Fig. 2

Genomic distribution of B73- and F2-specific regions. PAV distributions along all chromosomes for 10 Mb sliding windows and 1 Mb steps. Each panel represents a different chromosome with chromosome number indicated on top. Grey boxes indicate position of peri-centromeric regions. For each chromosome, top panel: fraction of window covered by B73 genes, number of F2/B73 SNPs per window, PAVs (F2-specific and B73-specific regions). Numbers are scaled relatively to the highest value across the whole genome for each feature type. Bottom panel: fraction of window covered by B73 reads and F2 reads with mapping quality > 30 (no scaling was applied). Asterisks highlight regions of low diversity between F2 and B73. Greek letters represent regions with particular patterns (from visual inspection). Regions with Ω abundant SNP and scarce PAV; ω abundant SNP and abundant PAV; Δ abundant F2-specific regions and scarce B73-specific regions; δ scarce F2-specific regions and abundant B73-specific regions