> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002522.md).

# Which controls should be used when sequencing low diversity libraries on a MiSeq?

Illumina recommends adding PhiX at 1% to all sequencing runs as an internal control.

For low-diversity libraries, spike in higher percentages of phiX to add base diversity to the run. The percentage of PhiX to depends on the diversity of the library, and requires optimization.

* Monotemplates may require 30% PhiX.
* Real Time Analysis (RTA) v1.17.28 or later requires a minimum of 5% PhiX spike-in for low-diversity libraries, when using MiSeq v3 reagents for sequencing.
* MiSeq v2 runs require higher phiX spike in than MiSeq v3 runs.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2522), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002522%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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