Table 2. Quality parameters and typing results of SARS-CoV-2 genome sequences.
| Case | Sequencing run | SARS-CoV-2 coverage | Typing results | ||||
|---|---|---|---|---|---|---|---|
| Reads | Bases (Mbp) | Covered positions (bp) | Coverage breadth (%) | Mean depth | Clade | Lineagesa | |
| A1 | 6.4 × 106 | 967 | 0 | 0 | 0 | NA | NA |
| A2 | 8.8 × 106 | 1,328 | 29,869 | 99.9 | 87.3 | V | B.2 |
| A3 | 7.2 × 106 | 1,086 | 29,896 | 100 | 172 | S | A |
| A4 | 6.2 × 106 | 932 | 19,384 | 64.8 | 2.73 | G | B.1 |
| A5 | 8.1 × 106 | 1,216 | 29,715 | 99.4 | 14.5 | V | B.2.1 |
| A6 | 7.7 × 106 | 1,159 | 29,901 | 100 | 4,867 | V | B.2.1 |
| A7 | 1.4 × 107 | 2,130 | 29,862 | 99.9 | 27.8 | V | B.2.1 |
| S1 | 7.1 × 106 | 1,072 | 29,873 | 99.9 | 70 | V | B.2.1 |
| S2 | 6.0 × 106 | 908 | 27,696 | 92.6 | 27.7 | V | B.2.1 |
| S3 | 1.4 × 107 | 2,094 | 26,853 | 89.8 | 11.9 | Vb | B.2.1 |
| S4 | 6.9 × 106 | 1,047 | 28,241 | 94.4 | 23.3 | V | B.2.1 |
| S5 | 8.3 × 106 | 1,260 | 29,903 | 100 | 7,199 | V | B.2.1 |
| S6 | 7.6 × 106 | 1,141 | 0 | 0 | 0 | NA | NA |
| S7 | 6.0 × 106 | 904 | 0 | 0 | 0 | NA | NA |
| S8 | 4.6 × 107 | 7,006 | 0 | 0 | 0 | NA | NA |
NA = not available.
aLineage classification scheme proposed by Rambaut et al. (14) using Pagolin software version 1.1.14 and the lineage database version 2020-05-19; bS3 strain had the G26144T variant but not the G11083T variant.