Pangenome-wide association study (PGWAS) of tetracycline and erythromycin resistance. (A) Manhattan plot of unitigs mapped to Spn23F. Locus tags and gene names for features in peaks: (1) Spn23F01130 (capD), Spn23F01140 (epsC); (2) Spn23F01760 (ruvA), Spn23F01770 (tag), Spn23F01780 (putative protease); and (3) Tn916. Gene coverage by significant unitigs associated with tetracycline (B) and erythromycin (C) resistance identified by pyseer and mapped by ggCaller, with known causative genes marked by red asterisks. Number of mapped queries per kilobase pair was calculated by binning genes matched to queries by ggCaller with the same annotation, and then taking the ratio of the number of queries mapped to the total sequence length of the bin. Core genome phylogenies with resistance and causal gene annotations generated by ggCaller are available in Supplemental Figure 9.