Figure 3.

Allele frequency histogram. Visualization of mapping results of Dwarf Cavendish Illumina reads against the Pahang v2 reference sequence, used for the determination of SNV frequencies. The frequencies of the reference allele at SNV positions are displayed here, excluding those positions at which the Pahang reference sequence deviates from an invariant sequence position of Dwarf Cavendish. Black vertical lines indicate allele frequencies of 0.33, 0.5, and 0.66, respectively. SNVs in the duplicated segment on the long arm of chromosome 2 (magenta) are distinguished from all other variants (lime). Within the duplicated segment on chromosome 2, the frequency of the reference alleles is often 0.75 or 0.25 indicating the presence of three similar alleles and one diverged allele.