Diversity Outbred Genotype Data

Diversity Outbred Genotype Data

Description 

Diversity Outbred mice have been genotyped on the Mouse Universal Genotyping Array (MUGA) and the MegaMUGA. The MUGA contains 7,854 markers with a mean spacing of 329 kB. The MegaMUGA contains 77,808 markers with a mean spacing of 33 Kb.

Data

Raw Genotype Data

These directories contain the raw files produced by GeneSeek (Lincoln, NE).

MUGA files

MegaMUGA files

Array Intensities and Genotypes

The directories below contain the X and Y intensities and allele calls for the MUGA and MegaMUGA.

MUGA

MegaMUGA

Reconstructed Genotypes

Each file is a binary Rdata file that contains a matrix of genotype probabilities produced by the hidden Markov model in DOQTL. Dimensions are number of markers (rows) by 36 genotypes (columns).

MUGA genome reconstructions

Allele call based reconstructions

Intensity based reconstructions

 

MegaMUGA genome reconstructions

Allele call based reconstructions

Intensity based reconstructions

Publications 

Gatti DM, Svenson KL, Shabalin A, Wu LY, Valdar W, Simecek P, Goodwin N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW and Churchill GA
G3. 2014;4(9):1623-33
Logan RW, Robledo RF, Recla JM, Philip VM, Bubier JA, Jay JJ, Harwood C, Wilcox T, Gatti DM, Bult CJ, Churchill GA, Chesler EJ
Genes Brain Behav. 2013 Feb 21. doi: 10.1111/gbb.12029