Indel

An indel is a genetic variant caused by the insertion or deletion of one or more nucleotides in the genome. Indels can range from a single base pair to larger segments and are a common form of genetic variation across species.

Indels are classified as insertions or deletions. In coding regions, the effect depends on the net change: in-frame indels (multiples of three nucleotides) add or remove amino acids without shifting the reading frame, while frameshift indels disrupt the downstream protein sequence. Indels outside coding regions can affect regulatory elements or RNA structure and influence gene expression. Larger indels may span exons or regulatory regions and are often treated as structural variants.

Detection relies on sequencing and alignment. Short-read data identify many small indels but can misalign near repetitive sequences; specialized callers and local assembly improve accuracy. Long-read sequencing and split-read approaches help identify larger indels. In variant data formats such as VCF, indels are described relative to a reference genome as insertions or deletions, with coordinates and changed sequence recorded.

Indels contribute to genetic diversity and to disease when they disrupt coding or regulatory regions. Examples include disease-causing deletions or insertions in specific genes, such as the cystic fibrosis ΔF508 three-base deletion. Indel polymorphisms are also used as genetic markers in population genetics and evolutionary studies.