**Intro:**
Yeast chromosome 12 contains a really long region of rDNA. There are about 150-200 or greater copies of a 9.1kb repeat, so about 1.5M bases in total, which is the majority of the chromosome. The published yeast reference genome has only 2 copies of the repeat. 

**My situation:**
I just did whole genome sequencing of some yeast clones. I have on about 70X coverage in most of the genome. If you figure that there are 200 copies of the rDNA repeat on chromosome 12, but only 2 copies represented in the reference sequence, then in this region I should see a read depth of roughly 70*100 = 7000. And in fact, this is pretty much what I see, here's a plot of read depth in that area. To generate this plot I mapped reads with `bwa` and then used `samtools depth` and then plotted in R. 

![enter image description here][1]

**My question:**
The plot looks obviously artificially cut off at a read depth of ~8000--why? I didn't specify any limits in creating the plot. **So where is the cutoff happening?** Is it something samtools depth is doing? Something bwa did? Or something about how the reads are generated during Illumina sequencing? 

Last thing to mentions: the highest value is not exactly 8000, there are a few positions with depths of 8002, just to make things weirder. And I've shown just one example, but it happens on to all clones I sequenced. 

Thanks for any help!


  [1]: https://i.imgur.com/I2ReY5E.jpg
    Usage: samtools depth [options] in1.bam [in2.bam [...]]
    Options:
      (...)

       -d/-m <int>         maximum coverage depth [8000]. If 0, depth is set to the maximum
                           integer value, effectively removing any depth limit.
      (...)