Variants in genomic context.

<p>(A) Density of SNPs around variant breakpoints by variant type. The dashed lines show the SNP density at the same loci but in DGRP lines that do not have the variant. (B) and (C) Density of SNPs near indels with minor allele count 2 to 4 (B) and 11 to 19 (C). The dashed lines show the SNP density at the same locus for DGRP lines without the indel. If indels were mutagenic, one would expect enrichment for low allele count SNPs near the high allele count indels; instead, the allele count of the neighboring SNPs closely matches that of the indel. (D) Density of variants (reference bases affected per Mb) in selected genomic regions. (E) Number of indels in coding regions by indel size. Insertions are in red and deletions in blue. Bars representing indel sizes that are a multiple of three are coloured dark red and blue, respectively.