Table 1 Summary statistics for each sequencing experiment
From: CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
Routine samples | Rapid response samples | |||||
|---|---|---|---|---|---|---|
CoronaHiT-ONT | ARTIC LoCost | CoronaHit-Illumina | CoronaHiT-ONT | ARTIC LoCost | CoronaHiT-Illumina | |
No. of samples | 95 | 95 | 95 | 59 | 59 | 59 |
Run time (h) | 30 | 30 | 25.4 | 18 | 18 | 24.4 |
Yielded bases (Gb) | 10.3 | 8.5 | 43.9* | 6.3 | 4.8 | 48.6* |
Bases deplexed (Gb) | 9.6 | 8.0 | 15.7 | 5.7 | 4.5 | 7.3 |
Reads sequenced (> Q7) | 24764627 | 15733349 | 113756312 | 13044532 | 8824469 | 53678322 |
Average PHRED score | 13.47 | 13.11 | 33.15 | 13.2 | 12.98 | 33.48 |
Average coverage (X) | 1145X | 1719X | 4649X | 1104X | 1421X | 3010X |
Standard deviation of coverage (X) | 698X | 1683X | 4352X | 439X | 1145X | 3496X |
Average read length (bases) | 374 | 448 | 135 | 413 | 457 | 135 |
Average (median) mapped length | 205.24 (195) | 386 (386) | 134.63 (150) | 241.25 (244) | 383.88 (385) | 131.43 (150) |
Samples passing GISAID QC | 66 | 59 | 74 | 44 | 40 | 44 |