We set the haplotype display threshold to zero to show all possible diplotypes (haplotype pairs) for patient number 3 (see Fig. 19.2. We see that while four diplotypes are possible, the first one:

0,0,1,1,0,1,1,1,0,1,1
1,0,1,1,0,1,0,1,0,0,1

has an estimated probability of 1.0 of being the actual diplotype. Sometimes there will be ambiguity after EM convergence, and more than one diplotype will have a probability within the display threshold.

See 19.5 below for a further explanation of diplotypes.

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