Here we list known bugs for the integrated release 2026-07, released in July 2026.
Known bugs as of September 2026:
| Mismatch between linked data for Ensembl gene IDs between legacy and new versions | |
| Affects: Live site, archives | Expected fix: TBC |
| Description: We are investigating cases of Ensembl gene IDs which linking to mismatched gene linked data between 116 and earlier versions and the new Ensembl integrated release 2026-07. The following genomes are affected: Gadus morhua – GCA_010882105.1 Sus scrofa – GCA_015776825.1 Sus scrofa – GCA_017957985.1 Oryzias latipes hni – GCA_002234715.1 Oryzias latipes hsok – GCA_002234695.1 Bos taurus – GCA_002263795.4 Corvus moneduloides – GCA_009650955.1 Equus asinus – GCA_016077325.2 Melopsittacus undulatus – GCA_012275295.1 Ovis aries – GCA_016772045.2 Scophthalmus maximus – GCA_013347765.1 Ficedula albicollis – GCA_000247815.2 We are still investigating the proportion of IDs that are mismatched between release versions. Ensembl gene IDs are unique to the genome in which they are annotated and the date of annotation. | |
| Workaround: No current workaround. Caution should be taken in mapping IDs from the above genomes from versions 116 and earlier to new Ensembl 2026-07. | |
| Faults identified with stable IDs in Macaca fascicularis GCA_011100615.1 | |
| Affects: Live site 2026-07 | Expected fix: TBC |
| Description: We have identified processing errors that have affected stable IDs in Macaca fascicularis – GCA_011100615.1. This genome will be suppressed and re-released. | |
| Workaround: No current workaround. | |
| Incorrect paths in the the new FTP structure JSON index | |
| Affects: Live site | Expected fix: within four releases |
| Description: There are incorrect paths in the new FTP structure JSON index – species.new_ftp_structure.json These may be due to incorrect dates for a directory, or due to an error in the file compression pipeline for that species data. Please take note of this when parsing the new FTP structure documentation and folders. | |
| Workaround: No current workaround. | |
| Genome browser tracks missing for 20 genomes | |
| Affects: Live site | Expected fix: within two releases |
| Description: Several genomes have faulty or missing tracks, and genome displays in the Genome browser app will not work as expected. Tracks missing include essential transcript and GC tracks. Name Accession – ID geneset-date provider-name: schistocerca_cancellata GCF_023864275.1 2023-03 NCBI RefSeq octopus_sinensis GCF_006345805.1 2022-03 NCBI RefSeq adineta_vaga GCA_000513175.1 2017-02 Genoscope hyla_sarda GCA_029499605.1 2023-09 Ensembl daucus_carota GCA_001625215.1 2016-06 USDA carcharodon_carcharias GCA_017639515.1 2021-10 Ensembl artibeus_jamaicensis GCA_004027435.1 2020-08 Ensembl macaca_thibetana GCA_024542745.1 2022-09 Ensembl marmota_flaviventris GCA_003676075.2 2020-05 Ensembl vicugna_pacos_huacaya GCA_000767525.1 2020-05 Ensembl onychomys_leucogaster GCA_949786385.1 2023-09 Ensembl bubalus_bubalis GCA_003121395.1 2020-06 Ensembl rhizomys_pruinosus GCA_009823505.1 2020-05 Ensembl sternotherus_odoratus GCA_032164245.1 2023-10 Ensembl bombyx_mori GCF_030269925.1 2024-08 NCBI RefSeq hypsopygia_costalis GCA_937001555.2 2023-02 Ensembl anas_zonorhyncha GCA_002224875.1 2020-04 Ensembl melolontha_melolontha GCA_935421255.1 2022-09 Ensembl felis_catus GCA_018350175.1 2021-08 Ensembl bombyx_mandarina GCF_003987935.1 2022-07 NCBI RefSeq | |
| Workaround: No current workaround. Tracks for these genomes will be regenerated. | |
| Genome browser tracks missing due to circular regions in four genomes | |
| Affects: Live site | Expected fix: within two releases |
| Description: Four genomes are missing essential tracks for contigs, simple features, and transcript information. Name Accession – ID geneset-date provider-name: adineta_vaga GCA_000513175.1 2017-02 Genoscope bombyx_mandarina GCF_003987935.1 2022-07 NCBI RefSeq bombyx_mori GCF_030269925.1 2024-08 NCBI RefSeq daucus_carota GCA_001625215.1 2016-06 USDA | |
| Workaround: No current workaround. Tracks for these genomes will be regenerated. | |
