text: user122: 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 |?
  
  
  user298: 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: 
  
  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.
  
original_text: 122: <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.stack.imgur.com/j4i86.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/j4i86.png" alt="enter image description here"></a></p>
   298: <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.stack.imgur.com/JktnE.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
  