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Table 1 The level of inflation in the mean and median test statistics of the association tests

From: The effect of rare variants on inflation of the test statistics in case–control analyses

  All variants Variants < 20 heterozygotes Variants ≥ 20 heterozygotes
  λ at median λ at mean λ at median λ at mean λ at median λ at mean
LRT 1.905 (1.903-1.906) 1.172 (1.171-1.172) 3.047 (3.047-3.047) 1.270 (1.270-1.271) 0.992 (0.991-0.992) 1.002 (1.001-1.002)
Wald test 0.311 (0.310-0.311) 0.580 (0.580-0.580) 0.017 (0.017-0.017) 0.343 (0.343-0.343) 0.990 (0.989-0.991) 0.987 (0.987-0.988)
Score test 1.902 (1.900-1.904) 1.004 (1.004-1.004) 2.198 (2.198-2.198) 1.008 (1.008-1.009) 0.991 (0.990-0.992) 0.997 (0.996-0.997)
  1. The level of inflation in the test statistics of the likelihood ratio test, Wald test and score test measured at the median test statistic and the mean statistic. The inflation factor (λ) is calculated by comparing the observed test statistic to the expected test statistic at a given point in the χ2 distribution. Inflation was measured for datasets including all variants, only variants with less than 20 heterozygotes in the sample and only variants with at least 20 heterozygotes in the sample. Each value of λ was averaged across 1000 simulated datasets. All intervals are 95% confidence intervals. A normal level of inflation is indicated by λ = 1.