Fig. 1

Illustration of paired-end reads covering a heterozygous SNV (reference allele is denoted by 0 and the variant allele as 1) in a diploid genome. The reads can be grouped into clusters of different sizes based on their alignment coordinates. Two reads that start and end at the same position but carry different alleles (0 and 1) at the heterozygous site (a) are highly likely to correspond to natural duplicates, i.e. independent DNA fragments. In contrast, a pair of read duplicates that have identical alleles at the heterozygous site (b) could correspond to PCR duplicates or natural duplicates