Fig. 7.

Single-reference callers achieve higher recall for samples in the same phylogroup as the reference genome, but not for rare loci. A Pandora recall (black line) and snippy recall (colored bars) of pan-variants in each of the 20 samples; each histogram corresponds to the use of one of 5 exemplar references, one from each phylogroup. The background color denotes the reference’s phylogroup (see Fig. 4 inset); note that phylogroup B1 (yellow background) is an outgroup, containing no samples in this dataset. B Same as A but restricted to SNPs present in precisely two samples (i.e., where 18 samples have neither allele because the entire locus is missing). Note the differing y-axis limits in the two panels