Whole-genome sequences of wild-derived European Mus strains capturing natural genetic diversity

Wild-derived mouse strains (WDS) preserve naturally occurring genetic variation that is largely absent from classical laboratory strains and therefore represent an important resource for evolutionary and biomedical research. We present whole-genome sequencing data for 30 European mouse samples representing two subspecies of Mus musculus and four closely related Mus species. The dataset comprises 13 strains of M. m. domesticus, 13 strains of M. m. musculus, and one strain each of M. spretus, M. spicilegus, M. macedonicus, and a wild specimen of M. cypriacus. Genomes were generated using paired-end Illumina sequencing, and raw sequence reads together with associated metadata have been deposited in public repositories. Principal component analysis confirms the expected taxonomic relationships among strains and demonstrates that the collection captures substantial natural genetic diversity across European house mice. By linking whole-genome sequences with living wild-derived strains maintained as experimental resources, this dataset complements existing phenotypic and genetic information and provides a foundation for studies of genotype–phenotype relationships, evolutionary genomics, hybridization, and biomedical genetics. This repository includes the joint call short variant VCF for these 30 samples. Illumina sequenced reads (pe150) from each sample were mapped to the mouse reference genome using bwa, folllowed by single sample variant calling with DeepVariant (--model_type WGS). Sample-level VCFs were then merged into a single joint call set using GLNexus. No quality, site, or sample-level filters have been applied to the VCF file in this data archive. Raw sequencing reads are available under SRA BioProject Accession PRJNA1476327.