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Table 7 Comparing errors in estimation of allele frequencies by filtering off rare SNPs.

From: Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction

MAF cutoff SNPs Analysed Correlation MAD error 95% CI
1% 405478 (81%) 0.982 0.031 (0.0433-0.0435)
5% 355095 (70.94%) 0.976 0.032 (0.0449-0.0452)
10% 306552 (61.24%) 0.969 0.032 (0.0449-0.0452)
15% 260485 (52.04%) 0.961 0.031 (0.0439-0.0442)
20% 218147 (43.58%) 0.949 0.030 (0.0425-0.0428)
  1. Actual allele frequencies obtained from individual genotyping were compared with estimated allele frequencies from pooled genotyping at various minor allele frequency cutoffs.