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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

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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.

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    $\begingroup$ 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/… $\endgroup$ Commented Mar 19, 2018 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! $\endgroup$ Commented Mar 19, 2018 at 16:53

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