[Genome] SNP

[Heather Trumbower]

Scott:

You are correct, we adjust the dbSNP coordinates to match our zero-based 
start, one-based end convention.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Mon, 2 Jul 2007, Davidson, S. wrote:

> Hi UCSC,
> I wonder if you can clear something up for me.
> I'm looking at Human Mar. 2006 Assembly and I'm interested in the SNP
> track.
>
> I was looking at the source data used to create this track, in
> particular the b126_SNPContigLoc_36_1.bcp.gz file from dbSNP.
> I noticed that the coordinates given for the SNPs don't match the
> coordinates displayed on the browser.
> For example (the first SNPs in the file):
>
> snp    dbsnp_coordinate    UCSC_coordinate
> rs3        31344841                    31344842
> rs4        31345221                    31345222
>
> However when I looked within UCSC text files from the table browser I
> saw that these SNPs are noted as having a chromstart and chromend
> positions
>
>        chromstart    chromend
> rs3    31344841    31344842
> rs4    31345221    31345222
>
> This suggests that dbSNP uses a different coordinate convention to the
> zero based start one based end that UCSC employs, am I right in thinking
> this?
>
> Thanks in advance,
> Scott
>
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