Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains

Analyses were performed among strains classified into the following four categories: (1) all inbred strains analyzed, (2) all M. musculus strains, (3) all wild-derived M. m. domesticus strains, and (4) classical strains. The table shows the length of high-quality sequence, the number of variants per kilobase, and the SE of the rate. Variants were divided into insertions/deletions and substitutions. Discrimination between microsatellites and insertions/deletions was performed on the basis of the presence/absence of more than four adjacent tandem repeats of the inserted/deleted sequence, respectively. This threshold was determined empirically by comparing the frequency of mononucleotide runs of different sizes in the sequenced region and the frequency of insertions/deletions observed in runs of each size. For runs of less than five nucleotides, the probability of observing insertions/deletions is roughly equal to their frequency. For runs of five or more nucleotides, the probability of an insertion/deletion is 10 to a 100 times greater than expected.