[Genome] A question about SNPs

[Shan Yang]

Hi, 

I used the snp128 data for my research. And I found many cases where the start of SNP is greater than the end of SNP. If it is an indel, it may make some sense, however, a lot of these cases are single nucleotide change like this one shown here. 
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=107011994&o=36266&t=36266&g=snp128&i=rs4030808&c=chr1&l=36264&r=36268&db=hg18&pix=1200

What is the explaination to this?

My guess is that dbsnp data came from various sources and some of them use 0 start, half close region and some of them use 1 start, close region. When you put them on genome browser, you treat them all as 0 start and half close, thus, when you convert them into 1 start, closed region, you'll add 1 to the start coordinate and keep the end coordinate. Thus, if start=end in the original coordinate, they will be start = end +1 in the genome browser.

I don't know if this is right, but all the cases I've seen here all have start = end +1 problem.

Thanks!

Shan



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