Collaborative Cross and Diversity Outbred Reference Data

CC/DO Founder Names, Letters, and Colors

Strain	JAX Stock No.	Letter	Color (hex)	Color (RGB)	Color
A/J	000646	A	#F0E442	240, 228, 66
C57BL/6J	000664	B	#555555	85, 85, 85
129S1/SvImJ	002448	C	#E69F00	230, 159, 0
NOD/ShiLtJ	001976	D	#0072B2	0, 114, 178
NZO/HlLtJ	002105	E	#56B4E9	86, 180, 233
CAST/EiJ	000928	F	#009E73	0, 158, 115
PWK/PhJ	003715	G	#D55E00	213, 94, 0
WSB/EiJ	001145	H	#CC79A7	204, 121, 167

Purchasing Genetically Diverse Mice

Purchase Collaborative Cross Mice (Search for “Collaborative Cross” to view available strains)
Purchase Diversity Outbred Mice

Genotyping

Collaborative Cross mice genomes are available below.
Diversity Outbred mice may be genotyped using the GigaMUGA through Neogen. They are currently the only vendor who can process the GigaMUGA.

Diversity Outbred Genome Report

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)

MUGA
MegaMUGA
GigaMUGA

Founder Denovo Genome Assemblies
Founder Pseudogenomes (i.e. SNPs & Indels inserted)
Genomic Variants

Mouse Universal Genotyping Array Series

MUGA

MUGA Reference Quality Control Process

Marker positions

File	GRCm38	GRCm39	Description
Marker positions	muga_uwisc_v1.csv	muga_uwisc_v2.csv	CSV file. 7,854 rows. Contains cM values.
Marker file metadata	muga_uwisc_dict_v1.csv	muga_uwisc_dict_v2.csv	Column descriptions for marker file.

CC/DO Founders

Founder Sample Metadata
- Founder Metadata: 48 rows, 5 columns. Contains sex and strain background for each sample. (6 DO samples excluded).
Founder Consensus Genotypes
- Genotypes: Gzipped CSV file. 7,762 rows, 9 columns. Genotypes encoded as one letter: A, C, G, T, H, or N.
Founder Probe Intensities
- X Channel: Gzipped CSV file. 7,762 rows, 9 columns.
- Y Channel: Gzipped CSV file. 7,762 rows, 9 columns.

All Reference Samples

Reference Sample Metadata
- Sample Metadata: CSV file. 55 rows, 4 columns.
Genotypes
- Genotypes: Gzipped CSV file. 7,762 rows, 55 columns. Genotypes encoded as one letter: A, C, G, T, H, or N.
Probe Intensities
- X Channel: Gzipped CSV file. 7,762 rows, 55 columns.
- Y Channel: Gzipped CSV file. 7,762 rows, 55 columns.

MegaMUGA

MegaMUGA Reference Quality Control Process

Marker positions

File	GRCm38	GRCm39	Description
Marker positions	mm_uwisc_v1.csv	mm_uwisc_v2.csv	CSV file. 77,808 rows. Contains cM values.
Marker file metadata	mm_uwisc_dict_v1.csv	mm_uwisc_dict_v2.csv	Column descriptions for marker file.

CC/DO Founders

File	Link	Description
Founder metadata	MegaMUGA_founder_metadata.csv	CSV file. 175 rows, 5 columns.
Consensus genotypes	MegaMUGA_founder_consensus_genotypes.csv.gz	Gzipped CSV file. 75,053 rows, 9 columns. Genotypes encoded as one letter: A, C, G, T, H, or N.
X channel intensities	MegaMUGA_founder_mean_x_intensities.csv.gz	Gzipped CSV file. 75,053 rows, 9 columns.
Y channel intensities	MegaMUGA_founder_mean_y_intensities.csv.gz	Gzipped CSV file. 75,053 rows, 9 columns.

All Reference Samples

File	Link	Description
Sample metadata	MegaMUGA_sample_metadata.csv	CSV file. 364 rows, 4 columns
Sample genotypes	MegaMUGA_genotypes.csv.gz	Gzipped CSV file. 75,058 rows, 354 columns. Genotypes encoded as one letter: A, C, G, T, H, or N.
X channel intensities	MegaMUGA_x_intensities.csv.gz	Gzipped CSV file. 75,058 rows, 354 columns.
Y channel intensities	MegaMUGA_y_intensities.csv.gz	Gzipped CSV file. 75,058 rows, 354 columns.

GigaMUGA

GigaMUGA Reference Quality Control Process

Marker positions

File	GRCm38	GRCm39	Description
Marker positions	gm_uwisc_v1.csv	gm_uwisc_v4.csv	CSV file. 143,259 rows. Contains cM values.
Marker file metadata	gm_uwisc_dict_v1.csv	gm_uwisc_dict_v4.csv	Column descriptions for marker file.

CC/DO Founders

File	Link	Description
Founder metadata	GigaMUGA_founder_metadata.csv	CSV file. 170 rows, 5 columns.
Consensus genotypes	GigaMUGA_founder_consensus_genotypes.csv.gz	Gzipped CSV file. 123,915 rows, 9 columns. Genotypes encoded as one letter: A, C, G, T, H, or N.
Chr Y Haplogroups	GigaMUGA_founder_consensus_genotypes_Y.csv	CSV file. 13 rows, 7 columns. Genotypes encoded as one letter: A, C, G, T.
Chr M Haplogroups	GigaMUGA_founder_consensus_genotypes_Mt.csv	CSV file. 20 rows, 6 columns. Genotypes encoded as one letter: A, C, G, T.
X channel intensities	GigaMUGA_founder_mean_x_intensities.csv.gz	Gzipped CSV file. 123,915 rows, 9 columns.
Y channel intensities	GigaMUGA_founder_mean_y_intensities.csv.gz	Gzipped CSV file. 123,915 rows, 9 columns.

