No T base in the Illumina report file

Question

[nehal1610.ranabhatt]

I just extracted the report of the Illumina SNP array genotyping using Illumina genome studio. To be specific, I extracted genotypes of the top strand for each locus. Interestingly, none of the loci displayed Thymine (T) as one of the alleles in a genotype. How can it be possible? Is it because the Illumina defined "Bottom" and "Top" in a certain way where "T" always gets the "bottom" strand designation?

Answer 1

[Istvan Albert]

Illumina uses a custom SNP designation.

Check the post:

Illumina'S Genome Studio Final Report: Forward Or Top Allele?

and the corresponding document here:

https://www.illumina.com/documents/products/technotes/technote_topbot.pdf

and the blog post:

http://onetipperday.sterding.com/2015/12/snp-allele-coding-schema.html