Fig. 2

Accuracy of mapping simulated paired-end reads to genome graphs that contained variants filtered for allele frequency at chromosome 25. a The top principal components of a genomic relationship matrix constructed from whole-genome sequence variants reflect the genetic diversity of the four cattle breeds considered. b Nucleotide diversity of the four breeds calculated in non-overlapping 10-kb windows for variants of chromosome 25. The values below each boxplot indicate the nucleotide diversity for the four breeds averaged across all sliding-windows. c Edge-to-node ratio of graphs that contained between 2046 and 293,804 variants filtered for allele frequency. d Proportion of incorrectly mapped reads for four breed-specific augmented genome graphs. Diamonds and large dots represent values from linear mapping using BWA mem and vg, respectively. The inset represents a larger resolution of the mapping accuracy for alternate allele frequency thresholds less than 0.1. e True-positive (sensitivity) and false-positive mapping rate (specificity) parameterized on mapping quality of the best performing graph from each breed. f Read mapping accuracy for breed-specific augmented graphs that contained variants that were either filtered for alternate allele frequency (triangles) or sampled randomly (circles) from all variants detected within a breed. The dashed and solid line represents the average proportion of mapping errors across four breeds using random sampling and variant prioritization, respectively. Colors indicate values obtained for different breeds. Results for single-end mapping are presented in Additional file 1: Fig. S2