I have searched through various websites, however, I am still rather confused with the difference between 'genotype' and 'alleles' since each site seems to be contradicting another site.

I would be much grateful if someone could please give me a concise and clear differentiation between 'genotype' and 'alleles'.

  • 1
    $\begingroup$ This question is duplicated a lot on this page (e.g. this), but since this is a re-occuring issue and I didn't find a reasonable AND concise answer on this site (or at least concise enough for my taste :P), I'm just gonna answer it here. $\endgroup$
    – markur
    Commented Sep 27, 2022 at 12:50

3 Answers 3


Please note that opinions on the exact wording of the following can differ a lot. You will have to find one for yourself that works best for you.

Gene = An element within the DNA/Genome with function(s)

Allele = A subtype of a gene with (or without) altered function(s) (due to function-changing mutation(s))

  • Every individual has two homologous versions (not exact copies) of every gene. 1 version on each chromosome (don't confuse with sister chromatids). This allows two versions (alleles) of the same gene to be present at the same time.
  • 1 allele is from mama, 1 allele is from papa. Both alleles often have a similar known functions, although they're rarely exact copies (unless your parents are siblings).
  • If two alleles have the same function, they may or may not be summarized as the same allele, depending on the aim of the study or how well the function of each mutation is characterized. Most textbook examples work with alleles with very defined functions ("wildtype vs. white").
  • A whole population of individuals has the same exact numbers of genes as a single individual (A human has just as many genes as the species humans). But the population has a multitude of alleles for each gene, while a single individual can have max two alleles per gene.

Genotype = A summary of genes and/or alleles per gene of an individual.

  • "Small differences among alleles of the same gene contribute to each person’s unique characteristics." (from thoughtco)

Phenotype = The observable functions/properties of an individual that are determined by its genotype


An allele is a variant of a gene, while a genotype is an (arbitrarily) specified combination of alleles, mostly stating the homo- or heterocygous presence or absence of certain mutation(s) in a certain gene or combination of genes. E.g. Genotype A: Gene A (wild-type allele | mutant allele), gene B (wild-type allele | wild-type allele).


According to a format guide, https://samtools.github.io/hts-specs/VCFv4.1.pdf:

Allele is representing single genetic haplotypes

Genotype is an assignment of alleles for each chromosome of a single named sample at a particular locus.

(A haplotype is a group of genes within an organism that was inherited together from a single parent. The word "haplotype" is derived from the word "haploid," which describes cells with only one set of chromosomes, and from the word "genotype," which refers to the genetic makeup of an organism. A haplotype can describe a pair of genes inherited together from one parent on one chromosome, or it can describe all of the genes on a chromosome that were inherited together from a single parent. This group of genes was inherited together because of genetic linkage)

(For human genome, a haplotype is defined as the combination of alleles for different polymorphisms that occur on the same chromosome, and for any given stretch of chromosomal DNA an individual will have two haplotypes, although at a population level there may be numerous haplotypes for any given stretch of chromosomal DNA.)


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