Genomic coverage of the entire Affymetrix 500 K chip set SNPs (purple, left-most bar) and annotated genomic coverage of Gentrepid (other bars) when pseudo-intervals are constructed around the SNPs using each approach tested. The bar graph on the left shows how many characterized genes in the genome are covered or represented for each approach tested. The approach most commonly used in GWAS, nearest, is indicated with an *. The Affy Chip set only covers 80% of the genes in the genome using this method. The BY approach has the higher total genome coverage, and this also holds when looking at the annotated coverage. The Venn diagram on the right shows the total overlap between the annotated (15,702) and characterized genes (27,499) in Gentrepid, with the greater portion of annotation from domain information. Parsed domains refer to the genes with Pfam domain information.
Ballouz et al. BMC Genetics 2011 12:98 doi:10.1186/1471-2156-12-98