What Does a Typical 16S Run Look Like on a MiSeq?

A typical 16S run on the MiSeq has the %Base and Q30 patterns shown below (in a 2x300 bp run). %Base

%Q30

The drop in the quality in the first cycles is due to the insert beginning with the sequencing of a locus specific primer.

Due to the low diversity of these libraries, the recommended cluster density for a 16S run is 30-40% lower than the standard density guidelines on the MiSeq.

For more information regarding low-diversity sequencing, review Illumina's Cluster Optimization Overview Guide and the Illumina Knowledge article How much PhiX spike-in is recommended when sequencing low diversity libraries on Illumina platforms?

For any feedback or questions regarding this article (Illumina Knowledge Article #7820), contact Illumina Technical Support [e-mail].