Mouse Diversity Genotyping Array - Annotation files

We have extensively annotated the array to help users interpret results, integrate array data with other genomic resources, and develop new uses for the array. Annotation and information regarding probe performance is provided below.


1. Re-annotation - Didion et al. 2012

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, Pardo-Manuel de Villena F, Churchill GA
BMC Genomics. 2012 Jan 19;13(1):34. PMCID: PMC3305361 [ Full Text ] [ software ] [ datasets 1 ] [ datasets 2 ]

Description of annotation files README (.txt) (includes minor correction to description of column 25 on 01/21/13)

Annotation of C57BL/6J - Probe Annotation files (.txt):


Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4

Chromosome 5
Chromosome 6
Chromosome 7
Chromosome 8

Chromosome 9
Chromosome 10
Chromosome 11
Chromosome 12

Chromosome 13
Chromosome 14
Chromosome 15
Chromosome 16

Chromosome 17 Chromosome 18
Chromosome 19
Chromosome X

Chromosome Y Mitochondria

Annotation of the Sanger strains - Probe Annotation files (.zip 60 MB):


129S1
A_J
AKR
BALB

C3H
C57BL
CAST
CBA

DBA
LP_J
NOD
NZO

PWK
WSB


 

2. Original Annotation - Yang et al. 2009

A customized and versatile high-density genotyping array for the mouse
Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, de Villena FP, Churchill GA.
Nat Methods. 2009 Sep;6(9):663-6. PMCID: PMC2735580. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Probe Annotation files (Version 2.0 Mouse Build 37):

SNP annotation file (.gz 155 MB)
IGP annotation file (.gz 113 MB)