[Genome] a question about dbSNP126 in genome browser and dbSNP127 at NCBI

[Brooke Rhead]

Hello Wenzhong,

We actually did not do any additional annotation on the function of the 
SNPs -- these annotations are from NCBI.  (We did do some additional 
annotations, but not of the 'function' field.)  If you look at the 
snp126 details page, our NCBI data sources are listed.  (To get to the 
details page, click on the track name, "SNPs (126)," just above the 
track control in the Genome Browser).  Scroll down to the "Data Sources" 
section to see which files from NCBI we used for the various fields in 
the snp126 table.  Here is the pertinent detail from that page for the 
functional classification information:

Functional classification was obtained from 
b126_SNPContigLocusId_36_1.bcp.gz.

The UCSC annotations are also described on the track details page.  The 
table that corresponds to our annotations is called 'snp126Exceptions'. 
  There is another small hg18 table called 'snp126ExceptionDesc' that 
describes what each of the exceptions in the first table means.

I hope this information is helpful.  Please write back to this list if 
you have any further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



wenzhong wrote:
> Hello , 
> 
>  
> 
> Can I please ask a question about dbSNP126 included in UCSC genome browser?
> 
>  
> 
> We did a brief comparison of the validated coding SNPs  in the dbSNP126 of
> UCSC and the dbSNP127 at NCBI: the # of common SNPs - 83046 IDs; unique in
> db126 of UCSC - 10838 IDs, and unique in db127 of NCBI- 16993 IDs. We looked
> at the 10838 IDs unique in db126 of UCSC and apparently most (if not all of
> them) do not have an annotation on 'Function' at NCBI, so your team
> apparently has done additional annotations on the SNPs. Can I please ask if
> there is a reference on these annotations, and is it based on RefSeq or UCSC
> KG? 
> 
>  
> 
> Thanks very much for the help!
> 
>  
> 
> --------------------------------------------------------------------------
> 
> Here is some additional details,
> 
>  
> 
> validated coding SNPs in dbSNP127 at NCBI:
> 
> synon 28675
> 
> nonsynon 28051
> 
> utr   43281
> 
> total 100039 (synon and nonsyn has 168 overlaps)
> 
>  
> 
> validates coding SNPs in dbSNP126 in Genome Browser:
> 
> synon 25677 (25294 unique IDs: 24927 IDs have unique genome mapping, 367 IDs
> have been mapped to multiple genomic location)
> 
> nonsynon 25505 (24878 unqiue IDs: 24281 IDs have unique genome mapping, 597
> IDs have been mapped to multiple genomic location)
> 
> utr  44297 (43894 unique IDs: 43511 IDs have unique genome mapping, 383 IDs
> have been mapped to multiple genomic location) 
> 
> total 93884 (synon and nonsyn has 182 overlaps)
> 
>  
> 
> common in two: 83046 IDs
> 
> db126.ni.db127 10838
> 
> db127.ni.db126 16993
> 
> ------------------------------------
> 
>  
> 
> Best regards,
> 
>  
> 
> Wenzhong
> 
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