GeneCov - How is gene coverage calculated?

In the Gene coverage tab, users can view the coverage rate of the genes included in the analysis manifest for each exon, whether a gene panel or exome.

Methodology

This module intersects the user manifest with RefSeq annotations for all genes included in the panel or the exome, keeping 10bp on each side in order to cover splice junctions, then proceeds to calculate coverage depth for each base included in this intersection.

Different thresholds are set in order to assign each exon a status (covered, warning, failed) according to the percentage of bases below these coverage thresholds.

• The status is defined from the base coverage in the exon including the adjacent 10bp.
• If UMIs are used, coverage is calculated after deduplication.

Choice of values

The user can select the coverage calculation method to be applied using the "Exon status criteria" drop-down menu at the top right of the page:

1. Mean Coverage (default): Uses the average coverage depth over the entire exon to determine coverage status.
2. Minimum Coverage:b> Uses the minimum fraction of bases that meet a specific coverage threshold. This ensures that a certain percentage of bases have at least the minimum required coverage depth.

Contact our Customer Care team (mailto:support@seqone.com) to set up your custom thresholds for "high / medium / low" exons.