- Summary Report: A cross-sample, combined report. This report summarizes key QC statistics such as read mapping summary and coverage statistics. See the Reports section for a detailed description.
- Shared_Variants: A track containing variants with >=50% frequency found in one or more samples.
- Consensus sequences: A folder containing the consensus sequence for each sample.
- Genome View: A track list containing:
- The reference SARS-CoV-2 genome MN908947.3
- The reference SARS-CoV-2 CDS regions
- Sample coverage graphs
- The reference SARS-CoV-2 gene regions
- The Shared_Variants track
An example is shown in figure 4.6.