TABLE 4.
Minimum coverage required to call walK, graR, vraG, and vraS mutations with BWA/BCFtools and Medaka in VISA clinical strain or minimum coverage required to exclude mutations from wild-type samples for test strains EUH15 and 107a
| Strain | Mutation | Coverage (×) for: |
|
|---|---|---|---|
| BWA/BCFtools | Medaka | ||
| 107 (VISA) | WalK A243T (26392) | 2 | 2 |
| GraR E15K (719060) | 2 | 2 | |
| VraG T217I (718728) | >500 | ||
| VraS A314V (2026309) | 2 | 5 | |
| EUH15 (VSSA) | WalK (26392) | 20 | 0 |
| GraR (719060) | 50 | 0 | |
| VraG (718728) | 0 | 0 | |
| VraS (2026309) | 80 | 0 | |
a
Mutation calls by BWA/BCFtools and Medaka given for test strains EUH15 and 107. Mutations and reference coordinates are given relative to USA300 FPR3757.