Table 4.
Limit of detection of stx gene subtype in a downsampled WGS data set for 19 strains 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 coverage | 40x coverage | 30x coverage | 20x coverage | 10x coverage | |||||||
| Blast | In silico | Blast | In silico | Blast | In silico | Blast | In silico | Blast | In silico | ||
| PCR | PCR | PCR | PCR | PCR | |||||||
| stx1a | 2 | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| stx1c | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 |
| stx1d | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 |
| stx2a | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 | 2 | 2 | 1 |
| stx2b | 3 | 2 | 3 | 2 | 3 | 2 | 3 | 3 | 3 | 3 | 2 |
| stx2c | 2 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| stx2d | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 2 | 3 | 2 |
| stx2e | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| stx2f | 7 | 7 | 7 | 7 | 7 | 7 | 7 | 7 | 7 | 7 | 6 |
| stx2g | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
see Table S1 for isolate identification.