Pe sample preparation kit

Whole-genome sequencing and data analysis were performed as previously described (Jankovic et al., 2013 (link)). In brief, 5µg of genomic DNA were sonicated to an average fragment size of 500bps and processed according to the Paired-End (PE) Sample Preparation kit protocol (Illumina). Upon quality assessment by Bioanalyzer (Agilent), the library was subjected to paired-end sequencing. Data were analyzed for structural variation (SV) discovery using the following programs: Hydra-SV (Quinlan et al., 2010 (link)), BWA aligner (Li and Durbin, 2009 (link)), Novoalign, the intersectBed software from BEDtools suite (Quinlan and Hall, 2010 (link)), RepeatMasker and RefSeq track from the UCSC Genome Browser. In order to clear artifacts resulting from genetic variation, we subtracted SVs that were similarly found in the genomes of C57BL/6 and 129/Sv mice (Jankovic et al., 2013 (link)), or of 17 other inbred strains of laboratory mice (Keane et al., 2011 (link)). Further, SVs were removed from final analysis if any of the two reads matched to repeats for >50%, if deletions were <1kb, or if their Final Weighted Support value was <2. Circular plots of genomic rearrangements were generated using Circos software (Krzywinski et al., 2009 (link)).