Probe_ID MASK.mapping MASK.typeINextBaseSwitch MASK.rmsk15 MASK.sub25.copy MASK.sub30.copy MASK.sub35.copy MASK.sub40.copy MASK.snp5.common MASK.snp5.GMAF1p MASK.extBase MASK.general

(1) Probe_ID: Probe ID
(2) MASK.mapping: whether the probe is masked for mapping reason. Probes retained should have high quality (>=40 on 0-60 scale) consistent (with designed MAPINFO) mapping (for both in the case of type I) without INDELs.
(3) MASK.typeINextBaseSwitch: whether the probe has a SNP in the extension base that causes a color channel switch from the official annotation (described as color-channel-switching, or CCS SNP in the reference). These probes should be processed differently than designed (by summing up both color channels instead of just the annotated color channel).
(4) MASK.rmsk15: whether the 15bp 3'-subsequence of the probe overlap with repeat masker, this MASK is NOT recommended.
(5-8) MASK.sub25.copy, MASK.sub30.copy, MASK.sub35.copy, MASK.sub40.copy: whether the 25bp, 30bp, 35bp and 40bp 3'-subsequence of the probe is non-unique.
(9) MASK.snp5.common: whether 5bp 3'-subsequence (including extension for typeII) overlap with any of the common SNPs from dbSNP (global MAF can be under 1%).
(10) MASK.snp5.GMAF1p: whether 5bp 3'-subsequence (including extension for typeII) overlap with any of the SNPs with global MAF >1%.
(11) MASK.extBase: probes masked for extension base inconsistent with specified color channel (type-I) or CpG (type-II) based on mapping.
(12) MASK.general: the recommended general purpose masking merged from "MASK.sub30.copy", "MASK.mapping", "MASK.extBase", "MASK.typeINextBaseSwitch" and "MASK.snp5.GMAF1p".