Viewing Single Sample Profiling Data

In the Cohorts and Metadata menu, you can easily manage and view all your samples. Create folders and move relevant samples into them to keep them organized. Click the folder icon on the left panel to see your folders and samples.

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Viewing Sample Results

From the Cohorts and Metadata menu, click on a sample name. You will see sample information, navigation controls at the top, and a table with microbial results.

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Number of Reads in Sample

The total number of reads in your sample is listed as well.

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Switching Databases

Click the drop down menu to select the database results to view:

• Bacteria
• Fungi
• Protists
• Antibiotic Resistance
• Virulence Factors
• MetaCyc
• Pfam
• EnzymeCommission
• CAZy
• GO Terms

** Filtered vs Total Results

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Filtered versus total results

You are able to view both filtered and unfiltered (total) results for your sample. Filtered results contain the calls that have met the threshold for high confidence that the organism called is in the sample. Unfiltered results contain additional calls that are below the filtering threshold and may need further validation to determine if they are truly present in the sample.

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When to use filtered results

You would typically use filtered results when you are looking at data where you want high confidence in your calls, like when working with clinical data. Many people use unfiltered (total) results when looking at environmental samples where there may be organisms whose genomes are more novel or diverge from most reference genomes.

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How filtering works

The filtering threshold which determines if results are considered significant is based on internal statistical scores determined by analyzing a large number of diverse metagenomes. Organisms listed in the filtered results are likely to be present in the sample. Unfiltered (total) results include those in the filtered results and usually additional organisms. Organisms listed in the unfiltered (total) results but not in the filtered results need further validation to determine if they are actually present in the sample - either by deeper sequencing of the sample followed by re-analysis or by orthogonal validation using targeted PCR or other methods.

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Taxonomy Switcher

The taxonomy switcher button allows you to select the taxonomic level results to view for both the sample dashboard table and the sample visualizations.

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Strain Level Statistics

To view strain level results click “Strain” on the taxonomy switcher at the top of the window. The dashboard table view provides a strain level report.

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Sample and Visualization Export

You can download your results as tab-separated files (which can be opened in Excel) or as PDFs. Click on “Export” and select the type of file you would like to download. Download should begin immediately. To download visualizations, navigate to the one of interest and click Export.