Overview of the filtering process within the amr.watch workflow applied to public genomes of priority bacterial pathogens available in the International Nucleotide Sequence Database Collaboration (INSDC) databases. The genome data are filtered in a series of steps, depicted from left to right in the table, with the numbers in each column representing a subset of those from the previous column.

For the pathogens that are grouped together, we initially accept genomes annotated in the ENA with any of the corresponding taxonomy IDs from the same group and use the Speciator assignments in subsequent processing.

Pathogen	ENA entries (run accessions)	Illumina paired-end entries	Filtered entries¹	Entries with geotemporal data²	Entries available for download in SRA	Entries associated with unique samples³	Assembled genomes	Genomes with correct species	Genomes that passed QC	Genomes with collection date post-2010
All Pathogens	1,580,477	1,404,693	1,391,702	784,704	781,314	752,122	720,739	627,878	616,012	558,900
A. baumannii	43,074	35,709	34,529	22,375	22,264	21,552	20,956	20,766	20,457	19,108
C. coli	166,259	161,511	159,972	106,496	105,598	105,001	101,264	32,106	30,608	29,500
C. jejuni	166,259	161,511	159,972	106,496	105,598	105,001	101,264	68,976	64,925	62,649
E. cloacae complex	18,754	16,614	16,437	12,101	12,101	11,134	10,670	10,473	10,267	9,805
E. faecium	42,480	40,961	40,649	25,384	25,384	24,453	24,188	24,018	22,970	21,771
E. coli	565,608	473,442	469,001	249,904	249,507	240,206	230,016	202,023	196,699	179,518
S. flexneri								10,420	10,095	9,301
S. sonnei								13,792	13,481	12,499
H. influenzae	16,279	15,089	15,027	6,170	6,168	5,991	5,397	5,386	5,248	4,634
K. pneumoniae	110,643	97,350	96,066	58,278	58,276	53,734	52,385	50,380	49,207	47,233
N. gonorrhoeae	72,927	70,187	70,099	46,053	46,053	43,342	40,102	39,732	38,434	37,658
P. aeruginosa	76,305	56,773	55,940	28,067	27,939	26,864	25,432	25,201	24,502	22,829
Salmonella Typhi	123,749	115,433	114,694	88,122	87,907	85,904	84,368	0	8,409	6,415
Salmonella Typhimurium								0	0	0
Salmonella Enteritidis								0	0	0
S. aureus	172,852	157,126	155,327	88,154	86,517	82,703	78,492	77,378	74,663	63,062
S. pneumoniae	171,547	164,498	163,961	53,600	53,600	51,238	47,469	47,227	46,047	32,918

Entries (runs) are filtered to include only those with two FASTQ files, ≥20x mean coverage (via assessment of the "base_count" field) and those associated with a single sample accession.
Entries (runs) are filtered to include those with a collection date that is decodable to at least the year and a sampling location that is decodable to at least the country level.
Entries (runs) are filtered to ensure only one run per sample accession is included (selecting the run with the highest number of bases via assessment of the "base_count" field).