Gene Coverage

Gene coverage information can be downloaded as an excel (xlsx) file from the user interface (UI) as mentioned in the relevant section in the Case Information page. In addition, the information is also available in a specific tab in the UI.

The view by default includes the columns with the information for depth at 5X, 10X, 20X, 30X, 50X 100X and 150X, the Min Depth, Max Depth and the Average depth for each gene, and default sorted by Gene column. Non-coding genes are labeled with an asterisk (*) to raise awareness to the user:

The user can reduce the number of columns visible by unselecting any depth information that is not relevant to be considered in the current analysis, filter by any values for a specific depth and change the sorting criteria. Any changes in the sorting or filtering applied will be showing on the top of the coverage information table as shown in the screenshot below:

Regarding coverage values, it is important to consider that gene coverage is influenced by the definition according to the secondary pipeline used to produce the data. In the case of using Nostos Genomics secondary pipeline the gene definition for coverage calculation is as follows:

WES/Panel:
- For coding genes: canonical transcripts, coding sequence (CDS) only, +- 5bp padding
  - Canonical transcript definition: (hg19: preferred source ENSEMBL, hg38: preferred source MANE)
- For non-coding genes: all exons, +- 5bp padding

WGS: Ensembl all transcripts, all exons and UTRs, +- 50bp padding