SNP and Indels
Single Nucleotide Polymorphisms (SNPs) and DNA insertions and deletions (indels), were identified using Genome Analysis Tool Kit 4 (GATK4) (4.3.0.0). Sequences were aligned with grcm38 (https://www.gencodegenes.org/mouse/release_M14.html) with BWA-2 (0.7.17-r1188). Duplicates were marked by using GATK4 MarkDuplicatesSpark. Samtools (1.16.1) was used for sorting the mitochondrial genome. Picard, R (4.2.0) and Samtools were used for Collect Alignment & Insert Size Metrics. GATK4 was used for Variants calling, Extract SNPs & Indels, Filter SNPs and Indels, and Base Quality Score Recalibration (BQSR). Further vcf files were aligned and marked for SNP and Indels using the integrative genome viewer (IGV) software (2.16.0).