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Table 1 Summary of the probes which are identified as having hybridization problems due to multimapping, SNPs, repeats, INDELs and unknown factors (note: some probes may belong to more than one category)

From: Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

  Infinium I Infinium II Total
Total number of probes on array 135,476 350,036 485,512
Probes which map to multiple genomic locations 5,971 13,863 19,834
Probes containing only known INDELs 1,935 4,348 6,283
Probes containing known repeat regions 8,438 30,305 38,743
Probes which have a SNP/INDEL at interrogated CpG 12,746 57,372 70,118
Probes containing known SNPs 52,175 117,342 169,517
Probes affected by unknown factors# 1,394 13,840 15,440
Total number of high-quality probes on array 52,817 119,770 172,587
Total number of potentially ‘noisy’ probes 82,659 230,266 312,925
  1. # ’Probes affected by unknown factors’ are considered as probes which have absolute beta difference between WGBS and HM450K bead array greater than 0.3.