Table 2 SNP-heritability of severe malaria susceptibility/resistance in Gambian population at different basic quality threshold using MLM
Population | Sample relatedness-threshold | SNP missingness-proportion | SNP differential-missingness Proportion | Prevalence | Covariate principal-components | No. Samples | No. SNPs | GCTA h2(% SE) | PCGC h2( SE) |
|---|---|---|---|---|---|---|---|---|---|
Gambia | – | 5% | – | 1% | 10 | 4920 | 1627656 | 37.8(.05). |  |
|  | 5% | 5% | 1 × 10−10 | 1% | 10 | 4128 | 1627656 | 30.5(.05) |  |
|  | 5% | 5% | 1x10− 5 | 1% | 10 | 4128 | 1607610 | 28.7(.05) |  |
|  | 5% | 5% | 1 × 10−3 | 1% | 10 | 4128 | 1570344 | 25.1(.05) |  |
|  | 5% | 2% | 1 × 10− 3 | 1% | 10 | 4128 | 1486554 | 20.1(.05) | 19.8(.07) |
|  | 5% | 2% | 1 × 10−3 | 1% | 15 | 4128 | 1486554 | 22.5(.05) |  |
|  | 5% | 2% | 1x10−3 | 1% | 20 | 4128 | 1486554 | 19.5(.05) |  |
|  | Phased | – | – | 1% | 10 | 4128 | 1627656 | 20.4(.06) |  |
Mandinka | 5% | 2% | 1x10−3 | 1% | 10 | 1281 | 1486554 | 24.2(0.6) |  |