Intermediate-sized structural variation between mouse strains due to endogenous retrotransposition. (A) Distribution of lengths of all variants identified here (ranging from 100 nt to 10 kb), predicted from WGS trace alignments. Each polymorphic integrant is present in the C57 reference genome and absent from at least one of the unassembled strain(s). (Legend) The percentages indicate the relative composition of each variant, identified by RepeatMasker as repetitive element sequences. (B) Classes of repeats in variants. Polymorphisms present in C57, containing >70% RepeatMasker content and ranging in length from 100 nt to 10 kb include: Alu, 5.4% of the total number of such variants; B2 SINEs, 19.2%; ERV1, 1.8%; ERV-K, 16.4%; ERV-L, 3.5%; L1, 38.8%; MaLR, 4.0%; simple repeats, 8.8%; and other, 2.0%. L1 retrotransposition is the most numerous cause of intermediate length variation between the strains.
