Structural variants on chromosome 17. Copy number variants (CNVs) were called in the sequence using a hidden Markov model (HMM), using both depth information and density of heterozygous SNPs (for amplifications). Deletions were called using aberrantly mapping pairs of reads. (a) Density of CNVs and deletions across chromosome 17 of A/J. CNVs called by the HMM are shown in dark red/green on the left-hand axis. Deletions called from aberrantly mapping read pairs are shown in bright red on the right hand axis. (b) As (a) but for CAST/Ei chromosome 17. Cut-out shows an example of output from the HMM for a region with two amplifications and a loss.