Fig. 1

Relationship between Mash distance (A) or taxonomic distance (B) and peak matching (PM) score. For panel A, the inverse Mash distance ([1 − mash] × 100, nearly equivalent to ANI (%)) was calculated and binned as shown on the x-axis. For panel B, taxonomic distances were obtained based on the GTDB r95 taxonomy; labels on the x-axis indicate taxonomic levels at which differences in PM scores are evaluated (for example, “strain” indicates pairs of genomes within the same species). PM scores were obtained from 200 randomly selected genomes matched against all genome entries in the GPMsDB (193,197 reference genome entries). Mass error tolerances of 50 (blue) and 200 ppm (red) were used for peak matching, and the resultant values were plotted as dots for given pairs of genomes. The distribution of the quantitative data is also shown as box plots, where the quartiles of the dataset are shown as boxes, while the whiskers extend to show the rest of the distribution, except for points that were determined to be “outliers” using a method that is a function of the interquartile range