5
$\begingroup$

I'm a little confused about how the position indices work in the browser. Based on the picture below, is base number 755440 an A or a G?

The general question is how do the indexing guides work? Is the base right under the | the one corresponding to the index or is it the one just before the |?

enter image description here

$\endgroup$
5
$\begingroup$

It's an A. The number refers to the position just before the |. This is clearer on different zoom levels, but I double checked by going to the very beginning of a chromosome:

chr7 position 1-15

As you can see in the image above, the | is always after the base it refers to. I also confirmed by checking a few random positions using another genome browser which places the positions unambiguously above each base.

For more details, see this UCSC blog post.

$\endgroup$
2
  • 2
    $\begingroup$ Yep and the reason for this is because we store everything internally as zero based coordinates but then display everything in a 1-based format. For more information see the following blog post: genome.ucsc.edu/blog/… $\endgroup$ – Christopher Lee Mar 19 '18 at 16:44
  • $\begingroup$ @ChristopherLee thank you! I had actually written out an answer stating that it must be the position after since bed files start at 0 and then thought to check, just to make sure, and was very much surprised that it was actually the position before! $\endgroup$ – terdon Mar 19 '18 at 16:53

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.