<p>I just assembled a plasmid using Illumina 2x250 PE. I am pretty confident that the assembly is fine.</p>

<p>I check by mapping the raw data to the assembly. In general I have a very high coverage (sometimes more than 1000x). Also I have very few unmapped pairs.</p>

<p>But I have some regions where the coverage drops to 10-20 fold coverage. This looks concerning, but I still think my assembly is fine because:</p>

<p>1. I this areas I also see barely unmapped pairs</p>

<p>2. I did not see more missmatches from the reads to the assembly sequence as in other regions</p>

<p>Now my questions:</p>

<p>1. What are the properties of sequences where Illumina gives a lower coverage? Any paper? Or a SW to check?</p>

<p>2. How else can I check if my assembly is fine in this low coverage areas?</p>

Check GC content. Illumina library prep can have problems with both, regions of high as well as low GC