A C T G T C G A C (T) 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] G G C I T (C) [G] t A (T) A (C) (G) T (C) C (C) T T A A T C A D C C G C T C A G A t G A C C A (C) T T A A C C G A C A (G) G C G C C G A C A C G T (T) A G (C) T (A) T D008 T G T C T T A G A T T C A C C G G G T T G C G A G (G) A C G [T] C 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 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 G T T C A G A t G 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 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 (A) 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 A C G T C T C C C G G T C A I C C G T G G G G G t G G C G C A T T C G C (C) (G) G C A G G C G C C G A C G T A T (C) A G T (T) (A) T D009 C T C T C (T) G A G A C T 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 A 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 (D) T T D t A T A C G T C T C C C G G T C A I C C G T G G G G G t G G C C C (A) (C) T C (G) C (C) (G) (G) C A G G C G C C G A (T) G C G T T (A) G T (G) G T C T C C C (C) G A G A C T G T C A A C T T G T A G A G G T C C C G A C C G C T G C A G C T G C C T G G C T D A T G T A G T T C G T G C C C C G A C C C G D A C G T C A G G T (I) T T [G] D A C A T A T G C G T T G G T T A D T C G T T C A G A t G A C C A (C) (T) T C (A) C (T) (A) (A) C G A A C G C T G A (C) G C G T T (G) G T (T) G T D010 (T) (G) (T) (T) T T G (G) (G) T (C) (T) A C (C) G G G T T (G) (T) (G) (G) (A) G (G) T C C (T) A C C (T) G (C) T (A) C A (G) T C G T C D G G T (C) I G T G T A A C (T) T G (T) A (C) (C) G (T) G A T C G G D A C A C C A (C) (G) C I T T D t A T A (T) (A) T (C) (C) (G) C C G G T (T) A I (T) C G T G G A (G) A t (G) G C C A A (C) T C G C T A G C G A A C G C T G A T G (T) G T T G G T (T) G T (C) (T) (C) (C) C T A (A) (A) A (T) (C) G T (T) G A C T T (A) (C) (A) (A) (G) A (A) C C T (C) G A A (C) G (T) C (G) A G (A) C C G C C D G G T (T) I G T A A A A T (C) C G (C) G (T) (G) 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 (C) (G) T (G) (T) (C) T T G G T (C) A I (C) C G T T C G (T) G t (A) A 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) G T T G G T (G) G T D011 T G T C T T A G A T T C A C C G (A) (C) 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 (D) (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 D C C G T T C A G A t G A C C A A (C) 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 (A) [(C)] T G T C T T A G A T T C A C C 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 C C T A T T C (I) (A) T G T A A T T C G 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 G T T C A G A t G A C C A A (T) T C G C T A G C G A A C G C T G A (T) G (C) G T T G G T T (G) [(T)] D012 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 D013 C T C T C T G A G A C T 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 A 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 T C C C G G T C A I C C G T G G G G G t G G C G C A T (C) C G C T (A) G C A G G (C) (G) C [C] G (A) C G (C) G T T A (C) (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 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 [G] T T C A G A t G A C C A A T (T) C A C T (G) G T A G G (G) (A) C C G (G) C G (T) G T T G (G) (C) T G (T) D014 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 (T) (A) 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 A C C G A T A G G C G C C G A C G T (G) T (C) (G) G T T G T D015 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 G T T C A G A t G 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 (C) 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 A T T G G (T) G G C D016 (T) (G) (T) (T) T T G (G) (G) T (C) (T) A C C G G G T T (G) (T) (G) (G) (A) G (G) T C C (T) A C C (T) G (C) T (A) C A (G) T C G T C D G G T (C) I G T G T A A C (T) T G (T) A (C) (C) G (T) G A