Fig. 3.

Downsampling a high-coverage aDNA sample. The comparative effect of downsampling on heterozygous variant calling following bwa aln and vg map alignment of reads from the ancient Yamnaya sample [26] with different parameters and mapping quality filtering thresholds, and including post-processing of bwa aln with the modified read filter [10]. a SNPs. b Indels (the modified read filter does not apply in this case)