# 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** ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-f43b0dd465637ea364a8df8c757181a81faa5a66%2Fimage1.png?alt=media) **%Q30**\ ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-2ce4c1c5507c923b46a8c92737f3e5fd2cb67e8c%2Fimage2.png?alt=media\&token=7e0f8bcb-ed94-476e-94b6-ec81166898d4) 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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