T C G G D A (C) A C C A (C) (G) C (I) T (C) G t A T A (T) (A) T (C) (C) (G) C C (G) G T C A (I) C C G T G G A G A t G G C C A A (C) T C G C T A G C G A A C G C T G A T G (T) G T T G G T (T) G T (C) (T) (C) (C) C T A (A) (A) A (T) (C) G T C G A C T T (A) (C) (A) (A) (G) A (A) C C T (C) G A A (C) G (T) C (G) A G (A) C C G C C D G G T (T) I G T A A A A T (C) C G (C) G (T) (G) C (C) G A T C G G D A (T) A C C C (G) (A) C (D) T (T) G t A C A (C) (G) T (G) (T) (C) T T (A) G T C A (D) C C G T T C G G G t G A 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) G T T G G T (G) G T D033 C T C C C T G A G (A) (T) (C) G T C (G) A C T T G T A (A) A G G T C C C A A C C G C T G A A G C (T) G C C D G T (C) T D A T G A (A) G (T) (C) (C) G (C) A (T) (C) C T (A) (A) (T) T (G) (G) D C C G T C (A) C G C I [(T)] C (D) (t) A (C) (A) T G T C C G (C) T G G (T) (T) A (I) (T) C G T T C G G G t G G C C (C) (A) T T C (A) C C (A) (G) C (A) (G) G C G C (C) G A C G (T) G T T (A) (G) T (T) (G) T C T C C C T G A A (T) (C) (T) G T C (A) A C T C G T A (G) A G G T G C C G A C C G C T G C A G C (C) G C T T A G (T) T D A C G T (G) A (C) (T) (T) G (T) G (C) (G) G C (G) (G) (C) C (C) (A) A A C G T C (C) G A T I [(C)] T (G) (D) A (T) (G) C A T G T C (T) C G G (C) (C) A (D) (C) C G T G G A G A t G A C C (A) (C) T T C (G) C T (G) (A) C (G) (A) A C G C (T) G A C G (C) G T T (G) (C) T (G) (A) C D034 C T C C C T G A G (A) (T) (C) G T C (G) A C T T G T A (A) A G G T C C C A A C C G C T G A A G C (T) G C C D G T (C) T D A T G A (A) G (T) (C) (C) G (C) A (T) (C) C T (A) (A) (T) T (G) (G) D C C G T (T) (A) C G C I [(T)] C (D) (t) A (C) A T G T C C G (C) T G G (T) (T) A (I) (T) C G T T C G G G t G G C C (C) A T T C G C C (A) G C (A) (G) G C G C (C) G A C G (T) (G) T (T) A G T T G T C T C C C T G A A (T) (C) (T) G T C (A) A C T C G T A (G) A G G T G C C G A C C G C T G C A G C (C) G C T T A G (T) T D A C G T (G) A (C) (T) (T) G (T) G (C) (G) G C (G) (G) (C) C (C) (A) A A C G T (C) (C) G A T I [(C)] T (G) (D) A (T) A C A T G T C (T) C G G (C) (C) A (D) (C) C G T G G A G A t G A C C (A) A T T C G C T (G) G C (G) (A) A C G C (T) G A C G (C) (A) T (C) A G T T G C D035 C T C T C T G A G A C T 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 A 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 T C C C G G T C A I C C G T G G G G G t G G C G C A (C) T C G C (T) (G) G C A G G C G C C G A C G T A T T A G T G G T 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 (T) C C A C (D) C T D t A T A C G T C T C C C G G T C A I C C G T G G G G G t G G C G C A (T) T C G C (C) (A) G C A G G C G C C G A C G T A T T A G T G G T D036 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 C (G) (A) (A) C G C (T) G A C G C G T (C) A G (C) 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 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 (A) (G) (G) G A T (C) C G C G C A T (T) A G (T) T G C D037 T G T C T T A G A T T C A C C G G G T T G C G A G (A) G C C (T) (C) (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 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 G T T C A G A t G 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 (A) T T G G T G (A) T T G T C T T A G A T T C A C C G G G T T G T A G A (G) G T C (C) (T) (A) 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 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 T C C (C) G G T 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 G C G C C G A C G T (G) T T A G T T (G) T D038 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 G (T) T G (C) 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 (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 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 (C) T G (G) T G G C D039 C T C C C T G A G A C T G T C G A 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 