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Number and percentage of SNPs excluded in quality control
| Criterion | HD (SNPs) | HD (%) | 50 k (SNPs) | 50 k (%) |
|---|---|---|---|---|
| Location* |
42,669 |
5.5 |
1,723 |
3.2 |
| Call rate |
104,602 |
13.4 |
9,253 |
16.9 |
| MAF |
173,564 |
22.3 |
13,728 |
25.1 |
| HWE |
20,529 |
2.6 |
16,740 |
3.1 |
| Total | 341,374 | 43.9 | 26,378 | 48.3 |
*The criterion location excluded SNPs without coordinated genomic known and not located in autosomal chromosomes.