All Reference Samples

File	Link	Description
Sample metadata	GigaMUGA_sample_metadata.csv	CSV file. 279 rows, 4 columns.
Sample genotypes	GigaMUGA_genotypes.csv.gz	Gzipped CSV file. 123,998 rows, 280 columns. Genotypes encoded as one letter: A, C, G, T, H, or N.
X channel intensities	GigaMUGA_x_intensities.csv.gz	Gzipped CSV file. 123,998 rows, 280 columns.
Y channel intensities	GigaMUGA_y_intensities.csv.gz	Gzipped CSV file. 123,998 rows, 280 columns.

R/qtl2 Support Files

File	GRCm38	GRCm39	Description
CC/DO variants	cc_variants.sqlite	cc_variants_grcm39_ens104.sqlite	SQLite database of CC/DO founder SNPs & Indels.
Genes	mouse_genes_mgi.sqlite	mouse_genes_ensembl104.sqlite	SQLite database of mouse genes.

Founder Denovo Genome Assemblies

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	EBI page	FASTA file	Gzipped FASTA file.
129S1/SvImJ	EBI page	FASTA file	Gzipped FASTA file.
NOD/ShiLtJ	EBI page	FASTA file	Gzipped FASTA file.
NZO/HlLtJ	EBI page	FASTA file (This file is not yet listed on the EBI website)	Gzipped FASTA file.
CAST/EiJ	EBI page	FASTA file	Gzipped FASTA file.
PWK/PhJ	EBI page	FASTA file	Gzipped FASTA file.
WSB/EiJ	EBI page	FASTA file	Gzipped FASTA file.

Genomic Variants

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	mgp.v5.merged.snps_all.dbSNP142.vcf.gz	mgp_REL2021_snps.vcf.gz	Gzipped VCF file.
SNPs Index	mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi	mgp_REL2021_snps.vcf.gz.csi	Tabix index. .tbi or .csi file.
Indels	mgp.v5.merged.indels.dbSNP142.normed.vcf.gz	mgp_REL2021_indels.vcf.gz	Gzipped VCF file.
Indels Index	mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi	mgp_REL2021_indels.vcf.gz.csi	Tabix index. .tbi or .csi file.
Deletions	REL-1606-SV/mgpv5.SV_deletions.bed.gz	Not available	Gzipped BED file.
Deletions Index	mgpv5.SV_deletions.bed.gz.tbi	Not available	Tabix index for BED file. *.tbi file.
Insertions	mgpv5.SV_insertions.bed.gz	Not available	Gzipped BED file.
Insertions Index	mgpv5.SV_insertions.bed.gz.tbi	Not available	Tabix index for BED file. *.tbi file.

These data are associated with Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements, Cell Genomics, 2023. Please cite this publication if you use this data.

File	GRCm38	GRCm39 (Ensembl 104)	Description
Structural Variants	Not available	merged_SV_VCF.zip	Gzipped VCF file.

Founder Pseudogenomes

These are FASTA files with SNPs and Indels from the Sanger variant files inserted into each genome. GRCm38.

Strain	File	Description
A/J	A_J.with_unplac_unloc.fa.gz	Gzipped FASTA file.
C57BL/6J	Mus_musculus.GRCm38.dna.primary_assembly.fa.gz	Gzipped FASTA file. Ensembl 102 reference.
129S1/SvImJ	129S1_SvImJ.with_unplac_unloc.fa.gz	Gzipped FASTA file.
NOD/ShiLtJ	NOD_ShiLtJ.with_unplac_unloc.fa.gz	Gzipped FASTA file.
NZO/HlLtJ	NZO_HlLtJ.with_unplac_unloc.fa.gz	Gzipped FASTA file.
CAST/EiJ	CAST_EiJ.with_unplac_unloc.fa.gz	Gzipped FASTA file.
PWK/PhJ	PWK_PhJ.with_unplac_unloc.fa.gz	Gzipped FASTA file.
WSB/EiJ	WSB_EiJ.with_unplac_unloc.fa.gz	Gzipped FASTA file.

Collaborative Cross Reference Data

We provide consensus genotypes and a qtl2-style allele probs object for use in genetic mapping. We also provide Chr M and Y genotype and founder funnel codes.

Collaborative Cross Analysis Pipeline

Data compiled from:
Srivastava et al. Genetics, 2017
Shorter et al. G3, 2019

File	Link	Description
Consensus Genotypes	CC_consensus_genotypes.csv	CSV file.133,948 rows, 77 columns. ACGT genotypes for 76 CC strains.
Founder Allele Probabilities	CC_diplotype_probs.rds	R binary file (*.rds). “allele probs” object in qtl2 format. 76 strains, 8 founders, 120,625 markers.
Chr M & Y Genotypes and Funnel Codes	cc_sample_metadata.csv	CSV file. 76 rows, 5 columns.