📖Understanding the BaseSpace HTML reports
Summary results
Sample Composition
The Sample Composition bargraphs show the proportion of reads classified to six broad categories for of all samples in the analysis run: Targeted Microbial, Untargeted, Ambiguous, Unclassified, Low Complexity, and Targeted Internal Control (RPIP, UPIP, VSP V2 only).
Summary Statistics
The Summary Statistics table summarizes sample QC metrics for all samples in the analysis run. Further details on each metric can be found by hovering over each column header.
Per sample results
Individual sample results 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.
1. Sample Quality Control
Version Information is a table with the application version, test type, and test version that were run. Running the latest version of the application is recommended.
Sample Composition is a bargraph showing the proportion of post-quality reads classified to six broad categories for the sample (RPIP, UPIP, VSP V2 only).
Read Classification is a dynamic plot that can be configured to show the following (RPIP, UPIP, VSP V2 only):
Targeted Microbial Reads - Relative (default): Bargraph of post-quality targeted microbial reads belonging to Viral, Bacterial, Fungal, Parasite and AMR categories, relative to post-quality targeted microbial reads only. Percentages are expected to sum to 100%. Hover over an individual bar to display the values.
Targeted Microbial Reads - Absolute: Bargraph of post-quality targeted microbial reads belonging to Viral, Bacterial, Fungal, Parasite and AMR categories for all post-quality reads in the sample overall. Hover over an individual bar to display the values.
Untargeted Reads - Relative: Bargraph of post-quality untargeted reads belonging to untargeted categories, relative to post-quality untargeted reads only. Percentages are expected to sum to 100%. Hover over an individual bar to display the values.
Untargeted Reads - Absolute: Bargraph of post-quality untargeted reads belonging to untargeted categories for all post-quality reads in the sample overall. Hover over an individual bar to display the values.
**Note that accurate sample composition and read classification results rely on selecting the correct enrichment panel. If you run an analysis that is not specific to the enrichment panel (e.g., VSP V2 analysis with VSP-enriched samples), reads from high background viruses that are not targeted by VSP probes (e.g., Measles virus) but that are targeted by VSP V2 probes will be reported as targeted viral reads.
Internal Controls is a table containing supported Internal Control options along with observed RPKM values (RPIP, UPIP, VSP V2 only).
QC Metrics is a table containing sample QC metrics. Dehosting refers to human reads only.
2. Microorganisms
Microorganism results are summarized in tables, separated by type (Viruses, Bacteria, Fungi, Parasites). Each table includes whether the microorganism is predicted present in the sample, as well as various alignment metrics. Further details on each metric can be found by hovering over each column header. The best-match Reference Accession(s) are provided for all RPIP, RVOP/RVEK, VSP, and VSP V2 viruses in the Viruses table. To see all best-match Reference Accession(s), click on the three dots (...) in the table and scroll down the page.
Reference Coverage is a dynamic plot showing the coverage depth across the viral genome for detected RPIP, RVOP/RVEK, VSP, and VSP V2 viruses. Select a virus from the dropdown list to view the coverage plot. Segments are concatenated for segmented viruses, and the targeted regions of the viral genome are indicated for RPIP viruses.
3. Antimicrobial Resistance Markers
Viral AMR (Variants) is a table with viral AMR variant results for Influenza A/B viruses (RPIP, RVOP/RVEK, VSP, and VSP V2 only)
Bacterial AMR (Genes) is a table witb bacterial AMR gene results (RPIP, UPIP only)
Bacterial AMR (Variants) is a table with bacterial AMR variant results (RPIP, UPIP only)
4. User Options
The User Options table summarizes user options selected during launch of the analysis.
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