#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
Y 2649856 . G A 42.7 PASS AA=.; GT:PL:DP:SP:GQ 0:0,9,81:3:0:99
question is: whats the point of knowing the location of the snp without an rs#? If the snp is found in this individual HG00096 would that be considered a type of private SNP?
The point is you have the genomic location and the variant.
It could be a private mutation, it could be a false positive.
Not all mutations are going to have rs#s.
I work with human genomes, trying to find the causes of inherited disease, and we're primarily interested in mutations no one has seen before, so the vast majority have no RSID. an RS# just means it has been reported to a database and has no bearing on the biological significance.
Also, take a close look at the HG00096 column, I think the leading GT==0 implies this individual has the reference G. Also be careful of the Y chromosome when calculating homozygosity.
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I agree with everything except "has no bearing on the biological significance". There are sites in dbSNP with some association to disease if you look carefully. I would agree that most are likely to be benign.
Yes I should word that more carefully. Any identified SNP could be studied and linked to function, but the existence of an ID number does not imply such functional knowledge exists. Perhaps vice-versa: any SNP with known function "should" have an ID#.