TABLE 2.
Minimum coverage required to call walK 646C>G mutation with BWA/BCFtools and Medaka in mutants or mutant mixtures or minimum coverage required to exclude mutation from wild-type samples for simulated, amplicon DNA, and culture mixturesa
| Proportion N384/N384-3 | Simulated (NanoSim) (×) |
Amplicon DNA (×) |
Culture (×) |
|||
|---|---|---|---|---|---|---|
| BWA/BCFtools | Medaka | BWA/BCFtools | Medaka | BWA/BCFtools | Medaka | |
| 100% N384 | 0 | 0 | 200 (exclude C > T) | NA | 0 (C > T at 10) | NA |
| 90% N384 | 5 | 5 | 10 | NA | 150 | NA |
| 10% N384-3 | ||||||
| 80% N384 | 5 | NA | ||||
| 20% N384-3 | ||||||
| 70% N384 | 10 | NA | ||||
| 30% N384-3 | ||||||
| 60% N384 | 5 | 5 | ||||
| 40% N384-3 | ||||||
| 50% N384 | 2 | 5 | 20 | 80 | 5 | 20 |
| 50% N384-3 | ||||||
| 40% N384 | 2 | 2 | ||||
| 60% N384-3 | ||||||
| 30% N384 | 2 | 2 | ||||
| 70% N384-3 | ||||||
| 20% N384 | 3 | 20 | ||||
| 80% N384-3 | ||||||
| 10% N384 | 2 | 2 | 2 | 2 | 3 | 3 |
| 90% N384-3 | ||||||
| 100% N384-3 | 10 | 10 | 2 | 2 | 2 | 2 |
a
Cases in which the mutation was never detected are listed as NA.