Fig. 5

Genetic variants from the graph topology. a Number of variant sites in each haplotype per genome. SNP = single-nucleotide polymorphisms, INS = insertions, DEL = deletions, M = millions. b Distribution of variants by size. c Variant sites distribution per variant type and impact for each pangenome class (n = 18 haplotypes). d Number of variant sites per gene locus in hemizygous genes (x-axis) and all the genes impacted by variants (y-axis) (n = 9 genomes). e Enrichment analysis results for the variant effects identified in the hemizygous genes when compared with all the genes impacted by variants. Boxes are colored with the average enrichment values (n = 9 genomes). For the boxplot representations in c and e, the middle bars represent the median while the bottom and top of each box represent the 25th and 75th percentiles, respectively. The whiskers extend to 1.5 times the interquartile range and data beyond the end of the whiskers are plotted individually as outlying points. f Pangenome features at the sex-determining region. V. arizonica B40-14 was used as representative for the region. For each allele (female and male), the density of allele-specific nodes, the repeats distribution, and the gene loci with the conserved variants are represented. The region is a sub-selection of the SDR spanning genes encoding VviYABBY3 to the WRKY transcription factor