Table 1 Probe types on GigaMUGA
Probe TypeNumberDescription
Haplotype discrimination54,250SNPs selected for maximal information content with respect to CC/DO founders; called by Sanger Mouse Genomes Project or lifted over from Mouse Diversity Array (MDA) (Yang et al. 2009)
Recombination hotspot46,020Same as above, but selected to flank a catalog of 25,000 recombination hotspots from Baker et al. (2015)
Wild alleles20,237SNPs predicted to be segregating in wild mice, from MDA and whole-genome sequencing of wild mice
Other existing13,036Other SNP probes carried over from MDA
ICR novel3693SNPs segregating within or between selection lines derived from the ICR:Hsd outbred stock, ascertained from whole-genome sequencing
CNV/SD2006Non-SNP probes targeted at segmentally duplicated regions, intended for exploring CNV
Sister strains1744SNPs segregating between closely related inbred strains
Target locus201Probes targeting specific endogenous loci (Xce, Vkorc1, R2d2, genes in the complement cascade); most are not designed as SNP probes
Transgene129Presence-absence probes for detection of exogenous engineered constructs