Fig. 5

SV genotyping comparison. Short reads from all 11 non-reference yeast strains were used to genotype SVs contained in the cactus graph and the VCF graph. Subsequently, sample graphs were generated from the resulting SV genotype sets. The short reads were aligned to the sample graphs and reads with identical mapping identity and quality across both sample graphs and an additional empty sample graph were removed from the analysis. The quality of the remaining divergent alignments was used to ascertain SV genotyping performance. The bars show the average delta in mapping identity (a) and in mapping quality (b) of divergent short reads aligned to the sample graphs derived from the cactus graph and the VCF graph. Positive values denote an improvement of the cactus graph over the VCF graph. Colors represent the two strain sets and transparency indicates whether the respective strain was part of the five strains set