Figure 2.

Pairwise SNP distance relationship between Illumina (COMPASS) and Nanopore (BCFtools) data

Each point represents the SNP distance between two isolates. The dashed line shows the identity line (ie, y=x). The isolate pairs shown are all pairs whereby the COMPASS distance is 20 or less. The red area and points indicate pairs with a Nanopore distance of more than 12 but an Illumina distance of 12 or less. These pairs are deemed false negative connections. The red area with stripes indicates pairs that are false negative connections at an Illumina threshold of five (Nanopore threshold of six), but not when the threshold is expanded to 12. These pairs are shown as square points. The grey area and points are the inverse—ie, false positive connections. Thus, the grey striped area shows pairs of samples that are false positive connections at an Illumina threshold of five (Nanopore threshold six), but not when the threshold is expanded to 12. SNP=single-nucleotide polymorphism.