Table 2.
Consensus-level accuracy of ONT whole-genome SARS-CoV-2 sequencing on patient specimens.
| Medaka | Medaka minus blacklista | Nanopolish | Nanopolish minus blacklista | |
|---|---|---|---|---|
| Cases analysed | 157 | 157 | 157 | 157 |
| Genome coverage (%) | 99.59 | 98.56 | 99.59 | 98.56 |
| Negative positions | 4,674,554 | 4,627,768 | 4,674,554 | 4,627,768 |
| Illumina variants | 1201 | 1162 | 1201 | 1162 |
| ONT variants | 1190 | 1159 | 1196 | 1164 |
| TPs | 1181 | 1155 | 1191 | 1160 |
| FNs | 20 | 7 | 10 | 2 |
| FPs | 9 | 4 | 5 | 4 |
| Sensitivity (%) | 98.33 | 99.40 | 99.17 | 99.83 |
| Precision (%) | 99.24 | 99.65 | 99.58 | 99.66 |
| Jaccard similarity (%) | 97.60 | 99.06 | 98.76 | 99.49 |
| Perfect concordance | 140/157 cases | 149/157 cases | 147/157 cases | 152/157 cases |
| Illumina SNVs | 1194 | 1162 | 1194 | 1162 |
| ONT SNVs | 1180 | 1155 | 1190 | 1160 |
| TPs | 1180 | 1155 | 1190 | 1160 |
| FNs | 14 | 7 | 4 | 2 |
| FPs | 0 | 0 | 0 | 0 |
| Sensitivity (%) | 98.83 | 99.40 | 99.66 | 99.83 |
| Precision (%) | 100 | 100 | 100 | 100 |
| Jaccard similarity (%) | 98.83 | 99.40 | 99.66 | 99.83 |
| Perfect concordance | 145/157 cases | 152/157 cases | 153/157 cases | 155/157 cases |
aBlacklist sites are error-prone low-complexity sequences (n = 15; 9–42 bp; see text for details).