Through whole-genome sequencing, we identified single nucleotide variants that distinguish aggressive BALB/cJ mice from control BALB/cByJ strains [82]. Sequencing libraries were prepared from high-quality genomic DNA using the TruSeq DNA PCR-Free kit (Illumina) and ultra-deep whole-genome sequencing (average 30X read-depth across the genome) was performed on a HiSeq X Ten System (Illumina). We developed an efficient data processing and quality control pipeline. Briefly, raw sequencing data underwent stringent quality control and was aligned to either the mm10 (BALB/cJ versus BALB/cByJ strain comparison). Isaac [83] was used to align reads and call single nucleotide variations (SNVs). We excluded SNVs that were covered by less than 20 reads, and that were not present in both animals from the same strain. SnpEff [84] was used to annotate SNVs and explore functional effects on gene function. SNVs differing between the two strains were annotated to a total of 1573 genes, which were subdivided into three different categories (intronic/exonic non-coding and synonymous variants (1422 genes), untranslated regions (90 genes), missense mutations and splicing variants (61 genes)).
