Ensembl Beta is in development, known bugs for this site will be listed below.

Known bugs as of November 2025:

Missing data from Western wild mouse SPRET_EiJ_v3 GCA_921997135.2 in release 2025-02
Affects: Integrated Release 2025-02	Expected fix: N/A, may be suppressed
Description: Due to missing data, gene visualisations in apps may fail for Western wild mouse SPRET_EiJ_v3 GCA_921997135.2.  This will be resolved in a future release and this release version may be suppressed from the site.
Workaround: No current workaround

Norway rat mRatBN7.2 genome in Integrated release 2025-02 is broken
Affects: Integrated Release 2025-02	Expected fix: N/A, will be suppressed
Description: Due to a site error, the Norway rat mRatBN7.2 genome from the 2025-02 Integrated release is not working correctly. This genome will be suppressed from site features to prevent use. There is a more up to date release of Norway Rat mRatBN7.2 from the 2025-07-14 partial release: https://beta.ensembl.org/species/d6c51c59-4863-4c1f-a738-bb838afa868e
Workaround: Please make use of the Norway Rat mRatBN7.2 from the 2025-07-14 partial release: https://beta.ensembl.org/species/d6c51c59-4863-4c1f-a738-bb838afa868e

Zimmermann’s shrew loaded incorrectly
Affects: Ensembl beta	Expected fix: within two beta releases
Description: Data for Zimmermann’s shrew (Crocidura zimmermanni) and the Crete spiny mouse (Acomys minous) imported from Genoscope were loaded incorrectly and will contain missing or incorrect data.
Workaround: Please use the older version of the genome: Zimmermann’s shrew (mCroZim1.1) https://beta.ensembl.org/species/183fb547-fe4f-483f-93a6-33e806d8ffb4

Broken Entity Viewer for some variants due to data mismatch
Affects: Ensembl Beta	Expected fix: within eight beta releases
Description: The Entity Viewer page is broken for some variants. Example link: https://beta.ensembl.org/entity-viewer/t2t-chm13/variant:1:53345:rs1295930465?allele=1&view=transcript-consequences Example for expected page: https://beta.ensembl.org/entity-viewer/t2t-chm13/variant:1:53345:rs1295930465?allele=0 This is due to a version mismatch in transcript between core and variation data.
Workaround: No workaround

Incorrect URLs from annotation provider links
Affects: Ensembl Beta	Expected fix: Within the next two beta releases
Description: Annotation provider links on the species homepage are formed of broken URLs. Example: Human T2T-CHM13v2.0 species homepage For more information on our gene annotation process, please see Ensembl Help and documentation
Workaround: No workaround

Genome Browser breaks for genomic patches
Affects: Ensembl Beta	Expected fix: within the next four beta releases
Description: The Genome browser page breaks when pointed to a gene that is located in a patch region. Example: Select Human Grch38 and open the genome browser Search for gene ENSG00000285479 The discovered gene is on a patch (HG1815_PATCH:312,916-1,046,066)
Workaround: Point Genome Browser to the location of the gene instead of the gene ID: * broken: (https://beta.ensembl.org/genome-browser/grch38?focus=gene:ENSG00000285479) * works: (https://beta.ensembl.org/genome-browser/grch38?location=HG1815_PATCH:997023-1020218)

Links to homologies data in FTP lead to incorrect directories
Affects: Ensembl Beta	Expected fix: within the next two beta releases
Description: In many species the link to the homologies FTP dumps are broken on the site.  For example: https://beta.ensembl.org/species/7c4e3698-a2c2-41e2-ac41-38323847c3e1 Leads to a folder which does not exist: https://ftp.ebi.ac.uk/pub/ensemblorganisms/Adineta_vaga/GCA_000513175.1/ Community/homology/2017_02 The files are present under the wrong directory. The correct directory is: https://ftp.ebi.ac.uk/pub/ensemblorganisms/Adineta_vaga/GCA_000513175.1/ community/homology/ Files can be found by going to the homology directory and browsing for the files. This bug should not be present for all new species, but the existing species will not be fixed immediately.
Workaround: Revert to the GCA directory in the FTP link and follow the correct directory paths e.g. https://ftp.ebi.ac.uk/pub/ensemblorganisms/Adineta_vaga/GCA_000513175.1/

Missing data for Adineta vaga –Rotifer AMS_PRJEB1171_v1
Affects: Ensembl Beta	Expected fix: Within next two beta releases
Description: Due to incomplete loading, data for Adineta vaga –Rotifer AMS_PRJEB1171_v1 is missing from the site. Some data may load but it is likely incomplete. Until this issue is resolved data should be obtained from the main site https://metazoa.ensembl.org/Adineta_vaga/Info/Index
Workaround: No current workaround in beta. Data is available via: https://metazoa.ensembl.org/Adineta_vaga/Info/Index

Ensembl Beta FTP gff3 files are uncompressed
Affects: Ensembl Beta	Expected fix: Existing files – within a few months time; new files – within the next two releases
Description: The gff3 files available via https://ftp.ebi.ac.uk/pub/ensemblorganisms/ are uncompressed due to a production system bug. Current uncompressed files will be fixed when the FTP structure is revised. New files generated within upcoming releases will be compressed.
Workaround: No current workaround.

Previous bugs which have been resolved (last updated November 2025):

If you find that a bug in the list below is still occurring, please contact the Ensembl Helpdesk

RESOLVED: Variant track view not displaying when zoomed in
Affects: Ensembl Beta	Expected fix: Within next two beta releases
Description: Variation tracks turn blank when zoomed into a gene via the genome browser app. This has been observed in T2T-CHM13.
Workaround: No current workaround.

RESOLVED: Norway Rat – Rattus norvegicus – mRatBN7.2 currently unavailable
Affects: Ensembl Beta	Expected fix: within the next two beta releases
Description: The Rattus norvegicus mRatBN7.2 genome on beta.ensembl.org is currently unavailable due a fault in the release process for this species.
Workaround: No current workaround. Please make use of other Rattus norvegicus genomes where applicable to your needs.

RESOLVED: Outdated regulatory annotation tracks for human and mouse
Affects: Ensembl Beta	Expected fix: within the next two beta releases
Description: The regulatory annotation tracks for human and mouse are showing data from an older release (March 2023) than the release version of Ensembl beta. The counts shown for regulatory features match the latest release, and hence these counts are incorrect.
Workaround: No current workaround on beta. Up to date regulation tracks are available via ensembl.org and ensemblgenomes.org/

RESOLVED: Incorrect counts on popular species display
Affects: Ensembl Beta	Expected fix: within next two beta releases
Description: The counts displayed within the black bubbles on the popular species grid of the https://beta.ensembl.org/species-selector page may not accurately represent the total count of genomes available for that species available in https://beta.ensembl.org
Workaround: No current workaround. Please use the species search bar to search across all species in https://beta.ensembl.org