--- title: Investigating exon coverage description: How to quickly check that all exons are covered? --- [Skip to content](https://docs.varsome.com/en/investigating-exon-coverage#main-content) English Show submenu for translations [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) [Customer portal](https://docs.varsome.com/support-requests?hsLang=en) [![varsome-new.png\]](https://docs.varsome.com/hs-fs/hubfs/varsome-new.png?height=40&name=varsome-new.png)](https://docs.varsome.com/en?hsLang=en) - Editions Show submenu for Editions - [VarSome.com](https://landing.varsome.com/varsome) - [VarSome Clinical](https://landing.varsome.com/varsome-clinical) - [VarSome Premium](https://landing.varsome.com/varsome-premium) - [VarSome API](https://landing.varsome.com/varsome-api) - [VarSome Insights](https://landing.varsome.com/varsome-insights) - About Show submenu for About - [The Company](https://saphetor.com/) - [Contact Us](https://landing.varsome.com/contact) - [Distributors](https://landing.varsome.com/distributors) - [Become a Partner](https://landing.varsome.com/become-varsome-partner) - [Community](https://varsome.com/community-contributions/) - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/) - Resources Show submenu for Resources - [Datasources](https://varsome.com/datasources/) - [Germline Classification](https://varsome.com/about/resources/germline-implementation/) - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) - [CNV Classification](https://varsome.com/about/resources/sv-implementation/) - [Help Center](https://docs.varsome.com/) - [Library](https://landing.varsome.com/whitepapers) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance) - Blog Show submenu for Blog - [Platform Updates](https://updates.varsome.com/en) - [Company News](https://news.varsome.com/en) - [VarSome Annotated](https://blog.varsome.com/annotated) Open main navigation Close main navigation - Editions Show submenu for Editions - [VarSome.com](https://landing.varsome.com/varsome) - [VarSome Clinical](https://landing.varsome.com/varsome-clinical) - [VarSome Premium](https://landing.varsome.com/varsome-premium) - [VarSome API](https://landing.varsome.com/varsome-api) - [VarSome Insights](https://landing.varsome.com/varsome-insights) - About Show submenu for About - [The Company](https://saphetor.com/) - [Contact Us](https://landing.varsome.com/contact) - [Distributors](https://landing.varsome.com/distributors) - [Become a Partner](https://landing.varsome.com/become-varsome-partner) - [Community](https://varsome.com/community-contributions/) - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/) - Resources Show submenu for Resources - [Datasources](https://varsome.com/datasources/) - [Germline Classification](https://varsome.com/about/resources/germline-implementation/) - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) - [CNV Classification](https://varsome.com/about/resources/sv-implementation/) - [Help Center](https://docs.varsome.com/) - [Library](https://landing.varsome.com/whitepapers) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance) - Blog Show submenu for Blog - [Platform Updates](https://updates.varsome.com/en) - [Company News](https://news.varsome.com/en) - [VarSome Annotated](https://blog.varsome.com/annotated) - English Show submenu for translations - [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new) - [Customer portal](https://docs.varsome.com/support-requests) - [Contact us](https://docs.varsome.com/en/kb-tickets/new) [Contact us](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) How can we help you? - There are no suggestions because the search field is empty. 1. [VarSome Help Center](https://docs.varsome.com/en?hsLang=en) 2. [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en) 3. [User Interface](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#user-interface) # Investigating exon coverage ## How to quickly check that all exons are covered? There's no direct way of seeing gaps in an exon's coverage, but you can get partway there by using the **Coding coverage report** as opposed to the [Region list coverage report](https://docs.varsome.com/region-list-coverage-report?hsLang=en): [![](https://docs.varsome.com/hs-fs/hubfs/image-png-Jan-14-2025-10-24-23-4196-AM.png?width=341&height=371&name=image-png-Jan-14-2025-10-24-23-4196-AM.png)](https://docs.varsome.com/hubfs/image-png-Jan-14-2025-10-24-23-4196-AM.png?hsLang=en) [![](https://lh7-us.googleusercontent.com/pblaWEFJdUP4NV06-5C6tOtwO-zGcxMlT7iQyC5I1DRJ3SKtzhaGv1Z1L3rDQGDqeg26fAuaXo6gq6SzO58cQw5JqFgiRZaezqiqkAYx58PEmqA6BDpODAZCqRyttu1VeZI5m4ZzkmmXZjUphmPKiNs)](https://lh7-us.googleusercontent.com/pblaWEFJdUP4NV06-5C6tOtwO-zGcxMlT7iQyC5I1DRJ3SKtzhaGv1Z1L3rDQGDqeg26fAuaXo6gq6SzO58cQw5JqFgiRZaezqiqkAYx58PEmqA6BDpODAZCqRyttu1VeZI5m4ZzkmmXZjUphmPKiNs) Clicking