List of haplotypes found in best reconstruction, with frequencies in parentheses. 1: T C A A A (71) 2: T C A G T (5) 3: C T G G T (26) 4: C T G A A (14) 5: C T A A A (14) 6: C T A G T (7) 7: T C G A A (19) 8: T T A A A (1) 9: T T G A A (15) 10: T C G G T (4) 11: T C A A T (1) 12: C T A A T (3) 13: T C A G A (1) 14: T C G G A (1) Summary of best reconstruction (numbers refer to the list of haplotypes given above) #1: (1,2) #2: (1,1) #3: (3,4) #4: (1,5) #5: (1,6) #6: (1,1) #7: (1,1) #8: (1,3) #9: (6,1) #10: (1,1) #11: (1,1) #12: (1,5) #13: (1,5) #14: (1,7) #15: (6,8) #16: (5,6) #17: (3,1) #18: (3,5) #19: (1,3) #20: (1,4) #21: (1,3) #22: (1,1) #23: (3,1) #24: (7,1) #25: (1,6) #26: (4,5) #27: (1,4) #28: (9,1) #29: (1,1) #30: (1,10) #31: (1,9) #32: (7,1) #33: (3,1) #34: (5,3) #35: (1,1) #36: (2,1) #37: (11,12) #38: (1,4) #39: (7,1) #40: (3,5) #41: (1,3) #42: (1,4) #43: (9,1) #44: (1,4) #45: (13,14) #46: (4,5) #47: (1,7) #48: (1,3) #49: (5,5) #50: (1,4) #51: (4,1) #52: (1,3) #53: (7,5) #54: (1,10) #55: (7,9) #56: (10,3) #57: (10,3) #58: (1,4) #59: (1,1) #60: (4,1) #61: (1,9) #62: (3,7) #63: (1,9) #64: (1,7) #65: (7,9) #66: (3,3) #67: (3,1) #68: (9,5) #69: (7,1) #70: (1,9) #71: (2,9) #72: (1,6) #73: (2,9) #74: (1,5) #75: (7,12) #76: (2,3) #77: (9,7) #78: (3,7) #79: (3,1) #80: (3,7) #81: (4,12) #82: (4,1) #83: (3,1) #84: (9,3) #85: (9,7) #86: (1,7) #87: (1,3) #88: (7,1) #89: (1,6) #90: (7,1) #91: (1,9) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: #1 T C A A A T C A G T #2 T C A A A T C A A A #3 C T G G T C T G A A #4 T C A A A C T A A A #5 T C A (A) (A) C T A (G) (T) #6 T C A A A T C A A A #7 T C A A A T C A A A #8 (T) (C) (A) A A (C) (T) (G) G T #9 (C) (T) A G T (T) (C) A A A #10 T C A A A T C A A A #11 T C A A A T C A A A #12 T C A A A C T A A A #13 T C A A A C T A A A #14 T C A A A T C G A A #15 (C) T A G T (T) T A A A #16 C T A A A C T A G T #17 C T G G T T C A A A #18 C T (G) G T C T (A) A A #19 T C (A) (A) (A) C T (G) (G) (T) #20 T C (A) A A C T (G) A A #21 T C (A) A A C T (G) G T #22 T C A A A T C A A A #23 C T (G) (G) (T) T C (A) (A) (A) #24 T C G A A T C A A A #25 T C A (A) (A) C T A (G) (T) #26 C T G A A C T A A A #27 T C (A) A A C T (G) A A #28 T T G A A T C A A A #29 T C A A A T C A A A #30 T C (A) A A T C (G) G T #31 T C A A A T T G A A #32 T C G A A T C A A A #33 C T G (G) (T) T C A (A) (A) #34 C T (A) A A C T (G) G T #35 T C A A A T C A A A #36 T C A G T T C A A A #37 T C A A T C T A A T #38 T C (A) A A C T (G) A A #39 T C G A A T C A A A #40 C T (G) G T C T (A) A A #41 (T) (C) (A) A A (C) (T) (G) G T #42 T C (A) A A C T (G) A A #43 T T G A A T C A A A #44 T C (A) A A C T (G) A A #45 T C A G A T C G G A #46 C T G A A C T A A A #47 T C A A A T C G A A #48 T C A A A C T G G T #49 C T A A A C T A A A #50 T C (A) A A C T (G) A A #51 C T (G) A A T C (A) A A #52 T C (A) (A) A C T (G) (G) T #53 T C (G) A A C T (A) A A #54 T C (A) A A T C (G) G T #55 T C G A A T T G A A #56 T C G G T C T G G T #57 T C G G T C T G G T #58 T C (A) A A C T (G) A A #59 T C A A A T C A A A #60 C T (G) A A T C (A) A A #61 T C A A A T T G A A #62 C T G G T T C G A A #63 T C A A A T T G A A #64 T C A A A T C G A A #65 T C G A A T T G A A #66 C T G G T C T G G T #67 C T (G) G T T C (A) A A #68 T T G A A C T A A A #69 T C G A A T C A A A #70 T C A A A T T G A A #71 T (C) A G T T (T) G A A #72 (T) (C) A A A (C) (T) A G T #73 T (C) (A) G T T (T) (G) A A #74 T C A A A C T A A A #75 T C (G) A (A) C T (A) A (T) #76 T C (A) G T C T (G) G T #77 T T G A A T C G A A #78 (C) (T) G G T (T) (C) G A A #79 C T (G) G T T C (A) A A #80 (C) (T) G G T (T) (C) G A A #81 C T G A A C T A A T #82 [C] T (G) A A T C (A) A A #83 (C) (T) (G) G T (T) (C) (A) A A #84 [T] T G A A C T G G T #85 T T G A A T C G A A #86 T C A A A T C G A A #87 T C (A) (A) A C T (G) (G) T #88 T C G A A T C A A A #89 (T) (C) A A A (C) (T) A G T #90 T C G A A T C A A A #91 T C A A A T T G A A Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = #1 = = = A A = = = G T #2 = = = = = = = = = = #3 = = = G T = = = A A #4 T C = = = C T = = = #5 T C = (A) (A) C T = (G) (T) #6 = = = = = = = = = = #7 = = = = = = = = = = #8 (T) (C) (A) A A (C) (T) (G) G T #9 (C) (T) = G T (T) (C) = A A #10 = = = = = = = = = = #11 = = = = = = = = = = #12 T C = = = C T = = = #13 T C = = = C T = = = #14 = = A = = = = G = = #15 (C) = = G T (T) = = A A #16 = = = A A = = = G T #17 C T G G T T C A A A #18 = = (G) G T = = (A) A A #19 T C (A) (A) (A) C T (G) (G) (T) #20 T C (A) = = C T (G) = = #21 T C (A) A A C T (G) G T #22 = = = = = = = = = = #23 C T (G) (G) (T) T C (A) (A) (A) #24 = = G = = = = A = = #25 T C = (A) (A) C T = (G) (T) #26 = = G = = = = A = = #27 T C (A) = = C T (G) = = #28 = T G = = = C A = = #29 = = = = = = = = = = #30 = = (A) A A = = (G) G T #31 = C A = = = T G = = #32 = = G = = = = A = = #33 C T G (G) (T) T C A (A) (A) #34 = = (A) A A = = (G) G T #35 = = = = = = = = = = #36 = = = G T = = = A A #37 T C = = = C T = = = #38 T C (A) = = C T (G) = = #39 = = G = = = = A = = #40 = = (G) G T = = (A) A A #41 (T) (C) (A) A A (C) (T) (G) G T #42 T C (A) = = C T (G) = = #43 = T G = = = C A = = #44 T C (A) = = C T (G) = = #45 = = A = = = = G = = #46 = = G = = = = A = = #47 = = A = = = = G = = #48 T C A A A C T G G T #49 = = = = = = = = = = #50 T C (A) = = C T (G) = = #51 C T (G) = = T C (A) = = #52 T C (A) (A) A C T (G) (G) T #53 T C (G) = = C T (A) = = #54 = = (A) A A = = (G) G T #55 = C = = = = T = = = #56 T C = = = C T = = = #57 T C = = = C T = = = #58 T C (A) = = C T (G) = = #59 = = = = = = = = = = #60 C T (G) = = T C (A) = = #61 = C A = = = T G = = #62 C T = G T T C = A A #63 = C A = = = T G = = #64 = = A = = = = G = = #65 = C = = = = T = = = #66 = = = = = = = = = = #67 C T (G) G T T C (A) A A #68 T = G = = C = A = = #69 = = G = = = = A = = #70 = C A = = = T G = = #71 = (C) A G T = (T) G A A #72 (T) (C) = A A (C) (T) = G T #73 = (C) (A) G T = (T) (G) A A #74 T C = = = C T = = = #75 T C (G) = (A) C T (A) = (T) #76 T C (A) = = C T (G) = = #77 = T = = = = C = = = #78 (C) (T) = G T (T) (C) = A A #79 C T (G) G T T C (A) A A #80 (C) (T) = G T (T) (C) = A A #81 = = G = A = = A = T #82 ? T (G) = = ? C (A) = = #83 (C) (T) (G) G T (T) (C) (A) A A #84 ? = = A A ? = = G T #85 = T = = = = C = = = #86 = = A = = = = G = = #87 T C (A) (A) A C T (G) (G) T #88 = = G = = = = A = = #89 (T) (C) = A A (C) (T) = G T #90 = = G = = = = A = = #91 = C A = = = T G = = Phase probabilities at each site with phase known positions indicated by = = = = 0.98 0.98 = = = = = = = = 0.98 0.98 0.98 0.98 = = = 0.98 0.98 = 0.77 0.77 = = = = = = = = = = 0.88 0.87 0.87 0.98 0.98 0.71 0.71 = 0.98 0.98 = = = = = = = = = = 0.98 0.98 = = = 0.98 0.98 = = = = = 0.98 = = 0.58 = = 0.98 0.98 = = = 0.98 0.98 0.92 0.92 0.92 0.92 0.92 = = 0.65 0.98 0.98 0.98 0.98 0.77 0.88 0.88 0.98 0.98 0.69 = = 0.92 0.92 0.73 0.98 0.98 = = = = = 0.96 0.96 0.77 0.88 0.88 = = 0.98 = = 0.98 0.98 = 0.83 0.83 = = 0.98 = = 0.98 0.98 0.56 = = = 0.92 0.98 = = = = = = = = = 0.56 0.98 0.98 = 0.98 0.98 = = = = 0.98 = = 0.98 0.96 0.9 0.88 0.88 = = 0.73 0.98 0.98 = = = = = = = = 0.98 0.98 0.98 0.98 = = = 0.98 0.98 0.67 = = = = 0.98 = = = = 0.81 0.98 0.98 0.87 0.87 0.77 0.98 0.98 0.98 0.98 0.69 = = = 0.98 0.92 = = 0.98 0.98 0.52 = = = = 0.98 = = = = 0.98 = = = = 0.98 = = 0.92 0.92 0.92 0.9 0.9 = = = = = 0.98 0.98 0.58 = = 0.96 0.98 0.65 = = 0.96 0.96 0.85 0.87 0.9 0.98 0.98 0.5 = = = = 0.62 0.98 0.94 = 0.98 = = = 0.98 0.98 = = = 0.98 0.98 = = = 0.98 0.98 0.69 = = = = = = = 0.98 0.98 0.63 = = = 0.98 0.92 = = 0.9 0.9 = 0.98 0.98 = 0.98 0.98 = = = = 0.98 = = = 0.98 = = = = = = = = 0.96 0.96 0.87 0.94 0.96 0.92 = 0.98 = = = = 0.98 = = = 0.92 0.98 = = = 0.85 0.9 0.98 0.98 0.73 0.73 = 0.98 0.98 = 0.85 0.85 0.98 0.98 0.98 0.98 = = = 0.98 0.98 0.67 = 0.83 0.98 0.98 0.75 = = = 0.98 = = = 0.88 0.87 = 0.98 0.98 0.98 0.98 0.87 0.96 0.96 0.85 0.85 = 0.98 0.98 = = 0.98 = 0.9 = 0.98 0.77 = = 0.87 0.87 0.75 0.98 0.98 = = = 0.98 0.98 = 0.98 = = = = = 0.98 = = 0.98 0.98 0.81 0.88 0.9 = = 0.98 = = 0.81 0.81 = 0.98 0.98 = = 0.98 = = = 0.98 0.94 = =