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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.