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Table 4 ACCORD Illumina Omni1-Quad Statistical Genotype QC Analysis Results

From: Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage

Step Samples Remaining SNPs Remaining Dropped (% of Remaining)
Post-Laboratory QC 32 1,140,419
(inc CNV probes)
 
Remove CNV probes
(not analyzed)
  1,048,713 91,706
Drop SNPs with 100% missing data 32 1,015,235 33,478
(3.3%)
Drop samples with > 1% missing data 32 1,015,235 0
(0%)
Total 32 1,015,235  
QC Statistic N Value Comments
Mean per sample Genotype Missing Rate (range; sem) 32 0.20%
(0.07-0.62%; 0.024%)
For all SNPs
   0.21%
(0.07-0.64%; 0.025%)
SNPs with < 100% missing genotypes
Median per sample Genotype Missing Rate 32 0.16%  
Mean per SNP Genotype Missing Rate
(range; sem)
1,015,235 0.21%
(0-37.5%; 0.0012%)
32 Samples
Median per SNP Genotype Missing Rate 1,015,235 0% 32 Samples
  1. The upper part of the table shows the samples and SNPs that were dropped at each step of the Statistical Genotype QC analysis and the total number remaining. The lower part of the table summarizes values of the key QC statistics in the samples and SNPs remaining after the QC steps.