Reference SNP(refSNP) of dbSNP

[CarlElit]

When I browse dbSNP for SNPs, I saw this info: "RefSNP Alleles: C/T". I know it indicates the alleles of the SNP. But what is the meaning of all syntax, such as "C/T", "C/T/A/T", "-/AT", etc? I could not find on the website...

When I use Bowtie to align these SNPs to human genome, I got quite a lot of instances whose reported position is very close to the desired position (+- 5). Is it possible that I did not consider the type of the alleles? Problem is sometimes even two SNPs seem to have the same alleles, but one is reported correct by Bowtie, but another is in correct...

[cariaso]

dbSNP actually does more than just true SNPs. This is (slightly) explained at

http://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=snpClass

C/T is a traditional SNP.
-/AT is an indel (either nothing, or the insertion of 2 bases 'AT')
C/T/A/T I think you're making that up and incorrect. You're probably thinking of something like rs3091244 which has more than 2 alleles, and is therefore written as A/C/T. However 2 occurences of a T in that list makes no sense to me.

A good example for these is rs332 which is a 3nt insertion of either
-/TCT/TTT

You may also find http://www.SNPedia.com to be a useful resource.

[CarlElit]

dbSNP actually does more than just true SNPs. This is (slightly) explained at

http://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=snpClass

C/T is a traditional SNP.
-/AT is an indel (either nothing, or the insertion of 2 bases 'AT')
C/T/A/T I think you're making that up and incorrect. You're probably thinking of something like rs3091244 which has more than 2 alleles, and is therefore written as A/C/T. However 2 occurences of a T in that list makes no sense to me.

A good example for these is rs332 which is a 3nt insertion of either
-/TCT/TTT

You may also find http://www.SNPedia.com to be a useful resource.

Thanks very much, cariaso. You are right, I make up "C/T/A/T", just to show an example...

So do you think the alleles will have effect when aligning SNPs to reference genome?