New alternative mouse strain hub and strain-specific annotations

[Yung-Chih Lai]

Hi Jairo,

I am glad to know this news. The 16 mouse genomes UCSC added are assembled genomes produced by Mouse Genomes Project. Totally, they produced 36 mouse genomes using short-read sequencing to identify SNPs, short insertions, and deletions, and larger structural variations relative to the C57BL/6J mouse reference genome. May I know whether UCSC will integrate the all 36 mouse genomes in the near future? Or UCSC only integrate de novo genome assembly? Many thanks.

Best,

Gary

On Sat, Jul 15, 2017 at 6:28 AM, Jairo Navarro Gonzalez <jnav...@ucsc.edu> wrote:

A mouse strain assembly hub is now available and shows an alignment of 16 assembled laboratory mice strains, including the reference mouse (mm10) as well as the reference rat (rn6). This hub contains some of the most common mice strains used in disease models such as NOD, BALB/c, and C3H. Each mouse strain in the assembly hub is displayed as the primary sequence along with strain-specific annotations. You can load this hub from our Public Hubs or the following page.

Along with the release of this assembly hub, a new track is available for mm10. The Mouse SNPstrack shows single nucleotide variants between the different strains of mice and all SNP and indel calls are relative to the reference mouse genome (GRCm38/mm10).

Special thanks to Joel Armstrong, Ian Fiddles, and Benedict Paten for the alignment generation, as well as Thomas Keane and the Mouse Genomes Project for providing the genome assemblies. Thanks to Hiram Clawson and Jairo Navarro for the development and release of this track and hub.

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Jairo Navarro

UCSC Genomics Institute

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[Jairo Navarro Gonzalez]

Hello Gary,

Thank you for using the UCSC Genome Browser and your question about the newly released mouse strain hub.

I believe your question is regarding the availability of the identified SNPs, indels, and structural variations for the 36 alternative mouse strains relative to the C57BL/6J mouse reference genome. I am happy to share that this data is already available on the Genome Browser and can be viewed using the Mouse SNPs track on mm10.

For example, loading this session will take you to the FTO gene on mm10 where three single nucleotide variants (SNVs) are present. Clicking on an item will take you to the details page for the SNV and will give you more information about which of the 36 strains contain that particular genotype.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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[Yung-Chih Lai]

Hi Jairo,

Yes, you are right. Many thanks for your information.

Best,

Gary