Figure 3

Number of revealed haplotypes is often an under-estimate of the actual number of underlying haplotypes. Four different hypothetical read mapping scenarios are shown for the block in Figure 1. All scenarios have same the number of reads at individual SNPs but differ in which of those reads span both SNPs. (A) 0-haplotype blocks. None of the reads spans the two SNPs therefore no haplotypes are deduced. (B) 1-haplotype blocks. A few reads span the two SNPs and they all show the same A.G haplotype. (C, D) 2- and 3-haplotype blocks arise when spanning reads show more haplotypes.