Understanding how and why genetic diversity varies between species and across the genome are questions at the heart of population genetics. Studies in multiple eukaryotic species have shown that nucleotide diversity is reduced close to conserved, functional elements. This variation in nucleotide diversity is consistent with models of Hill-Robertson Interference, suggesting that natural selection has played a role in generating the observed patterns. It has, however, proven difficult to distinguish between two mechanisms that can lead to variation in the amount of nucleotide diversity: background selection due to selection against deleterious mutations and recurrent selective sweeps of advantageous variants. Using whole genomes of Mus musculus castaneus individuals sampled from the species’ ancestral range we estimate the strength of selection acting on protein coding genes and conserved non-coding elements and construct a fine-scale recombination map. Using these we hope to tease apart the contribution of positive and negative selection to the patterns of nucleotide diversity across the genome.