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 probeThe 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. 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. 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: BlankThe genomic location of the variant was successfully mapped with no complications. No additional comments were required. No probe mappingsThe 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 mappingsThe 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.

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