The density of SFPs and genes across each chromosome of A. thaliana. SFP density is calculated for all accessions per base pair (bp) using a sliding window of 50 kbp and the density at each position is plotted on a log scale (shown in black). The gene density, calculated as coding bp per every 50,000 genomic bp is also calculated (shown in light blue). The olive regions show the position of the centromeres. Deletions are shown in red and are defined as 10 probes in a row that were called SFPs (~350 bp). In the figure, the number of deleted bp calculated in a 50 kbp window. We have defined a duplication to be at least 10 probes in a row with a log2-fold change of greater than 1 (2-fold increase in signal). In this figure, the number of duplicated bp is calculated in 50 kb windows across the chromosome (green).