Deletion

Deletion of a DNA segment can happen if it is bordered by direct repeats. These repeats can be introduced by insertion of same transposons in identical orientation. DNA will fold back in a closed loop structure with direct repeats positioned in a way two homologous chromosomes aligned in metaphase. This structure of DNA allows recombination to happen between two repeats resulting in a deletion of one repeat region and genes within the direct repeats.

Image taken from[1]