[Genome] About snp126

[Heather Trumbower]

Chun-Hsi:

We realized you were asking about population data.   We don't currently 
include allele frequencies in our data at genome.ucsc.edu.   However, you 
can find this data at dbSNP.  In our details page for each SNP displayed, 
we include a link to dbSNP.

So, if you are looking at rs10221297 in the UCSC genome browser, you can 
click on it to see the details we provide.  This link is 
http://genome.ucsc.edu/cgi-bin/hgc?g=snp126&i=rs10221297&c=chr10&l=50319&r=50330&db=hg18

In this case you will see the link to dbSNP at
http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs10221297
For this SNP there is no population data available.  An example of a SNP 
with population data is rs930557.

We are currently working on a track to display the allele frequencies for 
the HapMap SNPs.

If you wish to work directly with the dbSNP population data, you can use 
the SubPopAllele table available at via anonymous ftp at 
ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data.
Note this data is available for all submitted SNPs; to translate to 
reference (clustered) SNPs you can use the SNPSubSNPLink table.

We hope to incorporate this data within the next year or so.

Let us know if you have further questions.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Mon, 22 Jan 2007, Rachel Harte wrote:

> Hello,
>
> The easiest way to do this is to use our public mySQL server to query our
> database tables directly - see this page for help on doing this:
>
> http://genome.ucsc.edu/FAQ/FAQdownloads#download29
>
> There are a large number of SNPs in the snp126 table:
> mysql> select count(*) from snp126;
> +----------+
> | count(*) |
> +----------+
> | 12351941 |
> +----------+
>
> Therefore you may want to break the query down by class. Most SNPs are
> single base substitutions with a standard format:
> mysql>select count(*) from snp126 where class = 'single';
> +----------+
> | count(*) |
> +----------+
> | 10090600 |
> +----------+
>
> This query will count the number of instances of each observed
> substitution for the "single" class:
>
> mysql>select observed, count(observed) from snp126 where class = "single"
> group by observed;
>
> For insertions, you may wish to limit the size of the insertion so that
> you do not get too many rows of data returned:
> e.g.
> mysql> select distinct(observed) from snp126 where class = 'insertion' and
> length(observed) < 5;
>
> This is the most basic characterization of the snp126 data:
> mysql> select count(*), class from snp126 group by class;
> +----------+----------------+
> | count(*) | class          |
> +----------+----------------+
> | 10090600 | single         |
> |     5596 | in-del         |
> |        4 | het            |
> |     4321 | microsatellite |
> |     6486 | named          |
> |    51631 | mixed          |
> |    16809 | mnp            |
> |  1393040 | insertion      |
> |   783454 | deletion       |
> +----------+----------------+
>
> I hope that this helps you. Please let us know if you have further
> questions.
>
> Rachel
>
> Rachel Harte
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
> On Tue, 23 Jan 2007, pauhsi wrote:
>
>> How do I know the frequency or amount of every "observed" variation in snp126?
>>
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>