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Old 1st December 2016, 02:25 AM
ntk ntk is offline
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Nucleobase capitalization in RSRS polymorphism results

What is the significance of a lowercase derived nucleobase in a polymorphism? I have these in my RSRS results, but not rCRS.

e.g., why A16182c and A16183c, but G16390A under RSRS?

Whereas under rCRS, I have 16182C, 16183C, and 16390A.

(For that matter, why don't the rCRS polymorphisms include the reference base? But, at least it's internally consistent, and they are listed below, so there's no mystery there.)
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Old 1st December 2016, 01:08 PM
Ann Turner Ann Turner is offline
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Quote:
Originally Posted by ntk View Post
What is the significance of a lowercase derived nucleobase in a polymorphism? I have these in my RSRS results, but not rCRS.

e.g., why A16182c and A16183c, but G16390A under RSRS?

Whereas under rCRS, I have 16182C, 16183C, and 16390A.

(For that matter, why don't the rCRS polymorphisms include the reference base? But, at least it's internally consistent, and they are listed below, so there's no mystery there.)
By convention, the lower case bases signify a transversion. The chemical structures of the bases A and G resemble each other, and likewise C and T. This means that it's easier to substitute those bases for each other ("transitions"). The great majority of mutations are transitions. Any other substitution is called a transversion.
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