The details of the 9 genomic sequence contexts considered in GLM were summarized in Additional file 4. Briefly, general contexts including substitution types, immediate upstream and downstream bases, GC content, and homopolymer related features: whether the locus is within a homopolymer, the closest homopolymer length, the distance to the closest homopolymer, the local homopolymer base percentages and whether the alternative base is the same as the immediate upstream or downstream base are considered. These 9 features are the covariates included in the GLMs.
