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

[wenzhong]

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!

 

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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

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Best regards,

 

Wenzhong