Fig. 1

The amylase cluster genome region and structural variation. a Genomic organization and dotplot of the amylase gene cluster region in the mm10 reference genome (600 kb, representing positions chr3:113,050,000–113,650,000). The dot plot shows the internal repeats (boxed) and the annotation gap (visible as blank area). The gene annotations on the top are taken from the UCSC browser. It shows the sense strand, but the genes are encoded on the antisense strand. b Snapshots of the Bionano mapping results from the same genome region. The green bars represent the mm10 reference sequence, the blue bars the test genomes (C57Bl6, Fvb and PWK from top to bottom). cAmy2a copy number ranges in the individuals of different wild populations, based on sequencing read coverage data in the region including the Amy2a repeats of the reference genome mm10 (150 kb, dotted square in (a)). Note that reads from the Amy2b region would also map to this, but since this is a single copy locus, it would not contribute to the variance caused by copy number changes