View microbiome health research analysis results
If you use the AmpliSeq Microbiome Health analysis workflow, you can view the analysis results in Ion Reporter™ Software.
To visualize multiple analyses, see Visualize microbiome health research analysis results.
- In the Analyses tab, click Overview.
- Click Workflow filter, then select an AmpliSeq Microbiome Health analysis workflow to narrow the list to microbiome health research analysis results.
You can further refine the list of analyses with other filters, or click column headings to sort the list.
- Click the analyses name link.
The Analysis Results screen opens.
The following parameters are displayed.
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.
Total Reads—The total number of filtered and trimmed reads independent of length reported in the output BAM file.
Total Valid Mapped Reads—Total number of reads mapped to the reference sequences with good mapping quality (reads with alignment score greater than the min local alignment score threshold).
Mean read length—The average length of all reads from the BAM file.
- Select the Target Species tab, then click Source Data or Species Distribution.
- 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.
Note: Some of the primer pairs designed to detect the 73 targeted species can sometimes amplify strains of other non-targeted species. As a result, an additional 16 species can be reported as well. When such species are detected the species names are reported with (*), indicating that it is one of the non-targeted species.
- The Species Distribution view displays a bar chart of the abundance of the species that are detected.
- The Source Data view displays the parameters in the following table for each detected species.
Parameter
Description
Species name
Bacterial species.
Detected Target species abundance
Percentage abundance of the species in the sample.
Read Count
Raw read count.
Normalized read count
Read counts are normalized by the number of amplicons per sequence and the sampling depth per sample. Normalized read counts are comparable across different microbes and samples.
- Click 16s rRNA Gene tab, then select an option to view taxonomy data.
- To view a summary of the taxonomy data, click Source Data.
- To view bar charts of the abundance of detected species at the phylum, family and genus levels, click Microbe Distribution.
- To view a interactive taxonomy view of the detected species, click Interactive Taxonomy View.
You can adjust the taxonomy view as follows.- Enter a species to highlight that species in the Search field.
- Click Max depth to adjust the number of taxonomy classes that are displayed.
- Click Font size to change the font size of the characters.
- Click Chart size to change the size of the plot.
- Click Collapse to toggle the number of displayed taxonomy classes between 4 and 6.
- Click Snapshot to display the plot in a new window to enable saving the plot as a graphic.
- Click Link to display a link that can be copied for sharing or bookmarking
- Click ? to open the help system for generating the interactive taxonomy view
- To download data files, click Download Results.
A ZIP file containing the following files is downloaded to your local drive.