C C T A T (C) T D A T G T A A T T C C T (G) C C C C 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 A G T C A (D) C C G T T C A G A t G A C C A A T T C G C (C) (G) G C A G G C G C C G A C G C G T (C) A G C T G T 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 (T) C C A C (D) C T D t A T A C G T C T C C C G G T 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 A G G C G C C G A C G T A T (T) A G T T G T D040 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 I C C G T T C A G A t G A C C A C T T A A C C G A C A G G C G C C G A C G C G T T A G C 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 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 A G G G A T C C G C G C A T T A G T T G C Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = D001 T G T C T = A G A T T C A C ? ? ? G = = (G) C G A G A A C = T (T) = C A (T) = T C A A G = T = A = = T A T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = ? = = = = = = (T) = = = = ? = G = ? ? = = = = T = = = = = = = = = = = (C) = = C = = = = = = = (G) = = = = = = = = G T ? ? = G = (T) = = = C T C T C = G A G A C T G T ? ? ? C = = (A) T A G A G G T = C (C) = A C (C) = C T G C A = C = G = = D G G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = ? = = = = = = (C) = = = = ? = A = ? ? = = = = C = = = = = = = = = = = (A) = = A = = = = = = = (A) = = = = = = = = A C ? ? = A = (C) = = = D002 C T C = C = G A = = = = G T C A A C = = = T A G A G G T = C C ? A C C = C T G C A = C T G = = = G G C T D A = = = = G = = = G = = = = = = = = C = C = = = C G T ? ? = = T = = = ? D = = = = = = = = = = = G = = ? ? = T = G = = = = = = = = = C = = (A) = = = (G) = (T) A (G) C G A A = = = T = = = = C ? = (T) (G) = ? (G) = (C) T G T = T = A G = = = = A C T G G G = = = C G A G A A C = T T ? C A T = T C A A G = T C A = = = A T T C I G = = = = A = = = C = = = = = = = = T = G = = = T A C ? ? = = C = = = ? t = = = = = = = = = = = A = = ? ? = C = A = = = = = = = = = T = = (C) = = = (A) = (C) G (A) T A G G = = = C = = = = T ? = (C) (A) = ? (T) = (T) D003 = = = = = = = = = = = = = = T = = = = = = C G A G (A) A C = ? ? (A) C A T = T C A A G = T = A = = T A T = = = = = = = = = = = = C = = = = = = = = = = = = ? = T = = = A ? ? ? ? = C ? = = C = T A = G C G ? ? A (G) = = = (I) = = = (T) T C A = A = = A = = A C = = A A = C G A = A G = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = T A G A (G) G T = ? ? (G) A C C = C T G C A = C = G = = D G G = = = = = = = = = = = = G = = = = = = = = = = = = ? = C = = = C ? ? ? ? = T ? = = T = C G = C T C ? ? G (A) = = = (D) = = = (C) G G G = G = = G = = C A = = C G = T A G = G A = = = = = = = = (A) = = = = = = = = = = D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? (T) (A) = = = = = = = = = = = = A C = T A T = C = = = G T = = T T C C T G C C C C = = = = = = = = T = = = ? ? = = = = = = = A = = = = = = = = ? = = = = = = = = = A = = = = = = = = = T = = C = T = A = C G A T A G G = = = C = = = = = G = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? (C) (G) = = = = = = = = = = = = G T = D G G = T = = = A A = = C C T G C A T G G T = = = = = = = = C = = = ? ? = = = = = = = G = = = = = = = = ? = = = = = = = = = G = = = = = = = = = C = = A = C = G = T A G C G A A = = = T = = = = = A = = = = ? = = = D005 = = = = = = = = = = = = = = T = = = = = = = = = = (A) = = ? ? T A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = ? ? = = = = = = G = = = = = = = = = ? = = = ? ? = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = A = = = = = = = C = = = = = = = = = = = = = = C = = = = = = = = = = (G) = = ? ? C G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = ? ? = = = = = = A = = = = = = = = = ? = = = ? ? = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = G = = = = = = = T D006 = = = T = = = = = = = = = = = = = = = T A = = G = = = = C ? = (G) = = = = = = = C = A = = = = C = G G = C I G T ? T A = T T C = T G C C C C G A = C = G D A = A C = = = = = = T = = = = = A = = = = = = ? = = = T = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = (T) = T (A) = = (A) (G) = = = = = = = C = = = = = = = = = = = = = = = C G = = A = = = = G ? = (A) = = = = = = = A = G = = = = T = A T = T D A C ? A G = C C T = C A T G G T A G = T = A A C = G T = = = = = = C = = = = = G = = = = = = ? = = = C = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = (C) = C (G) = = (G) (C) = = = = D007 T G T C T = A G A T T C A C T = G G (C) = = C G A G A A C = ? (T) (A) C A = (G) T C A A G = T = = T = = = = = T = = = A A = = C C T = C A T G G T = = = = = = = = = = = = ? ? ? = = = (T) ? = G (C) = (T) (A) = (G) ? (G) ? = = G = = = = = = = T = = = = = = = = = = = (A) = C C G = T A G = G (A) A = = = T = = = G = A = (C) = = (T) = (G) = C T C T C = G A G A C T G T C = A C (T) = = T A G A G G T = ? (C) (G) A C = (A) C T G C A = C = = C = = = = = C = = = G T = = T T C = T G C C C C = = = = = = = = = = = = ? ? ? = = = (C) ? = A (T) = (C) (G) = (C) ? (C) ? = = A = = = = = = = C = = = = = = = = = = = (C) = T A A = C G A = A (G) G = = = C = = = A = G = (T) = = (C) = (A) = D008 T G T = T = A G A T T C A C = = G G = T = C G = G (G) A C = ? ? G C A T = T C A = G = T = = T C = G G = = I G T A = A = = = = = = (A) = = = = G A = C = G D A T A C = A ? ? = = T C G = = C = T A = G C G T ? A = = = = D = = = = T C A = A = = A = C A = = = = = = (T) (A) = = G A A = = = T = = = = = G = (T) G = = (G) (G) ? C T C = C = G A G A C T G T = = A C = C = T A = A (A) G T = ? ? A A C C = C T G = A = C = = C T = A T = = D A C G = G = = = = = = (G) = = = = A G = T = A A C C G T = C ? ? = = C T D = = T = C G = C T C C ? G = = = = I = = = = G G G = G = = G = G C = = = = = = (C) (G) = = A G G = = = C = = = = = A = (C) A = = (T) (A) ? D009 = = = T = (T) = = = = = = = = = G = = = = A = = = = = = = = = = = = = = = = = = = = A = C = = = D = = T C I G = = = = A = = = = = = = = = = = = T = G = = = = A C = C C A C (D) ? = ? t = T = C G = C T C C C = = = C = I C = = = G G G = G = = G = = C (A) (C) = = (G) = (C) (G) (G) = A G G = = = C = = (T) = = = = = (A) = = (G) = = = = = C = (C) = = = = = = = = = A = = = = G = = = = = = = = = = = = = = = = = = = = G = T = = = T = = C T D A = = = = G = = = = = = = = = = = = C = C = = = = G T = A G G T (I) ? = ? D = C = T A = G C G T T = = = T = D T = = = T C A = A = = A = = A (C) (T) = = (A) = (T) (A) (A) = G A A = = = T = = (C) = = = = = (G) = = (T) = = D010 (T) (G) (T) (T) T = G (G) (G) T (C) (T) A C (C) = G G = = (G) (T) (G) (G) (A) G (G) T = C (T) A C C (T) = (C) T (A) C A (G) T = = T = = = = = (C) = = = G T = = C (T) T = (T) A (C) (C) G (T) = = = = = = = = = = = = A (C) (G) = = = = = = = T = (T) (A) = (C) (C) (G) C C = = = (T) = = (T) = = = G G A (G) A = (G) G = C A = (C) = = = = = = = = = = = = = = = = = T = (T) = = = = ? = (T) = = (C) (T) (C) (C) C = A (A) (A) A (T) (C) G T (T) = A C = = (A) (C) (A) (A) (G) A (A) C = T (C) G A A (C) = (T) C (G) A G (A) C = = C = = = = = (T) = = = A A = = T (C) C = (C) G (T) (G) C (C) = = = = = = = = = = = = C (G) (A) = = = = = = = C = (C) (G) = (G) (T) (C) T T = = = (C) = = (C) = = = T C G (T) G = (A) A = G C = (T) = = = = = = = = = = = = = = = = = C = (C) = = = = ? = (G) = = D011 = = = = = = = = = = = = = = = = (A) (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = T = D G G = T (D) (G) = A A = = C C T = C A T G G T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = (G) = = (T) = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = (C) = (T) = = = = = = G (A) ? = = = = = = = = = = = = = = = = (G) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = C = T A T = C (I) (A) = G T = = T T C = T G C C C C = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = (A) = = (C) = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = (T) = (C) = = = = = = T (G) ? D012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D013 C T C T C = G A G A C T G T C = A C = = A T A G A G G T = C C G A C C = C T G C A A C = G = = D G G = = = = = = = = = = = = G = = = = = = = = = = = = = = C = = ? ? C A = ? = T D = = T = C G = C T C C C G = = = = I = ? ? = G G G = G = = G = G C = = (C) = G = = (A) = C = = = (C) (G) ? ? ? (A) = = (C) = = = A (C) (T) G = (C) T G T C T = A G 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 G T = A = = T A T = = = = = = = = = = = = C = = = = = = = = = = = = = = T = = ? ? G G = ? = C G = = C = T A = G C G T T A = = = = D = ? ? = T C A = A = = A = C A = = (T) = A = = (G) = T = = = (G) (A) ? ? ? (G) = = (T) = = = G (G) (C) T = (T) D014 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 = ? C C = C T G = A = C = G = T D = = = T D A C = A ? = C C T G C A T G G T A G = T = ? A C C G T ? C C A = = C T D = = T G C G = C T C C C G = C = = I = = G = G G G = G = = G C G C A = = = G = T A G C G A A = = = T = = = = C (A) = (T) (A) = = = = C 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 = ? A T = T C A = G = T = A = C T = = = C I G T = T ? = T T C C T G C C C C G A = C = ? D A T A C ? A G G = = T C G = = C A T A = G C G T T A = T = = D = = A = T C A = A = = A T C A C = = = A = C G A T A G G = = = C = = = = T (G) = (C) (G) = = = = T D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C = T A T = C = = = G T = = T T C C T G C C C C = = = = = = = = T = = ? = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = T = A = C G A T A G G = = = C = = = = = G = = = = (C) T = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = D G G = T = = = A A = = C C T G C A T G G T = = = = = = = = C = = ? = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = C = G = T A G C G A A = = = T = = = = = A = = = = (T) G = C D016 (T) (G) (T) (T) T = G (G) (G) T (C) (T) A C = = G G = = (G) (T) (G) (G) (A) G (G) T = C (T) A C C (T) = (C) T (A) C A (G) T = = T = = = = = (C) = = = G T = = C (T) T = (T) A (C) (C) G (T) = = = = = = = = (C) = = = A (C) (G) = (I) ? (C) = = = T = (T) (A) = (C) (C) (G) C C (G) = = = = (I) = = = = G G A = A = = G = C A = (C) = = = = = = = = = = = = = = = = = T = (T) = = = = = = (T) = = (C) (T) (C) (C) C = A (A) (A) A (T) (C) G T = = A C = = (A) (C) (A) (A) (G) A (A) C = T (C) G A A (C) = (T) C (G) A G (A) C = = C = = = = = (T) = = = A A = = T (C) C = (C) G (T) (G) C (C) = = = = = = = = (T) = = = C (G) (A) = (D) ? (T) = = = C = (C) (G) = (G) (T) (C) T T (A) = = = = (D) = = = = T C G = G = = A = G C = (T) = = = = = = = = = = = = = = = = = C = (C) = = = = = = (G) = = D033 = = = = = = = = G (A) (T) (C) = = = (G) = = = T = = = (A) = = = = C = = A = = = = = = = A = = = (T) = = C D G T (C) = = = T = A (A) G (T) (C) (C) = (C) A (T) (C) C T (A) (A) (T) T (G) (G) D C = = = = (A) C G C = ? C (D) (t) = (C) (A) T G = C C G (C) T = = (T) (T) = (I) (T) = = = T C G = G = = G = = (C) (A) = = = (A) = C (A) (G) = (A) (G) G = = = ? ? = = = (T) = = = (A) (G) = (T) (G) T = = = = = = = = A (T) (C) (T) = = = (A) = = = C = = = (G) = = = = G = = G = = = = = = = C = = = (C) = = T T A G (T) = = = C = T (G) A (C) (T) (T) = (T) G (C) (G) G C (G) (G) (C) C (C) (A) A A = = = = (C) G A T = ? T (G) (D) = (T) (G) C A = G T C (T) C = = (C) (C) = (D) (C) = = = G G A = A = = A = = (A) (C) = = = (G) = T (G) (A) = (G) (A) A = = = ? ? = = = (C) = = = (G) (C) = (G) (A) C D034 = = = = = = = = G (A) (T) (C) = = = (G) = = = T = = = (A) = = = = C = = A = = = = = = = A = = = (T) = = C D G T (C) = = = T = A (A) G (T) (C) (C) = (C) A (T) (C) C T (A) (A) (T) T (G) (G) D C = = = (T) (A) C G C = ? C (D) (t) = (C) = T G = C C G (C) T ? ? ? ? ? (I) (T) = = = T C G = G = = G = = (C) = = = = = = C (A) = = (A) (G) G = = = (C) = = = = (T) (G) = (T) = = = = = T = = = = = = = = A (T) (C) (T) = = = (A) = = = C = = = (G) = = = = G = = G = = = = = = = C = = = (C) = = T T A G (T) = = = C = T (G) A (C) (T) (T) = (T) G (C) (G) G C (G) (G) (C) C (C) (A) A A = = = (C) (C) G A T = ? T (G) (D) = (T) = C A = G T C (T) C ? ? ? ? ? (D) (C) = = = G G A = A = = A = = (A) = = = = = = T (G) = = (G) (A) A = = = (T) = = = = (C) (A) = (C) = = = = = C D035 = = = T = = = = = = = = = = = = = = = T A = = G = = = = C = = G = = = = = = = C = A = = = = C = G G = C I G T = T A = T T C = T (G) C C C C G A = C = G D A = A C (C) = = = = (I) T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = (T) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = C G = = A = = = = G = = A = = = = = = = A = G = = = = T = A T = T D A C = A G = C C T = C (A) T G G T A G = T = A A C = G T (T) = = = = (D) C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = (C) (A) = = = = = = = = = = = = = = = = = = = = = = = D036 = = = = = = = = = = = = 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 = = C = = = = = C = = = G T = = T T C C T G C C C C = = = = = = ? = T = = = (C) = = = = = = = = = = = = = (C) = = = = = = = = C = D C = = = = = = G = = G = = = = = = = = A = C G A = (G) (A) (A) C G C (T) G A = = = G = (C) = = (C) = = T = = = = = = = = = = = = 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 = = T = = = = = T = = = A A = = C C T G C A T G G T = = = = = = ? = C = = = (A) = = = = = = = = = = = = = (T) = = = = = = = = T = I T = = = = = = T = = A = = = = = = = = G = T A G = (A) (G) (G) G A T (C) C G = = = A = (T) = = (T) = = C D037 = = = = = = = = = = = = = = = = = = = = = C G A G (A) = C = (T) (C) (G) C A T = T C A A G = T = = T = = = = = T = = = A A = = C C T = C A T G G T = = = = = = = = T = = ? A (G) (G) = = = C G = = C = T A = G C G T (T) A = = = = (D) = = = = T C A = A = = A = (C) A = = = = = = = = = = = = A = = = T = = = = = (A) = = G = = G (A) = = = = = = = = = = = = = = = = = = = = = = T A G A (G) = T = (C) (T) (A) A C C = C T G C A = C = = C = = = = = C = = = G T = = T T C = T G C C C C = = = = = = = = C = = ? C (C) (A) = = = T D = = T = C G = C T C C (C) G = = = = (I) = = = = G G G = G = = G = (G) C = = = = = = = = = = = = G = = = C = = = = = (G) = = A = = T (G) = D038 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) A C C = C T G = A = C = = C T = A T = = D A C G = G = = = = = = = = = = = A G = T = A A C = G T = C C A = = = = = = = T G C G = C T C C C = = C (C) = = (C) = = = G G G (G) G = (G) G = G C = = = = = = = = = = = = = = = = = = = = = C = (T) = = (C) = = = = 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 (G) C A T = T C A = G = T = = T C = G G = = I G T A = A = = = = = = = = = = = G A = C = G D A = A C = A G G = = = = = = = C A T A = G C G T T = = T (T) = = (T) = = = T C A (T) A = (A) A = C A = = = = = = = = = = = = = = = = = = = = = T = (C) = = (G) = = = = D039 = = = = = = = = = = = = = = = = = G = T = C G = G A A C C T T = C A T = T C A = G = T = = = C T = = (C) = = = T = T A = T T C C T (G) C C C C G A = C = G D ? = A C (C) A G G = (I) T C G = = C = T A = G C G T T A = = = = (D) = = = = T C A = A = = A = C A = = = = = = (C) (G) = = = = = = = = = = = = = C G = (C) = = C = = = = = = = = = = = = = = = = = = = = C = C = T A = A G G T G C C = A C C = C T G = A = C = = = T D = = (T) = = = C = A G = C C T G C (A) T G G T A G = T = A A ? = G T (T) C C A = (D) C T D = = T = C G = C T C C C G = = = = (I) = = = = G G G = G = = G = G C = = = = = = (T) (A) = = = = = = = = = = = = = T A = (T) = = T = = = D040 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C = T A T = C = = = G T = = T T C C T G C C C C = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = A = = C = = C = = = = = = G = = G = = = = C = = A A = C G A = = = = C G C = G A = = = G = = = = C = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = D G G = T = = = A A = = C C T G C A T G G T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = G = = T = = T = = = = = = T = = A = = = = A = = C G = T A G = = = = G A T = C G = = = A = = = = T = = ? Phase probabilities at each site with phase known positions indicated by = 1 1 1 1 1 = 1 1 1 1 1 1 1 1 = = = 1 = = 0.54 1 1 1 1 1 1 1 = 0.98 0.82 = 1 1 0.54 = 1 1 1 1 1 = 1 = 1 = = 1 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.54 = = = = = = 1 = = = = = = = 1 = = = = = = = = = = = 0.72 = = 1 = = = = = = = 0.67 = = = = = = = = 1 1 = = = 1 = 0.51 = = = 1 1 1 = 1 = 1 1 = = = = 1 1 1 1 1 1 = = = 1 1 1 1 1 1 1 = 0.99 0.99 = 1 1 1 = 1 1 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 = = = = = = = = = 0.99 = = 0.81 = = = 0.78 = 0.85 0.9 0.79 1 1 1 0.99 = = = 1 = = = = 0.99 = = 0.67 0.5 = = 0.83 = 0.67 = = = = = = = = = = = = = = 1 = = = = = = 1 1 1 1 0.9 1 1 = = = 0.88 1 1 1 = 1 1 1 1 1 = 1 = 1 = = 1 1 1 = = = = = = = = = = = = 1 = = = = = = = = = = = = = = 0.95 = = = 1 = = = = = 1 = = = 1 = 1 1 = 1 1 1 = = 0.98 0.79 = = = 0.86 = = = 0.77 1 1 1 = 1 = = 1 = = 1 1 = = 1 1 = 1 1 1 = 1 1 = = = = = = = = 0.76 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.77 0.77 = = = = = = = = = = = = 1 0.99 = 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 1 1 1 1 1 1 = = = 1 = = = = = 0.99 = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = 0.86 = = = = 0.98 0.96 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = 0.94 = = = = = = = 0.93 = = = 1 = = = = = = = = = = = = = = = 1 1 = = 1 = = = = 1 = = 0.83 = = = = = = = 1 = 1 = = = = 1 = 1 1 = 1 0.98 0.98 1 = 1 0.99 = 1 1 1 = 1 0.96 1 1 1 1 1 1 = 1 = 0.99 1 0.99 = 1 1 = = = = = = 1 = = = = = 1 = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.69 = 0.9 0.64 = = 0.81 0.52 = = = = 1 1 1 1 1 = 1 1 1 1 1 1 1 1 0.97 = 0.97 1 0.52 = = 1 1 1 1 1 1 1 = = 0.63 0.75 1 1 = 0.5 1 1 1 1 1 = 1 = = 1 = = = = = 1 = = = 1 1 = = 1 1 1 = 1 1 1 1 1 1 = = = = = = = = = = = = = = = = = = 0.51 = = 1 0.5 = 0.52 0.52 = 0.51 = 0.51 = = = 1 = = = = = = = 1 = = = = = = = = = = = 0.63 = 1 1 1 = 1 1 1 = 1 0.66 1 = = = 1 = = = 1 = 0.96 = 0.51 = = 0.69 = 0.5 = 1 1 1 = 1 = 1 1 1 1 1 1 1 1 = = 1 1 = 1 = 1 1 = 1 0.57 0.97 1 = = = 0.97 1 1 1 = 1 1 1 = 1 = 1 = = 1 1 = 1 1 = = 1 1 1 1 = 1 = = = = = = 0.72 = = = = 1 1 = 1 = 1 1 0.99 1 1 1 = 1 = = = = 1 1 1 = = 1 = 1 1 = 1 1 1 1 = 1 = = = = 0.97 = = = = 1 1 1 = 1 = = 1 = 1 1 = = = = = = 0.86 0.83 = = 1 1 1 = = = 1 = = = = = 0.97 = 0.73 1 = = 0.85 0.64 = = = = 1 = 0.52 = = = = = = = = = 1 = = = = 1 = = = = = = = = = = = = = = = = = = = = 1 = 1 = = = 1 = = 1 1 0.99 1 = = = = 1 = = = = = = = = = = = = 1 = 1 = = = = 1 1 = 0.98 1 1 1 0.75 = = = 1 = 1 = 1 1 = 1 1 1 1 1 = = = 0.98 = 1 1 = = = 1 1 1 = 1 = = 1 = = 1 0.6 0.88 = = 0.61 = 0.63 0.7 0.61 = 1 1 1 = = = 0.99 = = 0.51 = = = = = 0.75 = = 0.58 = = 0.52 0.7 0.79 0.68 0.97 = 1 0.52 0.52 1 0.55 0.55 0.96 1 0.52 = 1 1 = = 0.63 0.75 0.76 0.63 0.69 1 0.74 1 = 1 0.83 1 1 1 0.79 = 0.79 1 0.59 0.91 1 0.54 1 = = 1 = = = = = 0.8 = = = 1 1 = = 0.95 0.73 1 = 0.83 0.94 0.79 0.65 0.99 0.6 = = = = = = = = = = = = 1 0.55 0.62 = = = = = = = 1 = 0.58 0.53 = 0.75 0.59 0.76 1 0.9 = = = 0.51 = = 0.5 = = = 1 1 0.99 0.53 0.96 = 0.51 1 = 0.98 1 = 0.72 = = = = = = = = = = = = = = = = = 0.91 = 0.67 = = = = = = 0.86 = = = = = = = = = = = = = = = = = = 0.51 0.5 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = 1 1 1 = 1 0.5 0.52 = 1 1 = = 1 1 1 = 1 1 1 1 1 1 = = = = = = = = 0.94 = = = = = = = = = = = = = = = = = = = = = = = 0.53 = = 0.53 = = = = = = = = = = = = = = = = = = 0.5 = = = = = = = = = = = = = = = = = 0.51 = 0.63 = = = = = = 0.99 0.56 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 0.99 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 0.99 1 1 = = = = 0.99 = = = = 1 1 1 = 1 = = 1 = 