Table 1 Description of scenarios of pre-imputation SNP filtering: Note that datasets contain different numbers of SNPs
From: Impact of pre-imputation SNP-filtering on genotype imputation results
Data subset | Number of SNPs | Quality criteria for SNPs contained in the data subsets |
|---|---|---|
HQ | 4658 | high quality : criteria MAF ≥ 0.1, CR = 1 and p(HWE) ≥ 10− 2 |
NQ | 7923 | Normal quality : MAF ≥ 0.01, CR ≥ 0.95 and p(HWE) ≥ 10− 6 |
LQ | 8472 | low quality: MAF ≥ 0.005, CR ≥ 0.5, p(HWE) ≥ 10− 2 |
NQ.MAF | 8310 | MAF ≥ 0.01 |
NQ.HWE | 9547 | p(HWE) ≥ 10− 6 |
NQ.CAR | 9194 | CR ≥ 0.95 |
HQ.MAF | 6344 | MAF ≥ 0.1 |
HQ.HWE | 9450 | p(HWE) ≥ 10− 2 |
HQ.CAR | 7148 | CR = 1 |
NQ.MAF.HWE | 8255 | MAF ≥ 0.01, p(HWE) ≥ 10− 6 |
HQ.MAF.HWE | 6261 | MAF ≥ 0.1, p(HWE) ≥ 10− 2 |
LQ.MAF | 8520 | MAF ≥ 0.005 |
LQ.HWE | 9574 | p(HWE) ≥ 10− 12 |
LQ.MAF.HWE | 8492 | MAF ≥ 0.005, p(HWE) ≥ 10− 12 |
BQ | 6337 | This data subset contains SNPs which fail NQ criterion and HQ |
ALL | 9602 | This data subset contains all available SNPs. |