List of haplotypes found in best reconstruction,
with frequencies in parentheses.

1: C C T C T I A (18)
2: C C T C T I C (2)
3: T C T C T D C (18)
4: T C T C T I C (1)
5: T T C T C I C (2)
6: T T C C C I C (4)
7: T C C C C I C (1)
8: C T C C C I C (1)
9: C T C T C I C (1)


Summary of best reconstruction
(numbers refer to the list of haplotypes given above)

D001: (1,1)
D002: (1,1)
D003: (2,3)
D004: (3,3)
D005: (1,1)
D006: (3,1)
D007: (3,4)
D008: (5,3)
D009: (3,1)
D010: (6,7)
D011: (6,3)
D012: (1,8)
D013: (1,3)
D014: (1,1)
D015: (1,1)
D016: (5,3)
D033: (6,3)
D034: (2,3)
D035: (3,1)
D036: (1,3)
D037: (6,3)
D038: (3,1)
D039: (9,1)
D040: (3,3)


Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:

D001
C C T C T I A 
C C T C T I A 
D002
C C T C T I A 
C C T C T I A 
D003
C C T C T I C 
T C T C T D C 
D004
T C T C T D C 
T C T C T D C 
D005
C C T C T I A 
C C T C T I A 
D006
T C T C T D C 
C C T C T I A 
D007
T C T C T D C 
T C T C T I C 
D008
T T C (T) C I C 
T C T (C) T D C 
D009
T C T C T D C 
C C T C T I A 
D010
 T  T C C C I C 
[T] C C C C I C 
D011
T T C C C I C 
T C T C T D C 
D012
C C T C T I A 
C T C C C I C 
D013
C C T C T I A 
T C T C T D C 
D014
C C T C T I A 
C C T C T I A 
D015
C C T C T I A 
C C T C T I A 
D016
T T C (T) C I C 
T C T (C) T D C 
D033
T T C C C I C 
T C T C T D C 
D034
C C T C T I C 
T C T C T D C 
D035
T C T C T D  C  
C C T C T I [A] 
D036
C C T C T I A 
T C T C T D C 
D037
T T C C C I C 
T C T C T D C 
D038
T C T C T D C 
C C T C T I A 
D039
C T C (T) C I C 
C C T (C) T I A 
D040
T C T C T D C 
T C T C T D C 



Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []
with phase known positions indicated by =

D001
= ? = = = = = 
= ? = = = = = 
D002
= = = = = = = 
= = = = = = = 
D003
C = = = = I = 
T = = = = D = 
D004
= = = = = = = 
= = = = = = = 
D005
= ? = ? = = = 
= ? = ? = = = 
D006
T = = = = D C 
C = = = = I A 
D007
= = = = = D = 
= = = = = I = 
D008
= T C (T) C I = 
= C T (C) T D = 
D009
T = = = = D C 
C = = = = I A 
D010
? T = = = = = 
? C = = = = = 
D011
= T C = C I = 
= C T = T D = 
D012
= C T = T = A 
= T C = C = C 
D013
C = = = = I A 
T = = = = D C 
D014
= = = = = = = 
= = = = = = = 
D015
= = = = = = = 
= = = = = = = 
D016
= T C (T) C I = 
= C T (C) T D = 
D033
= T ? = C I = 
= C ? = T D = 
D034
C = = = = I = 
T = = = = D = 
D035
T = = = = D ? 
C = = = = I ? 
D036
C = = = = I A 
T = = = = D C 
D037
= T C = C I = 
= C T = T D = 
D038
T = = = = D C 
C = = = = I A 
D039
= T C (T) C = C 
= C T (C) T = A 
D040
= = = ? = = = 
= = = ? = = = 



Phase probabilities at each site
with phase known positions indicated by =
= = = = = = = 
= = = = = = = 
1 = = = = 0.99 = 
= = = = = = = 
= = = = = = = 
1 = = = = 1 1 
= = = = = 1 = 
= 1 1 0.74 1 1 = 
1 = = = = 1 1 
= 1 = = = = = 
= 1 1 = 1 1 = 
= 0.97 1 = 1 = 1 
1 = = = = 1 1 
= = = = = = = 
= = = = = = = 
= 1 1 0.74 1 1 = 
= 1 = = 1 1 = 
1 = = = = 0.99 = 
1 = = = = 1 = 
1 = = = = 1 1 
= 1 1 = 1 1 = 
1 = = = = 1 1 
= 0.99 1 0.65 1 = 1 
= = = = = = =