Strain |
JAX Stock No. |
Letter |
Color (hex) |
Color (RGB) |
Color |
A/J |
A |
#F0E442 |
240, 228, 66 |
![]() |
|
C57BL/6J |
B |
#555555 |
85, 85, 85 |
|
|
129S1/SvImJ |
C |
#E69F00 |
230, 159, 0 |
|
|
NOD/ShiLtJ |
D |
#0072B2 |
0, 114, 178 |
|
|
NZO/HlLtJ |
E |
#56B4E9 |
86, 180, 233 |
|
|
CAST/EiJ |
F |
#009E73 |
0, 158, 115 |
|
|
PWK/PhJ |
G |
#D55E00 |
213, 94, 0 |
|
|
WSB/EiJ |
H |
#CC79A7 |
204, 121, 167 |
|
This report details the founder allele frequencies across the genome. This may be useful if you suspect are investigating a specific founder allele at a specific position.
https://jackson.jax.org/rs/444-BUH-304/images/2022-J.DO-Genetic-Diversity-Report.pdf
This page contains reference data for the Collaborative Cross (CC) and Diversity Outbred (DO) founders. You will find reference data for:
Mouse Universal Genotyping Array (MUGA)
Founder Denovo Genome Assemblies
Founder Pseudogenomes (i.e. SNPs & Indels inserted)
Genomic Variants
File |
GRCm39 |
Description |
|
Marker positions |
CSV file. 7,854 rows. Contains cM values. |
||
Marker file metadata |
Column descriptions for marker file. |
File |
GRCm38 |
GRCm39 |
Description |
Marker positions |
CSV file. 77,808 rows. Contains cM values. |
||
Marker file metadata |
Column descriptions for marker file. |
File |
Link |
Description |
Founder metadata |
CSV file. 175 rows, 5 columns. |
|
Consensus genotypes |
Gzipped CSV file. 75,053 rows, 9 columns. Genotypes encoded as one letter: A, C, G, T, H, or N. |
|
X channel intensities |
Gzipped CSV file. 75,053 rows, 9 columns. |
|
Y channel intensities |
Gzipped CSV file. 75,053 rows, 9 columns. |
File |
Link |
Description |
Sample metadata |
CSV file. 364 rows, 4 columns |
|
Sample genotypes |
Gzipped CSV file. 75,058 rows, 354 columns. Genotypes encoded as one letter: A, C, G, T, H, or N. |
|
X channel intensities |
Gzipped CSV file. 75,058 rows, 354 columns. |
|
Y channel intensities |
Gzipped CSV file. 75,058 rows, 354 columns. |
File |
GRCm38 |
GRCm39 |
Description |
Marker positions |
CSV file. 143,259 rows. Contains cM values. |
||
Marker file metadata |
Column descriptions for marker file. |
File |
Link |
Description |
Founder metadata |
CSV file. 170 rows, 5 columns. |
|
Consensus genotypes |
Gzipped CSV file. 123,915 rows, 9 columns. Genotypes encoded as one letter: A, C, G, T, H, or N. |
|
Chr Y Haplogroups |
CSV file. 13 rows, 7 columns. Genotypes encoded as one letter: A, C, G, T. |
|
Chr M Haplogroups |
CSV file. 20 rows, 6 columns. Genotypes encoded as one letter: A, C, G, T. |
|
X channel intensities |
Gzipped CSV file. 123,915 rows, 9 columns. |
|
Y channel intensities |
Gzipped CSV file. 123,915 rows, 9 columns. |
File |
Link |
Description |
Sample metadata |
CSV file. 279 rows, 4 columns. |
|
Sample genotypes |
Gzipped CSV file. 123,998 rows, 280 columns. Genotypes encoded as one letter: A, C, G, T, H, or N. |
|
X channel intensities |
Gzipped CSV file. 123,998 rows, 280 columns. |
|
Y channel intensities |
Gzipped CSV file. 123,998 rows, 280 columns. |
File |
GRCm38 |
GRCm39 |
Description |
CC/DO variants |
SQLite database of CC/DO founder SNPs & Indels. |
||
Genes |
SQLite database of mouse genes. |
These data were generated by the Wellcome Sanger Mouse Genome Project. The conditions of use laid out by the authors are as follows:
"In this study, we have produced reference quality chromosome scale genomes for both classical and wild derived inbred laboratory mouse genomes. These genomes were produced using third generation long reads and Hi-C. The genomes and gene annotation are also available via the Ensembl and UCSC genome browsers. The Mouse Genomes Project releases genome sequence data, SNPs and other variant calls as a service to the research community. 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 |
EBI Page |
FASTA file |
Description |
A/J |
Gzipped FASTA file. |
||
129S1/SvImJ |
Gzipped FASTA file. |
||
NOD/ShiLtJ |
Gzipped FASTA file. |
||
NZO/HlLtJ |
EBI page |
FASTA file (This file is not yet listed on the EBI website) |
Gzipped FASTA file. |
CAST/EiJ |
Gzipped FASTA file. |
||
PWK/PhJ |
Gzipped FASTA file. |
||
WSB/EiJ |
Gzipped FASTA file. |
These data were generated by the Wellcome Sanger Mouse Genome Project. The conditions of use laid out by the authors are in their README file.
File |
GRCm38 (Ensembl 78) |
GRCm39 (Ensembl 104) |
Description |
SNPs |
Gzipped VCF file. |
||
SNPs Index |
Tabix index. *.tbi or *.csi file. |
||
Indels |
Gzipped VCF file. |
||
Indels Index |
Tabix index. *.tbi or *.csi file. |
||
Deletions |
Not available |
Gzipped BED file. |
|
Deletions Index |
Not available |
Tabix index for BED file. *.tbi file. |
|
Insertions |
Not available |
Gzipped BED file. |
|
Insertions Index |
Not available |
Tabix index for BED file. *.tbi file. |
These are FASTA files with SNPs and Indels from the Sanger variant files inserted into each genome. GRCm38.
Strain |
File |
Description |
A/J |
Gzipped FASTA file. |
|
C57BL/6J |
Gzipped FASTA file. Ensembl 102 reference. |
|
129S1/SvImJ |
Gzipped FASTA file. |
|
NOD/ShiLtJ |
Gzipped FASTA file. |
|
NZO/HlLtJ |
Gzipped FASTA file. |
|
CAST/EiJ |
Gzipped FASTA file. |
|
PWK/PhJ |
Gzipped FASTA file. |
|
WSB/EiJ |
Gzipped FASTA file. |