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Table 2 Comparisons of observed and expected proportions of SNVs whose risk alleles were minor alleles in myopia

From: Are minor alleles more likely to be risk alleles?

MAF interval SNVs whose risk alleles were minor alleles SNVs whose risk alleles were major alleles Observed proportiona Statistical power of detecting minor alleles Statistical power of detecting major alleles Expected proportionb P-valuec (Original) P-valued (Considering the GWAS’s power imbalance) Lower limite (Considering the GWAS’s power imbalance) Upper limite (Considering the GWAS’s power imbalance)
(0, 0.1) 18 0 1.0 0.002 0.001 0.67 0.0000076*f 0.0015 *f 0.81 1.00
(0.1, 0.2) 3 3 0.5 0.100 0.059 0.63 1.00 0.68 0.11 0.88
(0.2, 0.3) 2 2 0.5 0.330 0.248 0.57 1.00 0.66 0.05 0.85
(0.3, 0.4) 0 2 0 0.507 0.444 0.53 0.50 0.22 0.00 0.84
(0.4, 0.5) 0 1 0 0.579 0.558 0.51 1.00 0.49 0.00 0.975
  1. The parameters for the statistical power calculation were chosen according to Meng et al. [18]: Cases = 190, controls = 1064, significance level = 5.0E-08, prevalence = 0.25, genotype relative risk = 1.60
  2. aProportion of SNVs whose risk alleles were minor alleles
  3. bExpected proportion of SNVs whose risk alleles were minor alleles (Considering the GWAS’s power imbalance)
  4. cP-value for the binomial test with the null hypothesis that the observed proportion is 0.5
  5. dP-value for the binomial test with the null hypothesis that the observed proportion is the expected proportion
  6. eLower and upper limits of the 95% confidence interval for the proportion by the Clopper–Pearson method with the null hypothesis that the observed proportion is the expected proportion
  7. f*P-value ≤0.01