[Genome] About snp126

[Rachel Harte]

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?
>