Table 2 The number of samples passing and failing the different QC thresholds 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 sequenced | 95 | 95 | 95 | 59 | 59 | 59 |
Consensus genomes | 98.95% (94) | 96.84% (92) | 100% (95) | 96.61% (57) | 91.53% (54) | 100% (59) |
Passing COG-UK QC | 80.00% (76) | 76.84% (73) | 82.11% (78) | 81.36% (48) | 74.58% (44) | 81.36% (48) |
Passing GISAID QC | 69.47% (66) | 62.11% (59) | 77.89% (74) | 74.58% (44) | 67.80% (40) | 74.58% (44) |
Failing COG-UK QC | 20.00% (19) | 23.16% (22) | 17.89% (17) | 18.64% (11) | 25.42% (15) | 18.64% (11) |
Failing GISAID QC | 30.53% (29) | 37.89% (36) | 22.11% (21) | 25.42% (15) | 32.20% (19) | 25.42% (15) |
Avg. (median) Ns of COG-UK passed | 1504 (354) | 1635 (121) | 688 (53) | 977 (606) | 1101 (339) | 911 (292) |
Avg SNPs of COG-UK passed | 7.99 | 7.99 | 11.0 | 18.3 | 18.2 | 20.4 |
No. of samples with known Ct ≤ 32 | 65 | 65 | 65 | 18 | 18 | 18 |
Consensus genomes (Ct ≤ 32) | 100% (65) | 100% (65) | 100% (65) | 100% (18) | 100% (18) | 100% (18) |
Passing COG-UK QC (Ct ≤ 32) | 98.46% (64) | 98.46% (64) | 98.46% (64) | 100%(18) | 94.44% (17) | 100% (18) |
Passing GISAID QC (Ct ≤ 32) | 95.38% (62) | 89.23% (58) | 98.46% (64) | 94.44% (17) | 88.89% (16) | 94.44% (17) |
Failing COG-UK QC (Ct ≤ 32) | 1.54% (1) | 1.54% (1) | 1.54% (1) | 0% (0) | 5.56% (1) | 0% (0) |
Failing GISAID QC (Ct ≤ 32) | 4.62% (3) | 10.77% (7) | 1.54% (1) | 5.56% (1) | 11.11% (2) | 5.56% (1) |
Avg (Median) Ns of COG-UK passed (Ct ≤ 32) | 682 (339) | 815 (121) | 111 (47) | 895 (339) | 911 (121) | 1064 (514) |
Avg SNPs of COG-UK passed (Ct ≤ 32) | 8.19 | 8.17 | 10.2 | 18.8 | 18.9 | 20 |