> 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/general/microarray-general-reference_material-list/000001423.md).
# What does Chr or MapInfo = 0 mean in Infinium Genotyping Array Manifest Files?
**Why are some markers mapped to Chromosome 0?**\
During Infinium manifest creation, each probe sequence is aligned/mapped to a reference genome build specified in the GenomeBuild column in the manifest. Based on this alignment, the genomic position of the single nucleotide polymorphism (SNP) or insertion/deletion (indel) coordinate is recorded in the MapInfo column, and the corresponding chromosome is indicated in the Chr column. In some cases, markers may be annotated with Chr = 0 and/or MapInfo = 0 in the manifest. These values indicate that a definitive genomic location could not be assigned. This can occur for the following reasons: **No valid mapping for the probe**The probe sequence does not align confidently to the reference genome build used during manifest creation. \*\*Multiple best-scoring mappings for the probe.\*\*The probe sequence aligns equally well to more than one location in the genome. In these cases, a unique genomic position cannot be determined with confidence, and the marker is not assigned to a specific chromosome or coordinate.\
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**Figure 1**. Example manifest illustrating loci annotated with Chr = 0.
**How to determine why a probe is mapped to Chr 0**
For loci assigned Chr = 0 and/or MapInfo = 0 in the manifest, additional details can be found in the Mapping Comments file, which is included in the product support files available on the [Illumina website](https://www.illumina.com). The Mapping Comments file provides the underlying reason for the Chromosome 0 designation for each probe. The MappingComment field may contain one of the following values: **Blank**The genomic location of the variant was successfully mapped with no complications. No additional comments were required. **No probe mappings**The Chr and MapInfo fields in the manifest are set to 0, as no valid alignments were identified for the probe sequence in the specified genome build. **Multiple mappings**The Chr and MapInfo fields are set to 0, as the probe aligns equally well to multiple genomic locations, and a definitive genomic location cannot be reliably determined. The possible mapping locations are provided in the Mapping Comments file as a semicolon-delimited list.\
**Figure 2**. Example of a mapping comments file showing probe mapping outcomes.
**Additional Resources**
* [Infinium genotyping manifest column headings](/microarray/general/microarray-general-reference_material-list/000001565.md).
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1423), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001565%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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