Sentence examples for missing genotype rates from inspiring English sources

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).

These maps had missing genotype rates of 1.9% (FTC) and 1.8% (BEPA).

The initial step of analysis is to perform a rigorous quality control procedure: high missing genotype rates (both per individual and per SNP) and deviations from Hardy-Weinberg genotype proportions are indicative of problems.

Among standard QC measures are the exclusion of single nucleotide polymorphisms (SNPs) with low call rates (e.g. <95%) and minor allele frequencies (e.g. <1%), excluding loci due to departures from Hardy-Weinberg equilibrium (HWE) and excluding samples with high missing genotype rates.

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

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.

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.

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.

Among 105 individuals, 3 were excluded because of low genotype rate (missing genotype rate > 10% per person).

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%.