APAV: An advanced pangenome analysis and visualization toolkit
Fig 3
Element-level analysis for Os04g0373400 gene in the rice genome.
(A) Coverage distribution of the gene and all CDSs. (B) The number of samples with gene/CDS absence and presence within each rice group. Significant associations are observed between the rice groups and CDS1, CDS3, and CDS4 (all p < 0.001, Fisher’s test). (C-E) The heatmap for element level PAVs in terms of PAV(C), coverage (D), and sequence alignment depth (E) of elements in the Os04g0373400 gene. The absent regions of corresponding samples are highlighted with red dashed boxes.