[Genome] snp128.txt vs web

[Pauline Fujita]

Hello Pierre,

The first record you found:

chr19 9270274 9270275

it is actually indicating a single base pair - due to our zero-based 
start position this actually just refers to the range 9270275 -9270275. 
For an  explanation of our zero-based start positions you can read this FAQ:

http://genome.ucsc.edu/FAQ/FAQtracks#tracks1

When you searched for "rs7254880" via the web interface it returned the 
original SNP, with an additional buffer of bases on either side. If you 
look at the range returned in:

Simple Nucleotide Polymorphisms (dbSNP build 128) (snp128)
rs7254880 at chr19:9270025-9270525

9270275 is actually right in the middle of this range.

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Pierre LINDENBAUM wrote:
> Hi UCSC,
>
> First of all, thanks for your great genome browser !
>
> Here is my question about a difference between your raw files and the 
> result seen on your browser:
>
> I just downloaded snp128.txt from your site for hg18:
>
> wget 
> "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp128.txt.gz";
>
> and grep-ed the snp named rs7254880
>
> gunzip -c snp128.txt.gz | grep rs7254880
>
> 655 chr19 9270274 9270275 rs7254880 0 + C C C/G genomic (...)
>
> ok, the position is on chr9 at 9270274
>
> but if I search now for rs7254880 via the web interface, it gives me
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg18&position=rs7254880
>
> Simple Nucleotide Polymorphisms (dbSNP build 128) (snp128)
> rs7254880 at chr19:9270025-9270525
>
> the position is now on chr9 at9270025 (!= 9270274 )
>
>
> why such a difference ?
>
> thank you in advance for your answer
>
> Pierre Lindenbaum
>
>
>
>
>
>
>
> .
>
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