Visualize microbiome health research analysis results
If you use the AmpliSeq Microbiome Health analysis workflow, you can visualize analysis results in Ion Reporter™ Software.
To view the analysis results from a single analysis, see View microbiome health research analysis results.
- In the Analysis tab, click Overview tab.
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Select the check box for each
analysis to be used for analysis, then click
Visualize.
You must select at least three analyses. A
minimum of three analyses are required for statistical analysis.
The Analysis Results screen opens to the Summary tab.
The Summary tab lists data for both the target species and the 16S rRNA gene. The Target Species Markers lists the total number of detected species. The 16S rRNA Gene Markers lists taxonomic data that is identified in the sample, and a value for Alpha Diversity. The alpha diversity results describe the diversity in a single sample at the species, genus, and family levels, and show the following metrics for each analyses.
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Pool QC—Pool QC is determined to be either PASS or FAIL. If the total number of valid mapped reads is greater than the threshold applied and the mean read length of all the reads from the BAM file is greater than the threshold, pool QC is determined to be PASS, otherwise FAIL. If pool QC is determined to be FAIL, it means that library pool failed and the results are not valid.
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Total Reads—The total number of filtered and trimmed reads independent of length reported in the output BAM file.
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Total Valid Mapped Reads—Total number of reads mapped to the reference sequences with good mapping quality (reads with alignment score greater than the minimum local alignment score threshold).
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Mean read length—The average length of all reads from the BAM file.
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- You can view results for individual samples, or view graphical representations of the selected analyses.
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To view target species data,
select the
Target Species
tab, then click the
Source Data
or
Heat Map & PCoA Analysis
sub tab.
-
The Ion AmpliSeq™ Microbiome Health Research – Target Species Pool detects 73 bacterial species that are associated with human disease. Click Download Results to download a file with a list of the 73 species.
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Click Source Data to view data on the abundance of each species in each of the selected samples.
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Click Heat Map & PCoA Analysis for a heat map of the abundance of the identified target species for each sample and a PCoA analysis plot, which shows Beta diversity results to describe similarities and dissimilarities between samples.
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To view taxonomy data, in the
16S rRNA Gene Markers
section, click
View Results
in row of a sample, then select one of the following sub tabs.
- To view a summary of the taxonomy data, click Source Data.
- To view a bar chart of the abundance of detected species at the phylum, family and genus levels and a heat map, click Microbe Distribution.
- To view the Alpha diversity values for each sample, click Alpha Diversity Analysis. Select any of the following options.
- To view Beta Diversity analyses of the selected samples, click Beta Diversity Analysis, then click a matrix or plot.
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To download data files, click
Download Results.
Note: The Alpha and Beta diversity data sets take longer to load. Click to save or open the file, depending on your browser settings.
A ZIP file containing the following files is downloaded to your local drive.
