Table 1 Number of variants and filters applied to them for various analysis
From: Exome-wide survey of the Siberian Caucasian population
Analysis | Number of variants | Filters |
|---|---|---|
PCA | 5948 | LD < 0.3, only autosomes, MAF = 0.05, LD window = 100kbp |
ADMIXTURE | 55,669 | LD < 0.2, only autosomes, LD window = 50kbp |
Fst (smartpca) | 65,436 | only autosomes, MAF = 0.05 |
Allele frequency difference | 117,010 (SNV) 5989(INDEL) | PLINK: --assoc fisher-midp mperm = 1,000,000 |