Infinium genotyping manifest column headings

The Infinium manifest file contains detailed information describing the content and design of each BeadChip. It is organized in a table, where each row corresponds to a specific marker/probe and each column provides associated information. Below is an overview of the key information for each single nucleotide polymorphism (SNP) or insertion/deletion (Indel) found in an Infinium genotyping manifests.

IlmnID: Provides a summary of the pertinent information about the SNP or Indel probe. Genome Build is zero if unknown. For Indels, Plus/Minus is reported instead of Top/Bot. Refer to the figure below:

Figure 1. Diagram with naming convention for probes.

ILMN Strand: The Top/Bot (for SNPs) or Plus/Minus (for Indels) designation of the ILMN strand (Design strand).

SNP: SNP alleles as reported by assay probes. Alleles on the Design strand (the ILMN strand) are listed in order of Allele A/B.

AddressA_ID: For Infinium I bead types, this is the Address ID for the probe specific for the A allele. For Infinium II bead types, the Address ID for the probe used for both A and B alleles (in this case, AddressB_ID and AlleleB_ProbeSeq columns are empty).

AlleleA_ProbeSeq: The sequence of the probe identified in AddressA_ID column.

AddressB_ID: For Infinium I bead types, the address ID for the probe specific for the B allele.

AlleleB_ProbeSeq: For Infinium I bead types, the sequence of the probe identified in AddressB_ID column.

GenomeBuild: The NCBI Genome Build referenced for information about this probe in this manifest.

Chr: Chromosome containing the SNP.

MapInfo: Chromosomal coordinates of the SNP.

Ploidy: Ploidy of the target organism. For humans, autosomes are diploid, mitochondria and Y chromosome are monoploid.

Species: Species targeted by the probes in this BeadArray.

Source: The database source of the SNP, if available (eg, dbSNP).

SourceVersion: The database (Source) version, if available, which was referenced for the SNP to create the manifest.

Source Strand: The Top/Bot (for SNPs) or Plus/Minus (for Indels) designation for the Source strand.

Source Seq: The sequence of the Source strand.

TopGenomicSeq (in *.csv version of manifest, but not in *.bpm): The sequence of the Top strand (for SNPs) or the Plus strand (for Indels).

BeadSetID: An identifier used in the manufacture of BeadChips.

Exp_Clusters: The number of clusters expected to be generated by each SNP: 1 for nonpolymorphic probes, 2 for mitochondrial DNA and Y chromosome loci, 3 for any other loci for a diploid organism.

Ref Strand: Plus/Minus (+/-) designation for the ILMN strand.

For more information on strand designations, refer to the following Illumina Knowledge articles and Technical Note:

• DNA strand designations

• Simple guidelines for identifying top/bottom (TOP/BOT) strand and A/B allele

• How to interpret DNA strand and allele information for Infinium genotyping array data

• “TOP/BOT” Strand and “A/B” Allele

For any feedback or questions regarding this article (Illumina Knowledge Article #1565), contact Illumina Technical Support [e-mail].