Identified AMR sequences through the CZ ID AMR pipeline will be summarized within an interactive AMR Sample Report Table. You can customize the table view and easily find AMR genes of interest by sorting and filtering results. Here we describe how to customize, sort, and filter the AMR Sample Report Table.
Customize the AMR Report Table View
The AMR Sample Report Table defaults to a list of data columns but you can add or remove columns by selecting the "plus" button to the right of the table. Use the dropdown menu to select (or de-select) column names you want to see on the table.
If you are adding columns, you can hide the Filter panel on the left-hand side to gain space for the table. To hide or show the Filter panel, simply click the Filter icon.
Hiding the Filter panel will make more room for the table.
You can also hide or expand "Contigs" or "Reads" column panels to help you focus on metrics of interest.
Sorting the AMR Report Table
By default, the AMR Repot Table is sorted based on gene name (first column) in alphabetical ascending order (from A to Z). However, you can sort the report by any of the column headers displayed on the table. The header used to sort the table will be highlighted in blue.
To sort the AMR Report Table, choose a data column by which to sort and click the column header. Downward arrow indicates column is sorted from Z to A for text entries (except Cutoff) and from highest to lowest for numerical entries (decreasing order). Click the column header to sort values in reverse order. The Cutoff column is sorted based on the stringency of the threshold used to call contig alignments to AMR genes (i.e., Perfect > Strict > Nudged). See AMR Report Metrics for header definitions.
Click column headers to sort the table by data or metric of interest.
Filtering AMR Results
The AMR Report Table shows all the AMR genes detected in a given sample. However, some of the genes may not be relevant given that some matches may have low-confidence (e.g., matches based on only one read). You may want to focus on a specific class of AMR genes or genes that were detected at a given abundance, coverage depth, and/or coverage breadth. The filter functionality of the AMR Sample Report makes it easy to focus on AMR genes with threshold values of interest.
To filter the AMR Report Table, open the Filter panel on the left-hand side of the page. This panel includes "Thresholds" and "Drug Class" filters.
To filter the report based on specific threshold values, click the "Thresholds" filter. A Configure Thresholds dialog box will appear. Use the dialog box to specify one or more value thresholds of interest.
The Filter panel is located on the left-hand side of the page. Available metrics to filter the AMR Sample Report Table are found within the Configure Thresholds dropdown menu.
Use the Configure Thresholds dialog box to specify value threshold(s) of interest.
Click the Apply button after selecting threshold(s). Applied filters will be listed within the Filter panel. In this example, the table was filtered to show AMR genes supported by at least two contigs and only two genes fell within the specified threshold.
If you are interested in filtering the report to focus on resistance against a specific drug glass, click the "Drug Class" filter. Select a drug class of interest from the dropdown menu.