Data in this release contains genotype data for 946 CFW mice for the GWAS for age-related hearing loss. The project is ongoing, and we plan to release the next version when more animals are tested and genotyped. 

Description of contents:
Variant Call Format
--genotypes_vcf.zip
--contents: chr*_bgl_flt.vcf.gz for chr01-chr19

–-Variant Call Format (VCF): specifies the format of a text file for storing gene sequence variations. A header begins the file and provides metadata describing the body of the file. The body is tab separated into 8 mandatory columns and an unlimited number of optional columns for other information on the samples.


Technical details:
--Rat Genome assembly: mRatBN7.2 (NCBI: GCF_015227675.2) 

All software used to generate the data in this object are noted below:

--fgbio
--cutadapt 
--fastqc
--BWA-MEM
--samtools
--picard MarkDuplicates
--bcftools
--STITCH
--stats

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.