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Finally, all arrays demonstrated a sample call rate >92% (average call rate of 99.75%).
Additionally, based on control samples that were run on each plate, pairwise concordances between technical replicates yielded >99% average pairwise concordance and >92% average call rate.
The average call rate for all samples was 97.18%.
The average call rate in the remaining samples was 99.4%.
The average call rate for stage II genotyping was 99.8%.
The average call rate per sample was >98%, whereas the average call rate per SNP was >95%.
An average call rate of 98.6% (range 97.2% to 98.9%) was observed.
The average call rate for both PLCO and NHS samples was 99.8%.
All SNPs showed high genotyping quality with an average call rate of 98.5%.
For the remaining 808,465 autosomal SNPs, the average call rate was 99.5%.
All sample call rates were greater than 0.95, and the average call rate of the sample was 0.993 (SD = 0.005).
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