alleles calculation and snp genotype nomenclature

Question

[melodyalaziz]

Hi

Please I want to know how to determine major and minor alleles and how to calculate them

The second thing I want to know the snp nomenclature how its ordering can be i.e rs2243248 which is first to write TG or GT genotype ..

i will be appreciated to help me the right way to write the genotype ordering letters ..

Many thanks

Meelad

Answer 1

[Alexander Skates]

Major/Minor alleles are determined by the allelic frequency. If you wanted to calculate them yourself, you would need population genotype data; you could download the genotypes from the 1000 Genomes or HapMap and calculate the frequency of each allele for a given SNP. Whichever occurred more often would be the major allele.

The order will be determined by the allele that was on the RefSeq strand (i.e. the strand that was sequenced for the reference genome).

This is all information that is easily available -- in the future make Google your first port of call!

[melodyalaziz]

thank you very much dear, but google is not the port of choice sometimes .