Answers.Body: <p>It's an A. The number refers to the position just before the <code>|</code>. This is clearer on different zoom levels, but I double checked by going to the <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&amp;lastVirtModeType=default&amp;lastVirtModeExtraState=&amp;virtModeType=default&amp;virtMode=0&amp;nonVirtPosition=&amp;position=chr7%3A1-33&amp;hgsid=660570179_mIq0EMY1BriaU5C7xNPQAELZSbzv" rel="nofollow noreferrer">very beginning of a chromosome</a>: </p>
  
  <p><a href="https://i.sstatic.net/JktnE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/JktnE.png" alt="chr7 position 1-15"></a></p>
  
  <p>As you can see in the image above, the <code>|</code> 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. </p>
  
  <p>For more details, see <a href="http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/" rel="nofollow noreferrer">this UCSC blog post</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-03-19T16:44:09.040Z
Answers.Text: 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: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/
Answers.UserDisplayName: Christopher Lee
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Answers.Text: @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!
Answers.UserDisplayName: terdon
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Answers.LastEditDate: 2018-03-19T16:53:54.747Z
Answers.UserDisplayName: terdon
Body: <p>I'm a little confused about how the position indices work in the browser. Based on the picture below, is base number 755440 an <code>A</code> or a <code>G</code>?</p>
  
  <p>The general question is how do the indexing guides work? Is the base right under the <code>|</code> the one corresponding to the index or is it the one just before the <code>|</code>?</p>
  
  <p><a href="https://i.sstatic.net/j4i86.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/j4i86.png" alt="enter image description here"></a></p>
  
Tags: <ucsc><genome-browser>
Title: How are positions visually indicated in the UCSC Genome Browser?
ThreadText: # How are positions visually indicated in the UCSC Genome Browser?
  
  (Asked by: username_0 on 2018-03-17)
  
  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](https://i.sstatic.net/j4i86.png)](https://i.sstatic.net/j4i86.png)
  
  **Tags:** ucsc, genome-browser
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-03-17. Score: 5 | Accepted answer
  
  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](https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr7%3A1-33&hgsid=660570179_mIq0EMY1BriaU5C7xNPQAELZSbzv):
  
  [![chr7 position 1-15](https://i.sstatic.net/JktnE.png)](https://i.sstatic.net/JktnE.png)
  
  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](http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/).
  
  > **Comments:**
  > **username_2**: 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: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/  
  > **username_1**: @username_2 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!  
  
  ---
  
  