📄Sample Report

The Sample Report contains at most four tabs: Sample QC, Virus Metrics, Nextclade Report, and Pangolin Report.

Sample QC

This tab contains tables and plots summarizing the sample.

Sample Summary Metrics

This table reports summary metrics for the sample, such as Status and Detected Amplicons. See here for their definitions.

Pre-processing Metrics

This plot displays counts of reads that fall into different categories. See here for their definitions.

Sequence Alignment

This plot displays the number of reads that mapped to each reference sequence. If there is a single reference sequence (e.g. SARS-CoV-2), one bar is shown.

Sequence Alignment Metrics

This table provides the number of reads that mapped to each reference sequence along with the genome and segment names of the reference sequence. The "Download CSV" button enables downloading the contents of the table as a text comma-separated value (CSV) file.

Virus Metrics

Example of a Virus Metric tab

Metrics by Virus

This table summarizes results for each viral genome generated in the sample with each row corresponding to a single viral genome. For segmented viruses like Influenza, a row will summarize information across multiple sequences generated for a single viral genome.

At the top is the "Download CSV" button, which enables downloading the contents of the table as a text comma-separated value (CSV) file.

The table itself contains rows for every viral genome with at least one sequence generated in the sample with the following columns:

1. Virus: Name of the viral genome

   • For custom references, this will be the part of the FASTA header before the first whitespace character for the corresponding reference sequence if no custom genome definition file is provided. If a custom genome definition file is provided, this will be the value of the genomeName column

2. % Callable: Percentage of bases in the reference sequence with coverage above the minimum read coverage depth for consensus sequence generation (10x by default). This is computed across all sequences belonging to the viral genome. See here for more information.
3. Median Coverage: Median coverage value (in number of reads overlapping each position) over the entire reference genome (not just the generated consensus sequence).

Metrics by Sequence

This table summarizes the results for each sequence generated in the sample. For segmented viruses like Influenza, there are typically multiple rows with the same virus name. Otherwise, this table contains similar information as the Metrics By Virus table.

At the top is the "Download CSV" button, which enables downloading the contents of the table as a text comma-separated value (CSV) file.

1. Virus: Name of the virus genome

2. Segment: Name of the segment to which the reference sequence corresponds. For non-segmented viruses, this is typically set to "Full".

3. Accession: Unique identifier of the reference sequence (text before first space in FASTA header if custom reference FASTA was provided)

4. % Callable: Percentage of bases in the reference sequence with coverage above the minimum read coverage depth for consensus sequence generation (10x by default). See here for more information on this metric.
5. Callable Bases: Number of bases in the reference sequence with coverage above the minimum read coverage depth for consensus sequence generation (10x by default)

6. Median Coverage: Median coverage value (in number of reads overlapping each position) over the entire reference genome (not just the generated consensus sequence).

7. Consensus Length: Length of the final consensus, without leading and trailing masked bases if sequence trimming is enabled. Sequence trimming can be disabled in the Input Form under Advanced Workflow Settings.

Consensus Coverage

Displays a trace of read coverage over each reference genome. On the top right is a drop-down menu that allows users to switch between genomes. The blue line represents the read coverage, with the coverage depth in log 10 of number of reads on the y-axis and the genomic position in the reference genome on the x-axis.

For segmented viruses like Influenza, coverage values for each segment is displayed in a horizontally stacked fashion. Grey blocks at the top show their boundaries.

Nextclade Report (optional)

This tab contains tables reporting the results of the Nextclade analysis performed on the generated consensus sequences in the sample. See here for more details.

Pangolin Report (optional)

This tab contains tables reporting the results of the Pangolin analysis performed on the generated consensus sequences in this sample. See here for more details.