# 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).\
\&#xNAN;**%Base**

![](/files/H3z9EazWNbtz1i55qLrJ)

**%Q30**\
![](/files/BHjjJnGnCgm1aem2hM31)

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](https://support.illumina.com/downloads/cluster-optimization-overview-guide-1000000071511.html) and the Illumina Knowledge article **How much PhiX spike-in is recommended when sequencing low diversity libraries on Illumina platforms?**

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #7820), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007820%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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