Figure 1.

Uncertainty in IBD Endpoints

(A) Allele discordances between two haplotypes are represented as crosses. We wish to estimate the endpoints of the IBD segment that covers the focal position in the middle of the longest identity by state (IBS) interval.

(B–D) Three of the possibilities for the shared IBD segment that covers the focal position.

(B) The IBD segment contains the first discordance to the right of the focal position.

(C) The IBD segment does not extend all the way to the discordances and has short flanking segments of IBS.

(D) Two moderately long IBD segments are adjacent. In this case, the second IBD segment is not of direct interest because it does not cover the focal position.