Segmental duplication

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Segmental duplication is a kind of mutation that causes redundancy in genomes. It is caused by an error in chromosomal splicing during genetic recombination: two chromosomes are cut in different locations, and the pieces are reattached in a way such that the stretch of DNA between the two locations is included twice. As a result, an organism's chromosome will contain two nearly-identical copies of the sequence, one from each parent, in immediate succession.

Detecting segmental duplications is in general a hard problem, posing challenges to WGA. Many assemblies, including the low-coverage kangaroo rat assembly, have had problems with it.

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