Minor allele frequency calculation
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Entering edit mode
9.6 years ago
Tark ▴ 50

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

Regards

SNP next-gen • 69k views
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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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Entering edit mode
9.6 years ago

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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Thank you for the clear explanation.

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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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Entering edit mode
9.3 years ago
Danielson ▴ 40

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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Entering edit mode
6.7 years ago
gpatil ▴ 10
=(2*Ref_allele)/(2*(Ref_allele + alternate_allele))
e.g. Population size 108, reference allele āAā = 70 and Alternate_allele āGā=38
=(2*70)/(2*(70+38)
=0.648
=1-0.648=0.352 MAF of alternate_allele