An overview of the procedure to characterize structural variants. A flow diagram of the different steps we used to characterize structural variants. (a) We first inspected 100 Mbp of next generation sequencing (NGS) data in 17 genomes. We examined chromosome 19 in its entirety and a random set of other chromosomal regions. (b) We identified 21 PEM patterns across 1,494 SV sites. We show two examples of PEM patterns, H1 and H2, as visualized using the LookSeq tool . The H1 deletion is on chromosome 1 and has strain distribution pattern 11110101 (1 means presence and 0 absence of the deletion) in the following strain order: A/J, AKR/J, BALB/cJ, C3H/HeJ, C57BL/6J, CBA/J, DBA/2J and LP/J. The H2 deletion is on chromosome 8 and is present in seven strains. (c) We randomly selected 662 SV sites for PCR-validation to investigate all PEM patterns and show the results for the two deletion SVs. (d) We randomly selected 261 SV sites for analysis of breakpoint sequence features using Sanger-based sequencing technology. We show sequencing data of a simple deletion of type H1 on chromosome 10 (20,467,348-20,467,894). Sequence analysis confirmed the deletion of 547 bp but also revealed an insertion of 34 bp.