Reference quality genomes
High quality reference genomes and annotation are available for seventeen inbred mouse strains. These data are released in accordance with the Fort Lauderdale agreement and Toronto agreements. As producers of these data we reserve the right to be the first to publish a genome-wide analysis of the data we have generated. The pre-publication data that we release is embargoed for publication except for analyses of single chromosomes in single strains or single gene loci across multiple strains. We strongly encourage researchers to contact us if there are any queries about referencing or publishing analysis based on pre-publication data obtained via this website (Email: mousegenomes@sanger.ac.uk OR the PI, Thomas Keane, tk2@ebi.ac.uk).
| Strain | Accession | Sex | Gene annotation |
| 129S1/SvImJ | GCA_921998555.2 | F | Ensembl |
| A/J | GCA_921998355.2 | F | Ensembl |
| AKR/J | GCA_922000895.2 | F | Ensembl |
| BALB/cJ | GCA_921997145.2 | F | Ensembl |
| C3H/HeJ | GCA_921997125.2 | F | Ensembl |
| C57BL/6NJ | GCA_921999865.2 | F | Ensembl |
| CAST/EiJ | GCA_921999005.2 | F | Ensembl |
| CBA/J | GCA_921998905.2 | F | Ensembl |
| DBA/2J | GCA_921998315.2 | F | Ensembl |
| FVB/NJ | GCA_921998635.2 | F | Ensembl |
| JF1/MsJ | GCA_921999095.2 | F | Ensembl |
| LP/J | GCA_947599735.1 | F | Ensembl |
| NOD/ShiLtJ | GCA_921998325.2 | F | Ensembl |
| NZO/HlLtJ | GCA_947593165.1 | F | Ensembl |
| PWK/PhJ | GCA_921998335.2 | F | Ensembl |
| SPRET/EiJ | GCA_921997135.2 | F | Ensembl |
| WSB/EiJ | GCA_921998345.2 | F | Ensembl |
Draft (short read) genomes
In 2018, we produced the first draft reference genomes for sixteen inbred strains (described in this paper). Whilst these genomes were informative for establishing the extent of non-reference haplotype variation and have very good representation for protein coding genes, we do not recommend using them for NGS analysis due to the lack of representation for common repeat sequences. These genomes can be found from Ensembl.