AF thresholds were determined using a high-resolution variant frequency framework and Hardy-Weinberg equilibrium calculation: 0.6% and 0.1% for recessive and dominant genes, respectively. Filtering AFs of variants linked to NSHL were obtained based on AFs reported in gnomAD and ExAC. We found that...
One of the most used values for filtering variants in a somatic mutation workflow is the Alternate Allele Frequency for each sample. This field is not always provided directly in the VCF data but don’t worry, VarSeq will automatically calculate the frequency using the provided allelic depth fiel...
SNPs with a frequency difference of more than 10% between the total (n = 1722) and the 2nd phase (n = 1099) data of KRGDB were excluded from the genetic score calculation. We used the average of composite genetic risk scores for the populations for correlation with the country-...
Genomic imprinting is an epigenetically regulated process wherein genes are expressed in a parent-of-origin specific manner. Many imprinted genes were initially identified in mice; some of these were subsequently shown not to be imprinted in humans. Such
The simulation was carried out using the Balding-Nichols model26, assuming a minor allele frequency of 0.3. For each setting, we predefined the risk for effective alleles of the causal SNPs by setting r = 1.15/1.2/1.3 as well as the level of population stratification between cohorts ...
calculated based on the SNP genotypes of each accession. The nucleotide diversity level,π, was calculated using the method mentioned above. Sliding 20-kb windows were used during the calculation with a 2-kb sliding step. ROD was computed using the formula, ROD=(πirrigated−πupland)/π...
However, the formula for var(WiZi) varies for different pedigree structures and can be very complicated; it also depends on the unknown frequency p of allele A. Instead, we choose to estimate var(WiZi) empirically. Since var(Zi)=1, if Wi were a constant, var(WiZi) would be W2i. This...
Next, the allele frequency of each site in the two control panels was calculated based on the genotypes of accessions, and ETASs for each elite variety were identified (Methods). In total, we identified 60,909 ETASs in the six elite varieties Guichao2 (2,598), IR64 (18,695), Minghui...