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Indels are insertions or deletions in a reference genome for an organism or cell that result in a net change in the number of nucleotides in the genome. They are relevant to many genetic mutations. One characteristic of present whole genome sequencing techniques is that they are relatively insensitive to indels. The term when used in evolutionary genetics may refer to more than one event separated in distance in the genome, but in molecular genetics refers to a single event localised to one portion of the genome. This confusion arises as in evolutionary genetics the events that lead to the difference might have been either an insertion or deletion as no reference genome is available. Microindels affect less than 50 nucleotides.

Humans usually have less than 300 frameshift indels, usually in non coding regions of the genome. In coding regions of the genome indels are usually multiples of 3 so are non-frameshift but are quite rare compared to base substitutions, perhaps being 10% of mutations.

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