SARS-CoV-2 sequencing clinical quality metrics for use on the Ion Torrent Genexus
| Quality Metrics | Failure Cutoff | Needs Review Cutoff | Pass Cutoff | |
|---|---|---|---|---|
| Run metrics | Loading (%) | <80 | N/A | ≥80 |
| Enrichment (%) | <95 | ≥95 | ||
| Library reads (%) | <80 | ≥80 | ||
| Final reads (%) | <30 | ≥30 | ||
| Final reads/lane | <8 000 000 | ≥8 000 000 | ||
| Mean raw accuracy (%) | <98 | ≥98 | ||
| Sample metrics | Total reads | <100 000 | 100 000–400 000 | >400 000 |
| Mean read length | <155 | ≥155–174 | ≥175 | |
| Uniformity of base coverage (%) | <80 | ≥80–<90 | ≥90 | |
| Average base coverage depth | <2000 | N/A | ≥2000 | |
| Percent reads on target (%) | <90 | ≥90–<95 | ≥95 | |
| Number of mapped reads | <50 000 | N/A | ≥50 000 | |
| Target base coverage at 20× (%) | <80 | ≥80–<90 | ≥90 | |
The metrics for quality control of SARS-CoV-2 sequencing on the Genexus can be divided into run-specific metrics and sample-oriented metrics. Most run metrics listed have hard cutoffs, while the sample metrics have a review window. Sequence data that “Pass” but need review should take all listed metrics into consideration and reference the qualitative metrics prior to reporting. NA, not available.