Fig. 1

Illustration of the types of balance measurement — SB, MB, and AB — with respect to read simulation, read mapping, and halpotype assignment. Note that the mismapped reads are excluded when calculating MB, and the reads assigned “Others” are also excluded when calculating AB. Columns indicate distinct types of bias event. “Loss\(^{*}\)” indicates a bias event due to reads with ALT alleles failing to align. “Loss\(^{**}\)” indicates a bias event due to reads mapping elsewhere than their true point of origin. “Flux” indicates bias from gaining mismapped reads from other sites. “Local” indicates that local repeat content, as well as sequencing errors, combine to make a gap placement ambiguous