Table 3.
Frequent non-synonymous variants observed in ≥ 15 samples (n = 47).
| Variant | AF range | # patients | # samples | ORF: effect |
|---|---|---|---|---|
| C17747T | 0.98–1 | 11 | 24 | ORF1ab: P5828L; helicase: P504L |
| A17858G | 0.98–1 | 11 | 24 | ORF1ab: Y5865C; helicase: Y541C |
| T28144C | 0.02–1 | 12 | 23 | ORF8: L84S |
| A23403G | 0.99–1 | 9 | 19 | S: D614G |
| C14408T | 0.02–1 | 10 | 17 | ORF1ab: P4715L; RdRp: P323L |
| G25563T | 0.03–1 | 8 | 15 | ORF3a: Q57H |
| C1059T | 0.95–1 | 7 | 15 | ORF1a: T265I; nsp2: T85I |
All variants called had at least 10 reads of support for the alternate allele. For the three variants with large ranges in allele frequency (T28144C, C14408T, G14408T), ≤ 3 outlier samples with variant AFs below 0.1 were present. When these samples are excluded, minimum AF increases to ≥ 0.99.