How to interpret duplication from MultiQC/FastQC? FastQC of my sample files, aggregated into a single plot by MultiQC. Blue represents unique reads. Black represents duplicate reads. The x-axis is the number of reads.

I see I have more duplicate reads than unique reads, how do I interpret this plot? This is my attempt:


  FastQC took the first 100,000 sequences in each sample (details).
  Generally, higher duplicated read percentage is welcome as it
  represents better sequencing depth and lower sequencing error
  contamination. This dsitribution in this plot looks reasonable and
  nothing unusual.
I would agree with your statement.  Typically the ratio of unique to duplicated reads is a function of input library complexity (number of input molecules) verse sequencing depth (the amount of molecules sequenced).  

In the example you gave you have about a 2:1 ratio of duplicates to unique reads which suggests that these libraries have been sequenced to their fullest and additional sequencing would yield few new unique reads.