Question: VEP result table, REF, ALT, CSQ meaning.
3.8 years ago by
dirranrak • 10
dirranrak • 10 wrote:
I got this result from VEP, I have some SNPs in the forward strand (1), reverse strand (-1) and no strand indication. I have these questions that I did not find the answers:
- Which of the REF or ALT allele is the minor or major allele?
- What is the CSQ?
- Why I have SNPs that have not been assigned to a strand and how can I fix it?
Chr Position ID REF ALT info Strand 1 864627 rs6681049 T A,C CSQ=A -1 9 138172039 rs9314655 G A CSQ=A 1 1 989518 rs6665000 C A CSQ=A
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