Table 2.
Thresholda | No. SNPb | Estimatec(SE) | LRd | p valuee |
---|---|---|---|---|
MAF > 0.01 | ||||
200 | 309,040 | 0.17 (0.11) | 2.29 | 0.07 |
20 | 297,198 | 0.13 (0.11) | 1.31 | 0.13 |
7 | 266,534 | 0.08 (0.11) | 0.59 | 0.22 |
4 | 226,165 | 0.06 (0.11) | 0.29 | 0.30 |
MAF > 0.05 | ||||
200 | 278,564 | 0.19 (0.11) | 3.42 | 0.03 |
20 | 267,043 | 0.16 (0.10) | 2.33 | 0.06 |
7 | 239,614 | 0.12 (0.10) | 1.33 | 0.12 |
4 | 203,698 | 0.09 (0.10) | 0.92 | 0.17 |
Excluding SNPs with more than the listed number of missing genotypes. Two hundred missing genotypes are approximately equal to a missingness rate of 5% (depending on sample size).
After filtering on the basis of SNP missing rate.
Estimate of genetic variance proportional to the total phenotypic variance on the observed scale.
Likelihood-ratio test statistic.
p values were calculated assuming that the LR is distributed as a 50:50 mixture of zero and under the null hypothesis.