UHTS and tiling array statistics for the investigated accessions. (a) Total number of short reads (35 bp for paired end runs; 36 bp for single end runs) obtained for each accession after quality filtering and calculated raw coverage (single end runs were performed for Eil-0, Lc-0 and Sav-0; additional paired end runs for Eil-0 and Lc-0; Tsu-1 and Col-0 reads from single end runs were obtained from published data). For Tsu-1, a subset of reads was retrieved (Tsu-1red) for comparative purposes. (b) Average coverage after MAQ mapping of the short reads onto the Col-0 reference genome and number of base-pairs in the reference genome with zero coverage. (c) Genomic tiling array statistics. Left: number of unique tiles with relative hybridization signal ratio <-1.0 (log2) calculated from the averages of two array hybridizations with divergent DNA versus two array hybridizations with the reference DNA. Middle: number of unique tiles with no UHTS coverage across all 25 bp of the tile. Right: intersection between the two groups of tiles. (d) Example plot of tiling array signal ratio (top panel) versus UHTS coverage (bottom panel). The entire gene (At1g31100) appears to be deleted in Eil-0, but appears to be intact in Lc-0. Please refer to Figure 3c for detailed plot labels.