Fig. 3

Allele frequency estimate (AFe) of the red versus the green pool of 180 accessions each plotted as delta-AFe values. The delta-AFe values for all detected variants (yellow dots) were plotted along the concatenated reference sequence sorted according to chromosome number. B. vulgaris chromosome 2 shows a clear difference peak close to it’s upper end (according to the standard orientation). Since the calculated AFe values become less reliable with less coverage, only variants supported by a mapped coverage of between 0.75 and 2.5 fold of the mean coverage of the respective chromosome were included in the plot