From 1000 genomes vcf:
1 191160243 rs68092106 TC T 100 PASS AC=1393;AF=0.278155
1 191160244 rs10801031 C T 100 PASS AC=1022;AF=0.204073
Seems a little suspicious that these have the same freq. Are these two rows reporting the same variant? Or can callers really distinguish between an indel and a SNP that perfectly overlaps the beginning or end of an indel?
TOPMed reports the similar results to 1000 genomes
https://bravo.sph.umich.edu/freeze5/hg38/variant/1-191191114-C-T
https://bravo.sph.umich.edu/freeze5/hg38/variant/1-191191113-TC-T
So I would guess they really are two different variants, unless this is a known issue with variant calling. I mean as long as it is sequence based I would think they could right?
1 answer
Seems a little suspicious that these have the same freq
They don't, and even if they did, it could be coincidence.
Are these two rows reporting the same variant?
No - one is a deletion (not an indel) and the other is an SNV. gnomAD clearly distinguishes between the two:
Actually this raises raises another question, I came across this example:
1 37176590 rs138644175 AC A 100 PASS AC=3143;AF=0.627596;
1 37176591 rs12723973 C A 100 PASS AC=2851;AF=0.569289;
It seems the deletion would occur in ~ 62 % of haplotypes, removing the C at position. It seems the SNV occurs in ~ 59% of haplotypes.
Considering the context: https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_000001405.25, I am not sure how you can have the described SNV ~59% of the time if the base it depends on is deleted ~62% of the time. Sorry feel a bit silly about this one.
They don't have to be part of the same 100% - the context is in the number of samples/chromosomes, not the total number in the cohort. The deletion could be 62% among 200 chromosomes and the 57% could be among a totally different or slightly overlapping 300 chromosomes. You'd need to look at this in each individual to see if there are any changes that don't make sense, like a hom-alt deletion AND a het SNV in the same diploid person.
Not to mention that gnomAD has wildly different frequencies on them:
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