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Minor allele frequency calculation

Hi everyone

I need to understand Minor allele frequency

A SNP with a allele (G) frequency of 0.40 implies that 40% of a population has G allele versus the most common allele (major allele), which is found in 60% of the population.

If a SNP allele frequency is 0.05 how will be calculate its percentage in the population

Please explain with calculation

Regards

snp next-gen
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updated by Ram Ram • written by Tark • Tark

The statement "which is found in 60% of the population" is incorrect, and should be corrected. It would be more correct to say "makes up 60% of the alleles in the population"

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written by stenemo88 • stenemo88

4 answers

If a SNP allele frequency is 0.05 in a population of 100 people:

Total number of alleles for each SNP: 100 * 2 = 200 (each individual has two alleles)

Total number of alleles for your SNP with a MAF of 0.05: 200 * 0.05 = 10

The minor allele is present ten times in your population. However, you don't know how many heterozygote and homozygote.

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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

What could be the solution if you want to know frequencies for homozygote and heterozygote ? Any databses that provide those infos ? Thanks !

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written by Amy • Amy

An explanation on MAF is given on ncbi: http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html#gmaf

Which states: "...In other words, if there are 3 alleles, with frequencies of 0.50, 0.49, and 0.01, the MAF will be reported as 0.49"

An example given: ""MAF/MinorAlleleCount:G=0.249/542". This means that for rs222, minor allele is 'G' and has a frequency of 24.9% in the 1000Genome phase 1 population and that 'G' is observed 542 times in the sample population of 1088 people (or 2176 chromosomes)."

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updated by Ram Ram • written by Danielson • Danielson 
=(2*Ref_allele)/(2*(Ref_allele + alternate_allele))
e.g. Population size 108, reference allele “A” = 70 and Alternate_allele “G”=38
=(2*70)/(2*(70+38)
=0.648 
=1-0.648=0.352 MAF of alternate_allele
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updated by Kevin Blighe Kevin Blighe • written by gpatil • gpatil

Hardy-Weinberg Equilibrium can be used for allele frequency calculation: https://www.k-state.edu/parasitology/biology198/answers1.html

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written by pltbiotech_tkarthi pltbiotech_tkarthi

OP was not asking for a tool to calculate AF but for an explanation. Your recent posting history is suspicious as it often has nothing to do with the toplevel question. Could you comment on that?

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written by ATpoint ATpoint

Yes, the toplevel question is concerning the tool for allele frequency, we can use the following tools for allele frequency based on HW equilibrium, isn't it? http://www.oege.org/software/hwe-mr-calc.shtml http://scienceprimer.com/hardy-weinberg-equilibrium-calculator https://wpcalc.com/en/equilibrium-hardy-weinberg/ here is the reference paper, which use HW equilibrium for AF https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570414/pdf/pone.0056472.pdf

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written by pltbiotech_tkarthi pltbiotech_tkarthi

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