• human: M_mapping+M_nonuniq+M_SNPcommon_5pt+M_1baseSwitchSNPcommon_5pt+M_2extBase_SNPcommon_5pt.
• mouse: M_mapping+M_nonuniq

Common masks:

• M_mapping: unmapped probes, or probes having too low mapping quality (alignment score under 35, either probe for Infinium-I) or Infinium-I probe allele A and B mapped to different locations
• M_nonuniq: mapped probes but with mapping quality smaller than 10, either probe for Infinium-I
• M_uncorr_titration: CpGs with titration correlation under 0.9. Functioning probes should have very high correlation with titrated methylation fraction.

Human masks (general and population-specific):

• M_commonSNP5_5pt: mapped probes having at least a common SNP with MAF>=5% within 5bp from 3'-extension
• M_commonSNP5_1pt: mapped probes having at least a common SNP with MAF>=1% within 5bp from 3'-extension
• M_1baseSwitchSNPcommon_1pt: mapped Infinium-I probes with SNP (MAF>=1%) hitting the extension base and changing the color channel
• M_2extBase_SNPcommon_1pt: mapped Infinium-II probes with SNP (MAF>=1%) hitting the extension base.
• M_SNP_EAS_1pt: EAS population-specific mask (MAF>=1%).
• M_1baseSwitchSNP_EAS_1pt: EAS population-specific mask (MAF>=1%).
• M_2extBase_SNP_EAS_1pt: EAS population-specific mask (MAF>=1%).
• ... more populations, e.g., EAS, EUR, AFR, AMR, SAS.

Mouse masks (general and strain-specific):

• M_PWK_PhJ: mapped probes having at least a PWK_PhJ strain-specific SNP within 5bp from 3'-extension
• M_1baseSwitchPWK_PhJ: mapped Infinium-I probes with PWK_PhJ strain-specific SNP hitting the extension base and changing the color channel
• M_2extBase_PWK_PhJ: mapped Infinium-II probes with PWK_PhJ strain-specific SNP hitting the extension base.
• ... more strains, e.g., AKR_J, A_J, NOD_ShiLtJ, MOLF_EiJ, 129P2_OlaHsd ...