Infinium genotyping manifest column headings
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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. See diagram below:
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 technical bulletins:
For any feedback or questions regarding this article (Illumina Knowledge Article #1565), contact Illumina Technical Support techsupport@illumina.com.
