Fig. 3

Impact of a single nucleotide polymorphism (SNP) on the peptide coverage of a protein fragment. Because tryptic peptides are non-overlapping, each read position is covered by exactly one tryptic peptide. A SNP modifies a single tryptic peptide, but all positions around the SNP covered by the modified peptide are no longer covered (correctly) after matching (53 read positions on average). Because k-mers are overlapping, each read position is covered by k peptides, except at the ends of the protein fragments. A SNP modifies k peptides, but apart from reduced peptide coverage around the SNP, only a single codon is no longer covered (correctly) after matching. The redundancy of the overlapping k-mers therefore makes up for a reduced impact of SNPs compared to non-overlapping tryptic peptides, at the cost of larger data volumes that need to be processed