Sentence examples for missing genotype rate from inspiring English sources

Similarly, 60,869 SNPs with missing genotype rate >5% and 10,889 SNPs with MAF<0.01 were excluded.

Multidimensional scaling (MDS) analysis used a total of 1317 SNP following removal of loci with missing genotype rate of >0.1 or MAF <0.01.

For genetic association studies, we required that each SNP have a missing genotype rate <10% and, in controls, have a Hardy-Weinberg p-value >0.001.

Missing genotype rate is 0.12% and typing error rate (as reflected by Mendelian inconsistency) is 0.11%.

Samples with a missing genotype rate of more than 5% (mothers) or 3% (children) were removed.

QC is applied as a sample missing genotype rate of > 3%, a SNP missing genotype rate of > 1%, Hardy-Weinberg Equilibrium (HWE) p-value ≤ 10-4, and minor allele frequency (MAF) < 1%.

All of the successfully resolved pedigrees were genotyped in the first sequencing run (164 SNP loci compared) despite this run having higher missing genotype rates (Table  2).

Ignoring the genotyping error rate and missing genotype ratio while simulating genotypes resulted in overestimating the assignment power, such that 78.1% and 75.8% of individuals were assigned at 14 markers, respectively, while only 67.0% were assigned when these empirical error rates were included in the simulations.

Missing genotype data rate was not significantly different between cases and controls.

Our quality control criteria are as follows: samples (i) with missing genotype call rate (>4%), (ii) with excessive heterozygosity (>30%), (iii) with gender inconsistencies, and (iv) from subject with cancer; SNPs with (i) missing genotype call rate (>5%), (ii) low MAF (<0.01), and (iii) Hardy-Weinberg equilibrium (P < 1 × 10−6) were excluded.

In addition, 28,445 markers with low genotype rate (missing genotype per SNP > 10%), 18,744 SNPs with < 1% minor allele frequency (MAF < 0.01), and 4,840 SNPs with Hardy-Weinberg departure (p < 0.001) along with the X chromosome were also excluded.