So, for a project I\'ve been working on (different story), I\'ve been looking at

Question

So, for a project I've been working on (different story), I've been looking at the HapMap Project, and their free online files. In their README file, they talk about how for each legend file for each chromosome/region, there is an rs id, an alelle coded 0, 1, and a base pair position.

Now it's fairly obvious after staring at this for a while that base pair position means where each nucleotide is located along the genetic sequence... is this correct?

And what do rs id, and the other words mean? Any help would be greatly appreciated!

Explanation / Answer

It's basically a unique identifier.

rs position 0 1
rs11089130 14431347 C G
rs738829 14432618 A G
rs915674 14433624 A G

The allele codes are the 3rd and 4th columns. An SNP is site where a different base is found in different versions of the same gene (different versions of genes are alleles). For a given SNP the different alleles are referred to as the 0 or the 1 allele. So in the table the first SNP, rs11089130, has two alleles: allele 0 has a C at the SNP position (14431347) whereas allele 1 has a G at that position. The allele code does not imply any biological significance.

I'm not sure what would happen if there were three alleles at an SNP, but presumably there would then also be an SNP coded as 2.

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