For each of the 212,560 SARS-CoV-2 genomes, we conducted mutation analysis. Based on published literature, the filtering criteria were as follows: (i) an allele frequency > 1 % within a cluster and (ii) presence in at least three genomes in that cluster. After the filtering process, we identified a total of 212,881 common mutations from 3,419 plasmid cluster.

Plasmid clusters along with the taxonomic information of their corresponding plasmids.

We detected 2,448 mutations in genes related to pathogenicity, contributing to a better understanding of pathogen–host interactions.

A total of 646 mutations were found in antimicrobial resistance genes, including those linked to known resistance phenotypes or potentially involved in resistance mechanisms.

We identified 2,717 mutations in genes linked to resistance against biocides and heavy metals, highlighting potential risks to public health and the environment.

A total of 4,156 mutations were identified in genes associated with known virulence functions, providing insights into bacterial pathogenicity.

ProtParam software is used for the analysis of physicochemical properties.

A total of 4,814 mutations were identified in genes associated with substrate uptake and detoxification, shedding light on bacterial adaptation strategies.