Indel

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An indel is a location, in an alignment between two (or more) sequences, in which one sequence contains bases and the other does not.

The term "indel" is a contraction of insertion and deletion. Insertions (not to be confused with inserts) and deletions are two sides of the same coin. If the sequences are lined up in their alignment, the base(s) that exist on one sequence constitute an insertion, while the corresponding empty space on the other sequence constitutes a deletion. For example, the following alignment contains one insertion on both sequences:

   ||      |
GGATCATCCGG CAT
GGA  ATCCGGCCAT

In a correct alignment, the appearance of an indel may mean one of two things. The indel may be a result of a sequencing error: one of the reads was incorrectly transcribed with an extra or missing base. Alternatively, the indel may reflect polymorphism in the underlying genome. Polymorphism of this type is responsible for frameshift mutations.

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