SNP tracks

[Marco Santagostino]

Dear Sir/Madam,

I have several questions about the SNP tracks
1 what are the differences between the track Common SNP, Flagged SNP,
Multi. SNP and All SNP?
Given that I need to check the occurrence of SNP among a list of
sequences for which I have the coordinates, and then compare it to the
occurrence in the human genome, which database is more suitable for the
seach with Table Browser?
2 Where do I find the statistics for each track (number of SNPs ecc...)?
3 Are these tracks deduced from the data of dbSNPs from NCBI? Do they
contains the data from the 1000Genomes Project?
4 I noticed that if I run a search with Table Browser of the SNP
contained in a subset of my sequences using the track All SNP(137),
table snp137, I obtained a number of SNP that is different from the one
that I obtain using the Variation Reporter tool at NCBI, why?

Thank you for the attention,

best regards,

Marco Santagostino


--
Marco Santagostino, PhD
Lab. Molecular and Cellular Biology
Dept. Biology and Biotechnologies, University of Pavia
Ferrata street, 9 - 27100 Pavia, Italy
Post Box: Ferrata street, 1 - 27100 Pavia, Italy
Tel.: +39 0382 985540
Fax: +39 0382 528496
e-mail: marco.san...@unipv.it

[Luvina Guruvadoo]

Hi Marco,

You can read more about the SNP track on its track description page.
This can be accessed by clicking on the gray bar to the left of the
track in the main display, or by clicking on the track title above its
pull down menu below the main display. See the SNP 137 track description
here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=19&g=snp137. This
should provide the answers to questions 1 and 3.

To answer the second part of question 1, it really depends on the
purpose of your analysis. You could use the "All SNP" track, but note
that it contains not only polymorphisms, but also rare SNPs, known
disease SNPs, and variants that are questionable because they map to
multiple locations in the genome.

For your last question, the usual reason for inconsistency between the
dbSNP website and ours is that they constantly update their web
database, while we only load our SNPs tracks once when they make
official release download files.

I hope this helps. If you have additional questions, feel free to
contact us again at gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group