0.97 1 = = 0.5 = 0.99 = = 0.86 = 0.98 = = = 0.52 0.52 = = = 0.53 = = 0.57 = = = 0.93 0.62 0.85 0.98 = 0.59 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 1 = = 1 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 = 0.99 1 1 = = 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 0.95 = = = 0.93 = 0.95 0.99 0.93 1 1 1 1 = = = 1 = = = = 0.97 0.66 = 0.6 0.55 = = = = 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 0.96 1 1 1 = = = 1 = = = = = 0.95 = = = = 0.72 0.99 = 0.95 0.53 0.7 0.79 0.68 0.97 = 1 0.52 0.52 1 0.55 0.55 0.96 1 = = 1 1 = = 0.63 0.75 0.76 0.63 0.69 1 0.74 1 = 1 0.83 1 1 1 0.79 = 0.79 1 0.59 0.9 1 0.55 1 = = 1 = = = = = 0.8 = = = 1 1 = = 0.94 0.73 1 = 0.83 0.94 0.79 0.65 0.99 0.6 = = = = = = = = 0.5 = = = 1 0.55 0.62 = 0.54 = 0.5 = = = 1 = 0.58 0.53 = 0.75 0.59 0.76 1 0.9 0.52 = = = = 0.51 = = = = 1 1 0.99 = 0.96 = = 1 = 0.98 1 = 0.72 = = = = = = = = = = = = = = = = = 0.91 = 0.67 = = = = = = 0.86 = = = = = = = = = = 1 0.74 0.67 0.5 = = = 0.62 = = = 0.99 = = = 0.54 = = = = 0.92 = = 1 = = = = = = = 1 = = = 0.67 = = 1 1 1 1 0.73 = = = 1 = 1 0.63 1 0.7 0.63 0.85 = 0.63 1 0.62 0.84 1 0.96 0.83 0.78 0.74 1 0.61 0.55 1 0.9 = = = = 0.52 0.93 1 1 = = 1 0.89 0.82 = 0.51 0.51 1 1 = 1 1 1 0.53 1 = = 0.52 0.53 = 0.57 0.7 = = = 1 1 1 = 1 = = 0.92 = = 0.62 0.51 = = = 0.5 = 1 0.9 0.5 = 0.7 0.62 1 = = = = = = = = 0.82 = = = 0.51 0.5 = 0.51 0.51 1 = = = = = = = = 1 0.74 0.67 0.5 = = = 0.62 = = = 0.99 = = = 0.54 = = = = 0.92 = = 1 = = = = = = = 1 = = = 0.67 = = 1 1 1 1 0.73 = = = 1 = 1 0.63 1 0.7 0.63 0.85 = 0.63 1 0.62 0.84 1 0.96 0.83 0.78 0.74 1 0.61 0.55 1 0.9 = = = 0.5 0.53 0.93 1 1 = = 1 0.89 0.82 = 0.51 = 1 1 = 1 1 1 0.53 1 = = = = = 0.57 0.7 = = = 1 1 1 = 1 = = 0.92 = = 0.62 = = = = = = 1 0.9 = = 0.7 0.62 1 = = = 0.58 = = = = 0.82 0.51 = 0.5 = = = = = 1 = = = 1 = = = = = = = = = = = = = = = 1 1 = = 1 = = = = 1 = = 0.99 = = = = = = = 1 = 1 = = = = 1 = 1 1 = 1 1 1 1 = 1 1 = 1 1 1 = 1 0.88 1 1 1 1 1 1 = 1 = 1 1 0.98 = 1 1 0.72 = = = = 0.5 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.82 = = = = 0.56 0.52 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 0.98 = 0.98 1 = = 0.87 1 1 1 1 1 1 1 = 1 0.94 1 1 1 0.84 = 1 1 1 1 1 = 1 = = 1 = = = = = 1 = = = 1 1 = = 1 1 1 1 1 1 1 1 1 1 = = = = = = = = 0.98 = = = 0.83 = = = = = = = = = = = = = 0.84 = = = = = = = = 0.99 = 1 1 = = = = = = 1 = = 1 = = = = = = = = 1 = 1 1 1 = 0.7 0.9 0.69 1 1 1 0.7 1 1 = = = 0.97 = 0.71 = = 0.79 = = 0.98 = = = = = = = = = = = = = = = = = = = = = 1 1 1 1 0.59 = 1 = 0.6 0.84 0.51 1 1 1 = 1 1 1 1 1 = 1 = = 1 = = = = = 1 = = = 1 1 = = 1 1 1 = 1 0.98 1 1 1 1 = = = = = = = = 0.91 = = = 1 0.58 0.57 = = = 1 0.98 = = 1 = 1 1 = 1 1 1 0.98 0.61 0.97 = = = = 0.61 = = = = 1 1 1 = 1 = = 1 = 0.56 1 = = = = = = = = = = = = 1 = = = 1 = = = = = 0.54 = = 1 = = 0.99 0.5 = 1 1 1 = 1 = 1 1 1 1 1 1 1 1 0.85 = 0.93 0.94 = 1 = 1 1 = 1 0.99 1 1 0.99 0.98 0.99 0.51 1 1 1 = 1 1 1 = 1 = 1 = = 1 1 = 1 1 = = 0.92 0.93 1 0.99 = 0.99 = = = = = = = = = = = 1 1 = 1 = 1 1 0.99 = 1 1 = 1 1 1 = = = = = = = 1 1 1 1 = 1 1 1 0.98 1 = = 1 0.74 = = 0.62 = = = 1 1 1 0.64 1 = 0.63 1 = 1 1 = = = = = = = = = = = = = = = = = = = = = 0.9 = 0.62 = = 0.74 = = = = = = = = = = = = = = = = = = = = = 0.97 = 1 = 1 1 = 1 0.95 1 1 1 1 1 = 1 1 1 = 1 1 1 = 1 = 1 = = = 1 1 = = 0.67 = = = 1 = 1 1 = 1 1 1 0.93 1 0.89 1 1 1 1 1 1 = 1 = 1 1 = = 1 1 0.79 1 1 0.99 = 0.67 0.99 1 1 = = 1 = 1 1 = 1 1 1 1 1 0.97 = = = = 0.78 = = = = 1 1 1 = 1 = = 1 = 1 1 = = = = = = 0.54 0.61 = = = = = = = = = = = = = 0.94 0.99 = 0.55 = = 0.91 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 = 1 1 1 = 1 = = = 1 1 = = 1 1 1 1 1 1 1 1 1 1 = = = = = = = = 0.96 = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = 1 = = 1 = = = = = = 1 = = 1 = = = = 1 = = 0.99 1 = 1 1 1 = = = = 1 1 1 = 1 1 = = = 0.99 = = = = 0.92 = = =