Table 1.
Sequencing read and genome assembly statistics including the total raw read pairs obtained and fraction captured from SARS-CoV-2 RNA, the fraction of 29,903 bp MN908947.3 genome sequence covered, depth of coverage, and number of variants detected relative to MN908947.3.
| Sample | Amplification | Enrichment | Number of Paired Reads | Reads from SARS-CoV-2 (%) | SARS-CoV-2 Genome Fraction (%) | Average Depth of Coverage | 0–100x Coverage (%) | 101–1000x Coverage (%) | >1000x Coverage (%) | # iVar Variants |
|---|---|---|---|---|---|---|---|---|---|---|
| Negative | ARTIC | No | 938,693 | 0.01 | 0 | 4.1x | 99.2 | 0.8 | 0.1 | n/a |
| Wuhan | Liverpool | No | 883,212 | 0.52 | 19.587 | 37.9x | 93.88 | 6.08 | 0.04 | 1 |
| Wuhan | Liverpool | Yes | 22,119 | 58.73 | 20.811 | 98.6x | 89.6 | 6.8 | 3.6 | 1 |
| Wuhan | Hexamers | No | 585,396 | 0.01 | 0 | 0.3x | 99.9 | 0.1 | 0.00 | n/a |
| Wuhan | Hexamers | Yes | 1536 | 1.56 | 0 | n/a | n/a | n/a | n/a | n/a |
| Wuhan | ARTIC | No | 2,271,152 | 73.86 | 59.104 | 15,604.0x | 10.6 | 35.5 | 53.9 | 5 |
| Iran | Liverpool | No | 813,975 | 90.13 | 98.53 | 6528.3x | 1.2 | 3.1 | 95.6 | 6 |
| Iran | Liverpool | Yes | 901,124 | 89.76 | 98.54 | 8214.4x | 0.7 | 0.2 | 99.1 | 6 |
| Iran | Hexamers | No | 1,091,011 | 2.77 | 99.89 | 215.3x | 0.43 | 99.56 | 0.00 | 7 |
| Iran | Hexamers | Yes | 619,661 | 89.17 | 99.83 | 4383.9x | 0.2 | 0.3 | 99.6 | 7 |
| Iran | ARTIC | No | 1,935,748 | 88.25 | 99.31 | 14,032.7x | 0.2 | 1.7 | 98.1 | 7 |