> 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/microarray/non-human-methylation/microarray-non-human-methylation-reference_material-list/000009599.md).

# What are the ctl Probes in the Infinium Mouse Methylation Array Manifest?

In the Infinium Mouse Methylation Array, the probe prefix (for example, **cg** in probe *cg00101675*) indicates the probe type. The majority of probes are prefixed with **cg**, which designates CpG-targeting probes. The complete list of probes included in the Infinium Mouse Methylation Array is available in the manifest CSV file.

Probes with the **ctl** prefix are control probes incorporated into the BeadChip to assess Infinium assay performance and data quality. These control probes are also used to estimate background signal and support data normalization during downstream analysis.

**References:**

* [Infinium Mouse Methylation Beadchip Manifest Column Headings](/microarray/general/microarray-general-reference_material-list/000005894.md)
* [Infinium Mouse Methylation BeadChip GenomeStudio Controls Dashboard Interpretation](/microarray/general/microarray-general-reference_material-list/000005666.md)
* [Infinium Mouse Methylation BeadChip Product Files](https://support.illumina.com/array/array_kits/infinium-mouse-methylation-beadchip-kit/downloads.html)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9599), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009599%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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