The mechanisms of structural mutation are generally inferred from sequence information at junction/breakpoint of the rearrangements. Four major mechanisms can account for the majority of SVs: non allelic homologous recombination (NAHR), non homologous end joining (NHEJ), fork stalling and template switching (FoSTeS), and L1-mediated retrotransposition (Zhang et al., 2009b)(Figure 2).
