Aggregate Summary Page
The 16S Metagenomics app provides a comparison of all samples on the Aggregate Summary page. You can view interactive charts showing comparisons of sample results or download aggregate result files.
| • | Aggregate Results |
The aggregate results section contains summary files for download. The PDF Aggregate Summary Report contains tables showing the same information as in the BaseSpace report. The CSV files contain the number of reads classified to each classification by sample, organized by taxonomic level of the classifications.
| • | Sample Information |
The Sample Information table provides the Sample Number, Sample ID, and statistics about genus-level classification rate and primary analysis for each sample.
|
Statistic |
Definition |
|---|---|
|
Number reads PF |
The total number of reads with an index sequence matching this sample that passed quality filtering |
|
% Reads PF Classified to Genus |
(# Reads with Genus-level classification) / (# Reads PF) * 100 |
| • | Principal Coordinate Analysis (PCoA) |
Principal coordinate analysis shows similarity between normalized relative abundance of all samples. The PCoA is generated using Classical MDS on a Pearson covariance distance matrix generated from per-sample normalized classification abundance vectors. You can select the maximum level at which to compare samples by adjusting the scrollbar above the chart. Points are labeled with a shortened version of the Sample ID. You can mouse over any point to view the full Sample ID.
| • | Hierarchical Clustering Dendrogram |
The dendrogram shows a hierarchical clustering of samples based on genus-level classifications. Mouse over the bar charts to view taxonomic labels.
| • | Species Diversity Results |
|
Statistic |
Definition |
|---|---|
|
Shannon Species Diversity |
The species-level Shannon diversity value for the sample (see en.wikipedia.org/wiki/Shannon-Wiener_index for details). |
|
Number of species identified |
The number of unique species classifications in the sample, only including reads classified to the species level. |