Figure 9

Relationship of diploid clustering to mean genic read depth in F. × ananassa ‘Winter Dawn’, displayed for PHR di-allelic SNPs (A) and for PHR SNP-SNPs (B). Black dot positions, which are identical in panels A and B, represent the mean read depth category (X axis), and the relative frequency of this read depth category (Y axis). The size of each dot is directly proportional to the fraction of di-allelic SNP (A) or SNP-SNP (B) markers that displayed diploid-like clustering. For example, the green arrow in (A) points to a large black dot with mean read depth category of approximately 28× (X axis) and a category frequency of approximately 0.01 (Y axis). The red arrow in (A) points to a small black dot corresponding to a mean read depth category of about 100× and a category frequency of about 0.015. The larger dot sizes (green arrows) occur in (A) in regions of comparatively low read depth, and in (B) in regions of comparatively high read depth. Conversely, smaller dot sizes occur in (A) in regions of comparatively high read depth, and in (B) in regions of comparatively low read depth (red arrows).