Table 4.

Classification of E. coli strains based on full-length and short-read 16S rRNA gene amplicon sequence variants

	Method	Classification	Best Hits
Zymo	V3V4	Escherichia/Shigella	994
	V4V5	Escherichia/Shigella	996
	FL-Representative	E. coli O157:H7	53
	FL-Full Complement	E. coli O157:H7	14
HMP	V3V4	Escherichia/Shigella	994
	V4V5	Escherichia/Shigella	996
	FL-Representative	E. coli	320
	FL-Full Complement	E. coli K12	32

The ASVs identified from the E. coli strains in the Zymo and HMP mock communities were used to classify the strains based on the V3V4 region alone, the V4V5 region alone, the representative (i.e. most abundant) full-length (FL) sequence, and the full complement of full-length sequences (Materials and Methods). Classification was based on a consensus across the best hits identified by exact BLAST hits against the NCBI nucleotide database (nt). The number of equally best hits is recorded.