<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>

CC BY-SA 3.0
2018-03-19T16:44:09.040Z
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/
Christopher Lee
CC BY-SA 3.0
2018-03-19T16:53:21.307Z
@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!
terdon
CC BY-SA 3.0
2018-03-17T13:54:59.637Z
2018-03-19T16:53:54.747Z
2018-03-19T16:53:54.747Z
terdon
<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>

<ucsc><genome-browser>
How are positions visually indicated in the UCSC Genome Browser?
# 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

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## 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**: @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!  

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