Fig. 1

Digital Unmasking of Nucleotide-conversions in k-mers: Legend: Possible base outcomes for a given nucleotide-conversion: match with reference (white), nucleotide-conversion scored as mismatch (red), nucleotide-conversion scored with nucleotide-conversion aware scoring (blue), low-quality nucleotide conversion (black) and filtered nucleotide-conversion (opaque) a Naïve nucleotide-conversion processing and quantification vs DUNK: The naïve read mapper (left) maps 11 reads (grey) to the reference genome and discards five reads (light grey), that comprise many converted nucleotides (red). The DUNK mapper (right) maps all 16 reads. b DUNK processes multi-mapping reads (R5, R6, R7, left) such that the ones (R3, R6) that can be unambiguously assigned to a 3′ interval are identified and assigned to that region, R5 and R7 cannot be assigned to a 3′ interval and will be deleted from downstream analyses. R2 is discarded due to general low alignment quality. c False-positive nucleotide conversions originating from Single-Nucleotide Polymorphisms are masked. d High-quality nucleotide-conversions are quantified normalizing for coverage and base content