what is 0 in the plink .bim file under allele1/2 column?

Question

[miaowzai]

Hello,

I have a bfile data that contains zero "0" in the allele column in .bim file. Both allele columns contain SNPs recorded as "0". I didn't find corresponding descriptions on plink website. Does it mean unknown allele? Why is there such thing?

example:

1 rs123 0 242345 0 A

1 rs234 0 24532 0 0

Thanks!

Answer 1

[chrchang523]

In a .ped + .map fileset, it's possible for a variant to have only one distinct allele (everyone's A A or 0 0), or even zero (everyone's 0 0). If a .bim file is generated from this type of data, it'll have 0 in place of each unknown allele code.

[miaowzai]

May I ask why this happens? Thanks!

[chrchang523]

Consider the simplest case, where you have just one sample. Whenever the sample has a homozygous call, you'll only see one allele code. Whenever it has a missing call, you won't see any allele codes.