on that option will bring up a popup where you can choose a gene list and then download a coverage report for the genes in that list. Please note that you will need to create the gene list before clicking on this option. To do so, click on **Gene Lists** in the top bar: ![](https://docs.varsome.com/hs-fs/hubfs/image-png-Jun-06-2025-07-28-53-1306-AM.png?width=670&height=64&name=image-png-Jun-06-2025-07-28-53-1306-AM.png) Then, click on **[Create new gene list](https://docs.varsome.com/en/create-a-gene-list?hsLang=en)** and enter your genes of interest and save it with a name of your choosing. You will now be able to generate coding coverage reports using that list. This file has a breakdown of coverage by exon. Although it won't directly pinpoint gaps, it will at least show the minimum coverage per exon, so if that is 0 you know there's a gap somewhere and can then use the *Gene Coverage* function to locate the target exon: [![Gene coverage](https://docs.varsome.com/hs-fs/hubfs/Gene%20coverage.jpg?width=600&name=Gene%20coverage.jpg)](https://docs.varsome.com/hubfs/Gene%20coverage.jpg?hsLang=en) Subsequently, click on the exon and so open the JBrowse window that shows the actual reads at that position: [![JBrowse view](https://docs.varsome.com/hs-fs/hubfs/Exon35%20gap.jpg?width=600&name=Exon35%20gap.jpg)](https://docs.varsome.com/hubfs/Exon35%20gap.jpg?hsLang=en) - [Registration & Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#main-content) - [User account management](https://docs.varsome.com/en/registration-billing?hsLang=en#user-account-management) - [Storage management](https://docs.varsome.com/en/registration-billing?hsLang=en#storage-management) - [Pricing and Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#pricing-and-billing) - [VarSome Clinical Tokens](https://docs.varsome.com/en/registration-billing?hsLang=en#varsome-clinical-tokens) - [Management of Samples and Analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#main-content) - [Uploading files](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#uploading-files) - [Managing Samples](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-samples) - [Managing Workflows](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-workflows) - [Launching analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#launching-analyses) - [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#main-content) - [Analyses](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#analyses) - [Results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#results) - [Filters](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#filters) - [Reporting](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#reporting) - [Quality Control](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#quality-control) - [Legal & compliance](https://docs.varsome.com/en/legal-compliance?hsLang=en) - [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#main-content) - [Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#troubleshooting) - [General](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#general) - [Filters](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#filters) - [User Interface](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#user-interface) - [Pipelines](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#pipelines) - [Features](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#features) - [Scientific articles](https://docs.varsome.com/en/scientific-articles?hsLang=en) - [VarSome API](https://docs.varsome.com/en/varsome-api?hsLang=en) [![VarSome Logo](https://docs.varsome.com/hs-fs/hubfs/VarSome%20Logo.png?width=200&height=47&name=VarSome%20Logo.png "VarSome Logo")](https://varsome.com) **Resources** [Query Examples](https://varsome.com/about/resources/examples/) [Germline Classification](https://varsome.com/about/resources/germline-implementation/) [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) [White Papers & Other Resources](https://varsome.com/library/) [Cite VarSome](https://varsome.com/about/general/varsome-citations/) [System Status](https://status.saphetor.com/) [Help Center](https://docs.varsome.com/en?hsLang=en) **Legal** [Terms of Use](https://varsome.com/information/legal/terms/) [Privacy Policy](https://varsome.com/information/legal/privacy/) [Information Security](https://varsome.com/information/legal/information-security/) Copyright © 2025, Saphetor SA