Question

Known Snps For C57Bl/6 And Cast/Eij

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11.0 years ago

dfernan ▴ 760

Hi,

I'd like to find ALL the SNPs and INDELS of CAST/EiJ with respect to C57BL/6 (I think this is mm10 reference assembly, am i correct?) mouse strain.

I have tried searching in pubmed dbsnp but i did not have much fortune...

Any help?

snp dbsnp • 5.0k views

ADD COMMENT • link updated 11.0 years ago by Larry_Parnell 16k • written 11.0 years ago by dfernan ▴ 760

score 3 · Answer 1 · 2013-05-07

3

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11.0 years ago

jts ▴ 240

The mouse genomes project at Sanger has SNP calls for many strains:

http://www.sanger.ac.uk/resources/mouse/genomes/

ADD COMMENT • link 11.0 years ago by jts ▴ 240

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Hi, thanks a lot! I found that data as well but my question is, does that data include all the reported SNPs for CAST/EiJ with respect to the latest assembly of C57BL/6?

ADD REPLY • link 11.0 years ago by dfernan ▴ 760

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There is a very detailed README file on the ftp:

ftp://ftp-mouse.sanger.ac.uk/current_snps/README

It says the reference version is GRCm38 (which is C57BL/6J).

ADD REPLY • link 11.0 years ago by jts ▴ 240

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great thanks! do you know if there are more SNPs databases, or these are all the SNPs out there for CAST/C57? thx again

ADD REPLY • link 11.0 years ago by dfernan ▴ 760

score 1 · Answer 2 · 2013-05-07

1

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11.0 years ago

Larry_Parnell 16k

At http://www.informatics.jax.org/strains_SNPs.shtml from the Jackson Lab you can find SNPs for given strains.

ADD COMMENT • link 11.0 years ago by Larry_Parnell 16k