Concordance in genotypes between replicates of the same subject within a genotyping platform and within a genotyping experiment.

<p>The averaged concordance values (the bars) and the corresponding standard deviations (the error bars) between replicates of a subject (coded by color as: blue for A, red for B, cyan for C, Magenta for D, Green for E, and Orange for F) genotyped in a genotyping experiment (indicated at x-axis) are plotted. The subject codes and the experiment ID for genotyping experiments are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044483#pone-0044483-t001" target="_blank">Table 1</a>.</p

Simulations results.

<p>Odds ratios were simulated for 50,000 times for each pair of a genotype concordance (from 0.94 to 1.00 with a step of 0.001) and a minor allele frequency (from 0.01 to 0.40 with a step of 0.01) by using a case population of 2,000 samples and a control sample size of 3,000 samples. Relationship between top 5% odds ratio of the 50,000 ones, concordance in genotypes, and minor allele frequency is depicted in <b>A</b>. The intersection curves at minor allele frequency values 0.05, 0.10, and 0.20 are shown in <b>B</b>.</p

Concordance in genotypes between replicates of the same subject genotyped by using different genotyping platforms.

<p>The averaged concordance values (the bars) and the corresponding standard deviations (the error bars) between replicates of a subject (coded by color as: blue for A, red for B, cyan for C, Magenta for D, Green for E, and Orange for F) genotyped by using different genotyping platforms (indicated at x-axis) are plotted. The subject codes and the experiment ID for genotyping experiments are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044483#pone-0044483-t001" target="_blank">Table 1</a>.</p