We estimated LD decay based on the coefficient of determination (r2) between any two loci using PopLDdecay (https://github.com/BGI-shenzhen/PopLDdecay). Tajima’sD,Fst, andθπwere calculated from sample allele frequency likelihoods in ANGSD over non-overlapping 2-kb windows. A summary of ...
Genotype data was imported into PLINK for quality control filtering. Variants with a call rate below 95% across samples, a minor allele frequency (MAF) < 0.01, or with significant deviation from Hardy–Weinberg equilibrium (HWE,pvalue < 1 × 10–6) were excluded prior to imputa...
SNP markers with a minor allele frequency (MAF) smaller than 0.01 and a missing percentage greater than 10% were removed. PCA was conducted in TASSEL v5.2.26 [39]. The software automatically converted the genotype data to numeric scores, and the missing data were imputed with the average sco...
by calculating the pairwise square correlation coefficientr2VS[33], correcting for the structure and kinship of the sample. Only sequence polymorphisms with less than 20% missing data and with a 0.2 minor allele frequency were analysed
Covariates were generated with a minor allele frequency of approximately 0.3, and, within any LD block, correlation between SNPs was again approximately 0.65, whereas SNPs not in the LD block were independent of one another. We assumed Hardy-Weinberg equilibrium. The gene consisted of 20 SNPs, ...
Of the SNPs tested, 29% were found to be polymorphic with a minor allele frequency >10%. A subset of the SNPs was genotyped through animal resources in order to look for association with age of puberty, facial eczema resistance or meat yield. Three SNPs were nominally associated with ...
conducting 10 repetitions at each K value. Admixture will use 16 processors for execution during each repetition, VCFtools will filter SNPs at an interval of 100bp, and the minor allele frequency filter in VCFtools will drop any loci with a minor allele frequency less than 0.05. Any individuals...
We used genome-wide association data from up to 11 685 participants with measures of circulating LDL-cholesterol concentrations across five studies, including data for 293 461 autosomal single nucleotide polymorphisms (SNPs) with a minor allele frequency of 5% or more that passed our quality ...
aMinor allele frequency (MAF) ofMLKL p.Ser132Proaccording to the gnomAD database, stratified by ancestry.bSequence alignment of conserved serine in the MLKL orthologs across different species.cMLKLWT,MLKLS132PandMLKLTSEEexpression was induced inMLKL−/−HT29 cells with 100 ng/ml doxycycline...
In each of the participating studies, genotype data were imputed using the 1000 Genomes Project reference panel (1KG; Phase 3) and filtered for a minor allele frequency (MAF) ≥ 0.5% and imputation quality score ≥0.3, retaining 11.8 million variants. Association testing was conducted on ...