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Quality control of TaqMan genotyping results included: thresholds for maximum individual missingness for each of the SNPs < 0.05, maximum genotype missingness for each of the individuals < 0.05 and the Hardy-Weinberg disequilibrium < 0.001 for the control group.
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For quality control, the genotype missingness frequency (GENO) was set to GENO <0.05 and the minor allele frequency (MAF) to MAF >0.05 when we selected SNPs from the DDD study.
Briefly, a total of 221 subjects and 83,423 markers were excluded for quality control reasons, including identity-by-descent, gender mismatches, genotype missingness, Hardy-Weinberg disequilibrium in controls, and low minor allele frequency.
Fourth, the maximum genotype distance between viable metabolic networks is almost as large as the diameter of genotype space itself, that is, to the maximum distance among all genotypes, regardless of their viability.
Morphological differences among P. maximum genotypes did not interfere in biomass accumulation.
From the sample of 2883 individuals, 4 had missing phenotypic information and 5 were removed for low genotyping (maximum SNP missingness rate >0.1).
Thresholds were set to exclude minor allele frequencies <.01, maximum minor allele frequencies of 1.0, maximum SNP missingness rate of 0.1 and maximum individual missingness rate of 0.1.
The maximum intra-genotype divergence in old genotypes was 7% (genotypes I and IV) whereas the maximum intra-genotype divergence in recent genotypes was 9% (genotype VIII).
The maximum amount of missingness in any one variable was 72%.
Also, the variable with the maximum amount of missingness had more than 10% of its values missing in over half of the 70 articles, where this was ascertained (36 articles).
must first be specified in order to conduct genotype-phenotype or MR analyses and to consider genotype-dependent missingness (scheme in Figure 4).
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