What Is Allele Frequency

Provides a quick introduction of allele frequency, which the number of alleles of a certain type, divided by the total number of alleles of all allele types in a population.

When we discuss human gene mutations, sometimes we are borrowing terminologies from general genetic studies. Here is the first example.

What Is Allele Frequency? - The allele frequency is the ratio of allele count of a certain type over allele count of all types in a population. Remember that an allele type refers to a variant form of a gene that are located at the same position, or genetic locus, on a chromosome. So higher allele frequency means more individuals carry this type of variant.

To get a better understanding of allele frequency, let's take a look at a simple case, where there are only 2 allele types "A" and "a" in a diploid population of 10 individuals. Each individual has 2 alleles combined in a chromosome. So we have a total of 20 alleles of both allele types in 10 combinations in the population:

```AA, aA, AA, aa, Aa, aA, aa, aa, aA, aa

With:
Number of "A":  7
Number of "a": 13
Total alleles: 20
```

To calculate allele frequencies of "A" and "a", we can count them and get their total numbers, then divid them by the grand total:

```Allele Frequency of "A":  7/20 = 35%
Allele Frequency of "a": 13/20 = 65%
```

Counting the number of alleles is not an easy job. It requires us to perform gene test on each individual to figure out the allele types in the chromosome.

But there is another way to calculate allele frequencies, if allele types "A" and "a" is a pair of dominant and recessive genotypes.

For example, assuming "a" is a recessive genotype in rabbit population. Only a rabbit with "aa" combination will be white. A rabbit with any other combinations, "Aa", "aA", or "AA", will be black. Obviously, "A" is a dominant genotype in this case.

Now we use the percentage of rabbits in each color to figure out allele frequencies using the Hardy-Weinberg (HW) equation:

```1 = p2 + 2pq + q2
1 = p + q

Where:
p is the allele frequency of "A"
q is the allele frequency of "a"
p2 is the percentage of "AA" sub-set
q2 is the percentage of "aa" sub-set
2pq is the percentage of "Aa" and "aA" sub-sets
```

If we look at our rabbit population again, we can associate rabbit color with each allele combination:

```AA,    aA,    AA,    aa,    Aa,    aA,    aa,    aa,    aA,    aa
Black, Black, Black, White, Black, Black, White, White, Black, White

With:
Number of Blacks:  6
Number of Whites:  4
Total rabbits:    10
```

Now we can figure out allele frequency of "a", q, from the percentage of White rabbits, q2:

```Percentage of White rabbits: q2 = 4/10 = 40%
Allele frequency of "a": q = sqrt(40%) = 63.25%
```

Then we can figure out allele frequency of "A", p, from the "1 = p + q" relation:

```Allele frequency of "A": p = 1 - 63.25% = 36.75%
```

As you can see, calculating allele frequencies can be simplified, if there are only 2 allele types forming a pair of dominant and recessive genotypes in a diploid population.