Genotypes for CFW mice for GWAS for age-related hearing loss (Version 1). In Genotype data from Crl:CFW(SW)-US_P08 stock of outbred mice

DNA was extracted from mouse spleen tissue using DNAdvance kit (Beckman Coulter). Multiplexed sequencing libraries were prepared using the Twist 96-Plex Library Prep kit (TWIST Bioscience), and then sequenced on a NovaSeq 6000 or NovaSeq X (Illumina). An average of ∼3.2 million reads per sample were obtained (paired end, 150 bp). The reads were aligned to the mouse reference genome GRCm38 (GCA_000001635.2). To generate genotypes at SNPs we used STITCH software (Davies et al. 2016) without reference panel, with the “niterations” parameter set to 40 and a position file as described below, to create a reference panel; then we ran STITCH again with the “niterations” parameter set to 1, using with the above result as a reference panel, filtered resulted genotypes by INFO score > 0.9, and then performed imputation using BEAGLE (Browning and Browning, 2016) . To construct the position file we used low-coverage sequencing data from earlier generations of CFW mice (Zou et al. 2022; Davis et al, 2016). The SNPs on X, Y, and MT chromosomes were not called. After genotypes were called with STITCH, the following SNPs were removed: (1) monomorphic SNPs, (2) SNPs that violate Hardy-Weinberg equilibrium with -log10(p) > 7, and (3) SNPs that have genotype missingness rate > 0.1 based on the results generated by STITCH.