Pasolli et al. [13]: genome fasta files were accessed from (http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html) on 2020-03-12. SGB annotations of genomes were taken from article supplementary files.

Almeida et.al [15].: genome fasta files were accessed from (ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/umgs_analyses/) on 2020-03-12.

Nayfach et.al [14].: genome fasta files were accessed from (http://bit.ly/HGM_all_60664_fna -O HGM_v1.0_all_60664_fna.tar.bz2) on 2020-03-12.

GenBank genomes were accessed on 30.07.2020 (www.ncbi.nlm.nih.gov/genbank/) [49]. GUNC results for 699,994 GenBank genomes were produced. RefSeq genome set was subsetted from GenBank. Genomes annotated as “derived from metagenomes” or “derived from environmental source” in the “excluded from refseq” column of the GenBank assembly metadata were considered as MAGs.

GTDB [2] genome metadata was accessed from (https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/95.0/) on 2020-08-17. Genomes were mapped to GenBank via GenBank accession IDs. Genomes annotated as “derived from metagenomes” or “derived from environmental sample” in the “ncbi_genome_category” column of the metadata table were considered as the GTDB MAGs subset.

The unfiltered set of 278,629 MAGs of the Global Microbial Gene Catalog dataset (GMGC, Coelho et al, in revision) is available at (gmgc.embl.de) [50].

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