[i] Intrachromosomal (LSV) calls represent variants where the ends of the HYDRA call were ≤1 Mb apart from one another on the same chromosome. TEV calls represent the union of variable transposon insertions in the B6 and DBA genomes. Ambiguous TEVs are cases in which the exact transposon class is uncertain because a recent mobile element was annotated on both ends of the HYDRA call. Distant insertions are either interchromosomal insertions or insertions of “distant” DNA (i.e., >1 Mb away) from the same chromosome. Gene features were classified as potentially affected if the HYDRA call overlapped with the annotation by at least 1 bp. Overlap with SDs was called if either end of the HYDRA call or 50% of its genomic span overlapped with an SD annotation. Note that unlike Figure 2B, the numbers in this table represent the final number of nonredundant variants, not the number of HYDRA breakpoint calls.