[Genome] dbSNP build 128

[Ann Zweig]

Hello Shan,

	dbSNP has mappings to several alternate collections of contigs, for 
example the Celera human assembly.  The files that you downloaded are 
probably from the recent release, which now includes Craig Venter's
genome too:

----------------
**** Major Changes in B129 ****

dbSNP b129 is mapped to  a new Human 36.3 assembly called HuRef

(Venter diploid genome) in addition to the NCBI reference and Celera
assemblies.
----------------

	Our browser is in NCBI 36 coords, so we only show the SNPs mapped to those.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Shan Yang wrote:
> Hi,
> 
> I have a question here about dbSNP build 128 of hg18 on genome browser. I tried to download the data from the link provided on the browser
> ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/
> (updated on 4/14/08-4/17/08)
> 
> Then I looked at the files I got. I randomly picked some locations in the chr_1.gz file, and am surprised to find that majority of the time, the location does not have a snp in browser.
> For example, the first 5 lines are like this:
> 
> 242     2       0       1       1       1       1       NW_927841       1       HsCraAADB02_8   3670230 19193787                0.18    0.24            2       0       1       36      36      C
> elera
> 242     2       0       1       1       1       1       NW_001838573    1       Hs1_WGA29_36    2491270 19115539                0.18    0.24            2       0       1       36      36      H
> uRef
> 242     2       0       1       1       1       1       NT_004610       18      Hs1_4767_36     3693803 20742048                0.18    0.24            2       0       1       36      36      r
> eference
> 538     2       0       1       1       1       1       NW_923572       1       HsCraAADB02_3   2845101 5275775 CHD5,KCNAB2                             0       0       1       36      129     C
> elera
> 538     2       0       1       1       1       1       NW_001838523    1       Hs1_WGA11_36    299275  5309775 CHD5,KCNAB2                             0       0       1       36      129     H
> uRef
> 
> 
> Among the 5 locations, 19193787, 19115539, 20742048, 5275775, 5309775, only 20742048 has a snp in the GB. 
> 
> Am I looking at the wrong file or there is anything wrong here?
> 
> Thanks!
> 
> Shan
> 
> 
> 
> 
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