Short answer
An allele is a sequence alternative at a genetic location. A genotype records which allele or alleles an individual has at a location, or more broadly across specified locations. At a simple autosomal locus, A is an allele; AA, Aa and aa are possible genotype notations. 1 2
Alleles are the versions being recorded; a genotype says which version or versions are present in the specified scope.
On this page
At a glance
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| Question | Allele | Genotype |
|---|---|---|
| Basic role | A variant option | An observed variant configuration |
| Single-locus example | A or a | AA, Aa or aa |
| Applies to | Sequence at a locus | Individual or sample and stated loci |
The table summarizes the cited definitions and the article’s stated scope. 1 2
What each thing is
Allele. One version of a sequence at a genomic location, often a gene. 1
Genotype. The variant or combination of variants an individual has at one or more specified loci. 2
Key differences
The words describe different levels. Two people may both have allele A, yet one may have genotype AA and the other Aa at that locus. A genotype requires a subject and an indicated region; an allele can be described as a version present in a population. 1 2
How to tell them apart
If you are naming a particular version, use allele. If you are recording what a person or sample carries, use genotype and say at which locus. The familiar two-letter notation is useful for a simple diploid locus but is not the format of every genetic result. 1 2
Where they overlap
Both describe DNA variation and depend on a defined genomic location. An allele contributes to a genotype; a genotype can contain multiple allele assignments. 1 2
Edge cases
Sex chromosomes, copy-number variation and microbial or viral genomes do not always fit a two-copy example. “Genotype” can also mean a much broader set of variants, so its scope must be specified. 1 2
Why the distinction exists
Separating a sequence alternative from an individual’s combination helps researchers discuss population variation and individual inheritance without mixing them. 1 2
Common misconceptions
A genotype is not simply another name for one allele. Nor does a two-letter classroom genotype exhaust the way real genomes vary. 1 2
Examples
At a simplified locus, A and a are alleles. A person whose two copies are A and a has genotype Aa there; their physical trait is a phenotype, another distinction. 1 2
Sources
Sources checked October 3, 2026.
- National Human Genome Research Institute — Allele. Definition and narration.
- National Human Genome Research Institute — Genotype. Definition.