Table 3.

Limit of detection of virulence genes in a down sampled WGS data set from 40 STEC and one hybrid STEC/EAEC O104:H4 by both a blast and in silico PCR approach.

Trait	Number of strains with trait by real-time PCR	Number strains determined from WGS data with indicated trait at different sequence coverage levels
		Original sequence coveragea		40x coverage		30x coverage		20x coverage		10x coverage
		Blast	In silico PCR	Blast	In silico PCR	Blast	In silico PCR	Blast	In silico PCR	Blast	In silico PCR
stx1	27	27	27	27	27	27	27	27	27	25	26
stx2	21	20b	19c	20	19	20	20	20	20	20	18
eae	26	26	26	26	24	26	26	24	20	8	9
ehxA	29	29	29	26	26	25	25	17	20	8	11

Strain identifiers listed in Table S1.

^aOriginal coverage was 40x to 267x.

^bFor the original sequence files, stx2 was missed in an E. coli O76:H19 using the genotyping plug-in that was detected by in silico PCR.

^cThe in silico PCR did not detect stx2 in 2 isolates though it was detected by the genotyping plug-in.