Summary outputs

  1. 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.

  2. Shared_Variants: A track containing variants with >=50% frequency found in one or more samples.

  3. Consensus sequences: A folder containing the consensus sequence for each sample.

  4. 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 16.6.

    Image sarscov2genomeview
    Figure 16.6: An example of the Genome View track list created from analysis of seven SARS-CoV-2 samples