Introduction

Genoox provides a comprehensive and customizable summary quality control report for sample read coverage.

To navigate to the coverage report, open a case, and search for "Coverage Report" from the left menu bar

Filters

Grouping

The Coverage report allows users to view coverage in different resolutions: Gene, Exon, Kit Region.

Coverage Region

"Coverage region" allows users to filter the report based on a pre-defined preparation kit (Library). Kit configuration is determined by the assay used to process the sample and produce the analysis, and can be defined using a "Custom Assay".

Panel

Virtual panels that are associated with the analysis assay can be used in order to filter the coverage report view based on genes \ regions from the panel.

Position

"Position" allows users to filter the view based on chromosomal position, including a sub-break down of exact positions, "Start" to "End" positions in a chromosome.

Qualified Coverage

📘Assay Threshold Customization

By default, qualified coverage is defined as x20 reads per base, however - this value
if fully customizable per analysis - and is determined by the assay configuration by which the analysis was processed

The qualified coverage menu allows users to filter the Coverage Report view based on the percent covered bases.

Region view

The area of the coverage report displays an aggregated coverage summary for a specific region. A region can be a gene an exon or a targeted region by the enrichment kit, according to the user selection.

Each region could be expanded by a mouse click to disclose specific coverage information on the region itself.

In the above image, we can review the coverage of the A4GALT Gene

Each Gene will contain a table (table structure description below) with regions in which there was insufficient coverage (below 20x by default). The exact threshold for considering a base as covered can be configured as part of the Assay.

Exon - The exon of the coverage region
chr - The chromosome of the coverage region
Start-End - Start to end position of the coverage region
Length - The length of the coverage region
Coverage - No. of reads of the coverage region
Targeted - indication whether the bases are targeted by the region or not ("v" sign marks that these bases are targeted by the kit and "x" that they are not)

Coverage Breakdown

Per each tile, a coverage breakdown summary is displayed to with summary of the coverage of the specific region.

The card displays:

Max - maximum depth (number of reads) found in the region
Med - median depth found in the region
Min - minimum depth found in the region
Avg - average depth found in the region

Bar Graph

The bar graph displays the percentage bases in the specific region which are above certain thresholds. The different thresholds can be configured in the assay configuration.

1 > - % of bases above 1x depth
5 > - % of bases above 5x depth
10 > - % of bases above 10x depth
20 > - % of bases above 20x depth

For example, in the above screenshot, 99% of the bases in the gene were covered with depth higher than or equal to 20x.