**We have encountered strange pattern in bam file that is generated from amplicon sequencing. (Nextera XT, illumina MiSeq).** 

As you can see at the middle of bam file, rectangular-shaped coverage is formed. Half of the reads finished at the right side of the rectangular; while other half of reads finished at the left side of rectangular. 

What can cause such abnormal coverage distribution? Any structural variant?

![enter image description here][1]
![enter image description here][2]
![enter image description here][3]
![enter image description here][4]

  [1]: http://i.imgur.com/Z2zFnj5.png
  [2]: http://i.imgur.com/uMrYmHO.png
  [3]: http://i.imgur.com/uAqsVEj.png
  [4]: http://i.imgur.com/ZVarV4M.png
**We solved the real cause of this pattern. It's duplication event of 200 bp area in that rectangular area.** We BLAST the unmapped parts of reads at the ends of rectangular area. And we found out that they are perfectly matched to region inside of this area.

![enter image description here][1]


  [1]: http://i.imgur.com/u6ZjM9E.png