NGS of single and multiple fosmid pools: whole genome coverage. (A) Sequencing a pool of 15,000 fosmids covers ∼15% of the genome. The probability that complementary haplotypes may co-occur within a pool is P < 0.0112, resulting in only a small percentage (1%–2%) of variants likely to be covered by fosmids from both haplotypes. The insert shows a specific example of 19 fosmids detected in the MHC region, concordant with the expected number of fosmids. (B) Additional sequencing of fosmid pools (coverage shown for 32 pools) results in increasing fosmid clone coverage and saturation with molecular haplotype sequence coverage across the entire genome. As shown by simulation, low coverage regions are primarily explained by limitations inherent in short read mapping (Supplemental Fig. S2).