Intraspecific genomic comparisons of 288 bacterial species
Filtering the MAGs generated by Pasoli et al., (2019) for MAGs belonging to SGBs represented by >100 genomes yielded 118,617 metagenome assembled genomes (MAGs) with >50% completeness and <5% contamination as estimated by CheckM (Parks et al. 2015) belonging to 287 bacterial species-level genome bins (SGBs). From these genomes, CoreCruncher (Harris et al., 2021) identified 566,958 core open reading frames (CORFs). Tajima’s D values and representative amino acid sequences for each of these CORFs are presented in Table S1.