i ve checked the SNP in that particular reference sequence.
for eg: rs6094752 in NM001174087. and the result is NM001174087.1:c.652C>T(from SNPdb in NCBI),
but when i saw the particular residue number in the reference sequence, according to the result the residue should be T, but instead of T , G is present. how can to interpret the result? Kindly help
when you have a code such as NM_001174087.1:c.652C>T it has plenty of information in it: it tells you where this variation is tagged (accession and version), the type of sequence for nomenclature (genomic, coding, ...) and the base change on that particular sequence (the original reference and the base substitution). having said that, you have to pay attention to all that pieces of information to extract your conclusions.
let me say in advance that I don't exactly understand what you mean with "the residue should be T", so I can only guess from 2 possible options:
you think that T should be the base to find in your variated sample, but you don't find that on dbSNP. if that is the case, let me tell you that dbSNP reports the reference sequence (both strands) and all the known possible variations in it, so the T would never be displayed in the reference, but only the original C as reported on the C>T code.
you found a G in that SNP position of the reference when it shouldn't. this may have been caused by a wrong position counting at your side (you may see that the reference C is surrounded by G at the previous and next position), or because you are looking at the appropriate position but on the negative strand (note that G is in fact the complementary base for the reference C in the possitive strand).
in any case, looking at the SNP you mentioned, I can assure you that the original base on the reference sequence is the C (on the possitive strand, where the SNP was reported), and that the base change is a T.
so has my answer solved your issue? I mean, do you clearly see the C on the reference possitive strand? do you understand that rs6094752 is defined as the change from that C to a T?
i m sorry @Jorge, i've got the clear idea after reading your wonderful explanation, but still facing difficulty with 652nd position in the sequence NM_001174087.1.
Ya i ve got an clear idea now.
Ya i ve got an clear idea now. Thankyou Jorge
but as u said @jorge, i ve taken the correct positive strand. NM_001174087.1
so has my answer solved your issue? I mean, do you clearly see the C on the reference possitive strand? do you understand that rs6094752 is defined as the change from that C to a T?
i m sorry @Jorge, i've got the clear idea after reading your wonderful explanation, but still facing difficulty with 652nd position in the sequence NM_001174087.1.
@jorge ya i got the solution for my problem.
@jorge ya i've got the solution for my problem