Why are some markers mapped to Chromosome 0?

Figure 1. Example manifest with Chr = 0 loci 

During manifest creation, the probe sequence is mapped to the genome build notated in the GenomeBuild column in the manifest. The SNP or indel coordinate is then recorded in the MapInfo column. If a marker is annotated with Chr = 0 or MapInfo = 0 in the manifest, there are two possible explanations:

1. No valid mapping for the probe.
2. More than 1 best-scoring mapping for the probe.

How do I find out why a probe is mapped to Chr 0?

For loci assigned a zero for Chr/MapInfo in the manifest, refer to the Mapping Comments file found in the product support files at Illumina.com. This file provides the reason for the notation:

• Blank – There were no complications in mapping the location of the variant.
• No probe mappings – The Chr and MapInfo fields in the manifest have been set to 0, as no valid alignments were identified for the probe sequence in the updated genome build.
• Multiple mappings – The Chr and MapInfo fields in the manifest have been set to 0, as multiple best scoring alignments were identified for the probe sequence. The locations of the multiple mappings are supplied as a semi-colon delimited list.

Figure 2. Example mapping comments file

Additional Resources

For more information about Infinium array manifest files, refer to the Infinium Genotyping Manifest Column Headings bulletin.