| Assembly statistics not being shown for species without chromosome level assembly | |
| Affects: Live site | Expected fix: within two releases |
| Description: Due to a display issue, assembly statistics are not being shown on the species homepage. This affects genomes with assembly levels that are not chromosome level (e.g. scaffold). e.g. https://beta.ensembl.org/species/ff7a2ba3-b5ce-4c24-b452-c0b56fcf16fa | |
| Workaround: No current workaround. | |
| Incorrect date directories in the new FTP structure for variation and homology data | |
| Affects: FTP | Expected fix: within two releases |
| Description: Due to a processing error, directories of dates for homology and variation data are incorrect for the new FTP structure released in June 2026. These directories have inconsistent dates. For example: The directory containing the homology file for Homo sapiens GRCh38 is incorrectly named: Index of /pub/ensemblorganisms/GCA/000/001/405/29/ensembl/2025_12/homology/2023_10_18 The homology file in this directory is from the 2025_12 update, so the correct path should be : https://ftp.ebi.ac.uk/pub/ensemblorganisms/GCA/000/001/405/29/ensembl/2025_12/homology/2026_04_09/ Please take caution of this when developing with the new FTP structure. | |
| Workaround: No current workaround. | |
| Issue in the automatic superseding of partial releases | |
| Affects: Partial releases | Expected fix: Autumn 2026 |
| Description: A web bug is causing partial releases which are meant to be superseded to persist if these have already been selected or if accessed via a saved URL. In future, when a partial release for a given genome is updated, it will redirect to the latest version of that data, and the previous versions will no longer be available. Data files for all releases remain available from the new Ensembl FTP site – https://ftp.ebi.ac.uk/pub/ensemblorganisms/ | |
| Workaround: The latest versions for partial releases may be selected by searching in the Species Selector | |
| Geneset FTP dumps are missing for select species | |
| Affects: FTP site | Expected fix: Autumn 2026 |
| Description: Geneset files on the new Ensembl FTP are missing for a selected number of genomes for the following organisms: Ovis aries Strigamia maritima Donax variegatus Yponomeuta padella Drosophila melanogaster Chrysolina graminis Melanotaenia boesemani Bruchidius varius, Xestobium rufovillosum Bruchidius varius, Crassostrea angulata Calliactis parasitica | |
| Workaround: No current workaround | |
| Missing data from Western wild mouse SPRET_EiJ_v3 GCA_921997135.2 in release 2026-07 | |
| Affects: Live site | 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 | |
| Zimmermann’s shrew and Spiny mouse loaded incorrectly | |
| Affects: Live site | Expected fix: N/A |
| 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: Live site | Expected fix: within eight partial releases |
| Description: The Entity Viewer page is broken for some variants. Example link: https://beta.ensembl.org/entity-viewer/GCA_009914755.4/variant:1:53345:rs1295930465?allele=1&view=transcript-consequences Example for expected page: https://beta.ensembl.org/entity-viewer/GCA_009914755.4/variant:1:53345:rs1295930465?allele=0 This is due to a version mismatch in transcript between core and variation data. | |
| Workaround: No workaround | |
| Missing data for Adineta vaga –Rotifer AMS_PRJEB1171_v1 | |
| Affects: Live site | Expected fix: N/A |
| 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 site https://metazoa.ensembl.org/Adineta_vaga/Info/Index | |
| Workaround: No current workaround in new site. Data is available via: https://metazoa.ensembl.org/Adineta_vaga/Info/Index | |
Previous bugs which have been resolved (last updated September 2026):
If you find that a bug in the list below is still occurring, please contact the Ensembl Helpdesk
| RESOLVED: Genome Browser breaks for genomic patches | |
| Affects: Live site | Expected fix: within the next four partial 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 ENSG00000285479The 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 | |