Table browser output of All SNPs(142) mm10: inconsistent SNP positions

[Emily Gibbons]

Dear receiver, 

I am working on removing overlapping SNP positions from my data using the snp142 table for mm10. I have noticed that some SNPs in the downloaded table are positioned one base before the SNP, where some are positioned one base after the SNP, when comparing the position in the browser. This has lead to inconsistencies in SNP removal for my data. 

I was wondering if there were patterns in mm10 SNP annotation that exists which could cause this to happen? 

Thank you for your help!

Emily 

[Matthew Speir]

Hello, Emily.

Thank you for your question about SNP data for mouse/mm10 in the UCSC Genome Browser.

The coordinates in our tables are zero-based start and a one-based end. This means that the start coordinates begin counting at zero. We add one to the start coordinate before displaying them in the Browser. However, for insertions the start and end coordinates output from the Table Browser will be the same. More details can be found in our FAQs or on our blog.

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.
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Matthew Speir

UCSC Genome Browser, User Support

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