📖Understanding the BaseSpace Reports

Summary

Sample Composition

The Sample composition bar graphs show the broad compositional makeup of all samples in the analysis run. If an internal control is used, this will show in the bargraph. It is typical to see that Untargeted reads comprise a large portion of the sample composition, particularly from samples where viruses make up a low portion of the overall genetic material, such as wastewater samples or viruses grown in host cells.

Summary Statistics

The table shows an overview of QC metrics for all the samples in the analysis run. One can click on the "Download CSV" link to directly access an excel compatible version. Further details on each metric can be found by hovering over each column header.

Sample Specific results

Individual sample composition can be further explored by clicking on "Report" under each sample name in the panel on the left. There are four tabs in the Sample Report: Sample Quality Control, Microorganisms, Antimicrobial Resistance Markers and User Options.

Sample Quality Control

• Version information provides a table with details as to the application run version, the analysis pipeline run and test version. We recommend running the latest version of the application.

• Sample composition summarizes the broad compositional makeup of the individual sample.

• Read Classification is a dynamic figure where one can choose select the following options:

  • Targeted Microbial Reads - Relative (default): This bargraph shows the compositional makeup of the targeted types relative to targeted microbial reads. Specifically, the percent of the targeted microbial reads belonging to Viral, Bacterial, Fungal, Parasite and AMR are broken down. Hovering over an individual bar shows the read value.

  • Targeted Microbial Reads - Absolute: This bargraph shows the compositional makeup of the targeted types within all reads (i.e. types within the absolute number of all reads). Hovering over an individual bar shows the read value, and for a given type will be the same value as shown in Targeted Microbial Reads - Relative.

  • Untargeted Reads - Relative: This bargraph shows the compositional makeup of the untargeted types relative to untargeted microbial reads. It is possible for reads not in the panel to be sequenced when there is a high concentration of background DNA/RNA.

  • Untargeted Reads - Absolute: This bargraph shows the compositional makeup of the untargeted types within all reads (i.e. types within the absolute number of all reads). It is possible for reads not in the panel to be sequenced when there is a high concentration of background DNA/RNA.

Note that accurate sample composition results rely on selecting the correct enrichment panel. If you run a viral panel analysis that is not specific to that panel (eg VSP-enriched samples through the VSPv2 pipeline), you may see unenriched viruses as on target, even if they are not in the panel design. For example - if your sample has a high level of measles and used the VSP Panel in library prep but the VSP V2 analysis, measles reads will be calculated as "on target" despite measles not being in the VSP enrichment panel.

Also note that sample composition metrics are not available for VSP or RVOP.

• Internal Controls provide a table with RPKM values if ICs were used in the wetlab workflow. If one selects an internal control but did not include it in their wetlab workflow/sequencing than this information may show as 0 and may lead to inaccurate RPKM scores.

• QC Metrics includes a table with defined metrics and their corresponding values. Dehosted Reads are human reads only. If another host is used, these would be removed as "off target" reads.

Microorganisms

• Microbes detected will be shown in the tables, separated by microbe type (virus, bacteria, etc). Each table includes whether the microbe is present, and various metrics. Hovering over each metric title will provide more details on the metrics. The best-match Reference Accession(s) for each virus is shown in the Viruses table. Non-segmented viruses will have a single accession number and segmented viruses will have one accession per segment. To see all of the accessions, click on the three dots (...) in the table and scroll down to see a list of all accession numbers.

• Certain microbes show their "Phenotypic Group". Each number represents a a predefined group.

  • Phenotypic Group 1: Microorganisms that are frequently considered part of the normal flora, colonizers, or contaminants but may be associated with disease in certain settings.

  • Phenotypic Group 2: Microorganisms that may represent normal flora, colonizers, or contaminants but that are frequently associated with disease.

  • Phenotypic Group 3: Microorganisms that are not generally considered part of the normal flora, colonizers, or contaminants and are generally considered to be associated with disease.

• Reference Coverage plots show the coverage depth across the consensus genomes of the viruses. There is a dropdown where the user can select which virus to examine. For segmented viruses (such as influenza), each segment is concatenated into one coverage plot.

Antimicrobial Resistance Markers

Viral Antimicrobial Resistance (AMR) results will be reported for Influenza viruses in the RPIP, RVOP/RVEK, VSP and VSP V2 analysis pipelines, and bacterial AMR marker results will be reported in the RPIP and UPIP analysis pipelines. Custom workflows and non-influenza viruses do not include AMR results. Note that this does not mean there are no AMR markers in the sample; rather, further analysis using a virus specific tool is recomended if other AMR markers are of interest.

User Options

This table summarizes which settings the user selected at launch of the analysis.