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!
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.