Reference Genomes

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: OR the PI, Thomas Keane,

We expect the gene annotation to be finalised and released by end of 2023 via the Ensembl Rapid Release browser.

StrainAccessionSexQVN-basesGene annotation
129S1/SvImJGCA_921998555.2FIn progress
A/JGCA_921998355.2FIn progress
AKR/JGCA_922000895.2FIn progress
BALB/cJGCA_921997145.2FIn progress
C3H/HeJGCA_921997125.2FIn progress
C57BL/6NJGCA_921999865.2FIn progress
CAST/EiJGCA_921999005.2FIn progress
CBA/JGCA_921998905.2FIn progress
DBA/2JGCA_921998315.2FIn progress
FVB/NJGCA_921998635.2FIn progress
JF1/MsJGCA_921999095.2FIn progress
LP/JGCA_947599735.1FIn progress
NOD/ShiLtJGCA_921998325.2FIn progress
NZO/HlLtJGCA_947593165.1FIn progress
PWK/PhJGCA_921998335.2FIn progress
SPRET/EiJGCA_921997135.2FIn progress
WSB/EiJGCA_921998345.2FIn progress

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.