Data download

Description	File link	Checksum (MD5)
MGE profiles	mges.txt.zip	07d131aeb9363f3d08b8e0fff8baed48
Nested MGEs	nested_is-tn_integrons.txt.zip	eb8c51fd1b35dab6ba8c4fea9f2a404f
Antibiotic resistance carrying MGEs	arg_mge.txt.zip	9dce4c681e00b84d514233dc3e8eefaa
Horizontal Gene Transfer data	HGT_data.txt.zip	2fb72f31e302a0dd80ed2475467e4748
Taxonomy	taxonomy.txt.zip	e96978aa9b0f57552c015c73fd7c56a5
Recombinase HMMs from proMGE (huh_y1, huh_y2, ser_tn, ser_ce, ser_lsr, cas1)	hmms.tgz	376b03ee2c4d19b9232da7c51cade8e9

Annotations of Mobile Genetic Elements (MGE) based on the proGenomes2 data (for species with at least 2 genomes).

• The profile HMMs used for recombinase annotations can be found at the SMART database by searching for the recombinase subfamily names in the keyword search
• The genomeID in the files are combination of NCBI taxid and sampleID - "taxid.sampleID"
• The proteinID in the files are combination of NCBI taxid, sampleID and proteinID - "taxid.sampleID.orfID"
• The MGE genome position is a combination of NCBI taxid, sampleID, contigID and genomic coordinates - “taxid.sampleID.contigID:start-end”
• All the underlying data (contigs, genes, proteins, functional annotation) with the accessions used in this analysis can be found on the proGenomes2 website by searching for the genus or specI cluster. The specI cluster search on the proGenomes2 page can also be used to connect the genomes to NCBI taxonomy