Overlap of deletions between two or more of the four accessions examined. (a) Venn diagram of the overlap between transposable element genes for which deletions (that is, tiling array signal ratio <-1.0 (log2) and no short read coverage for at least 100 bp) could be detected in the different accessions. (b) Same as (a), for protein coding genes. (c) Example plot of tiling array signal ratio versus UHTS short read coverage for a gene (At1g09840) in all four accessions. Top panels: tiling array signal ratio (log2), with the -1.0 threshold indicated by a red line. Bottom panel: corresponding short read coverage after MAQ mapping. A major deletion shared by two accessions (Eil-0 and Lc-0) and another shared by all four accessions are highlighted.