Fig. 3

Overlap of SNPs and indels between pangenome- and assembly-based discovery. a–c Overlap of small variations (SNPs and indels smaller than 50 bp) between pggb, cactus, and assembly-based discovery presented for a biallelic SNPs, b biallelic indels, and c multiallelic SNPs/indels. Variants in different classifications of genomic regions are indicated by colour of the stacked bar. d Number of small variations recovered from each haplotype from the pangenome and the assembly-based mapping. The faded and dark areas of the bars represent indels and SNPs, respectively. e Precision and recall of pggb and cactus for SNPs, indels, and multiallelic variants assuming the assembly-based calls are truth. The black WGS point represents gold-standard accuracy for 30 × sequencing coverage