Exact(3)
Quality control criteria included genotype call rate of >80%, less than 1 duplicate errors (5 duplicates in each 96 well-plate), and significant Hardy-Weinberg disequilibrium.
An amplicon contamination of amplified library DNA molecules from a previous sequencing run can also lead to duplicate reads in following runs, but these types of duplicate errors can normally be avoided by preventing cross-contamination of sequencing library samples.
The following exclusions were applied to identify a final set of 306 655 autosomal SNPs: call rate <97%, Hardy Weinberg equilibrium P < 10−5, more than two duplicate errors or Mendelian inconsistencies (for reference Centre d'Etude du Polymorphisme Humain trios), heterozygote frequency = 0 or SNP not found in HapMap.
Similar(57)
The genotyping error was estimated by genotyping 20%% of the samples in duplicate (error <1%%).
PD100Rint, EI was found reproducible with a duplicate error of 8.3% or 0.65 doubling doses (within 140 μg).
Estimation is based on comparison of duplicate error-prone genotypes: neither reference genotypes nor pedigree data are required.
Neurite outgrowth was performed in triplicate and each sample within an experiment was performed in duplicate (error bars indicate SD).
Experiments were performed in triplicate and each sample within an experiment was performed in duplicate (error bars indicate SD).
There were 574 successfully released STR markers with an overall duplicate error rate (3 CEPH sample duplicates on each of 18 plates) of 0.1% and an overall Mendelian error rate of 2% on 99.7% of samples.
SNPs that could not satisfy the following criteria were excluded: (i) a minimum call rate of 90%; (ii) no duplicate error; (iii) Hardy-Weinberg equilibrium greater than P > 0.001.
Neurite outgrowth was performed in triplicate and each sample within an experiment was performed in duplicate (error bars indicate SD) DOI: http://dx.doi.org/10.7554/eLife.09811.017 We further examined the role of the GR of ALK in FAM150A/B binding.
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