I have a plink format data (bim/bed/fam) from data provider. As far as I know, the sequencing was done by Illumina exome SNP beadchip. I didn't call the genotypes.
There are some variant IDs startwith "exm". They do have rs numbers when I look'em up. What are these SNPs? Why use "exm"?
Also, I found some duplicated monomorphic positions, like:
1 exm1771279 2435759 0 G
1 exm2277033 2435759 0 C
I checked the genotypes for both calls and the file says all people have GG for exm1771279 and all people have CC for exm2277033. However, they are at the same site. How is this possible?