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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.
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BMC Genomic Data

ISSN: 2730-6844

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