WGS of Peromyscus maniculatus: liver tissue sample
DNA was extracted from ear punch tissue samples using Gentra Puregene Tissue Kits. The purity of extracted DNA was assessed by measuring 260/280 absorbance ratios with a NanoDrop Spectrophotometer and sample concentrations were measured using the Qubit dsDNA HS Assay. Prior to library preparation, the presence of high-molecular weight DNA was confirmed using agarose gel electrophoresis. Library preparation and sequencing were conducted by the University of Wisconsin-Madison Biotechnology Center. Sequencing libraries were constructed with the Illumina DNA Library Prep using 100-500 ng of input DNA per sample. Purified and pooled libraries were sequenced on the Illumina NovaSeq X Plus platform to generate paired-end 150 bp reads. Samples were sequenced to a targeted coverage of 30X per individual. As a quality control measure, four mice were re-sequenced: one male each from Saturna (FSB85), Pender (FSB114), and Maple Ridge (FSB42) as well as a single female from Maple Ridge (FSB6). These technical replicates were sequenced using unique libraries, allowing us to capture the effects of sequencing/genotyping error introduced at all laboratory and bioinformatic steps downstream of PCR-based library preparation. Reads generated for these four technical replicates have FASTQ filenames with "DUPLICATE" appended to the sample name. Each mouse was sequenced across multiple lanes, ranging from 17-18 lanes per individual. Distinct sequencing lanes are denoted in FASTQ filenames by the L00* identifier.