Fig. 5
Boxplots of O n (average log odds of being an outlier across the 65 SNP probes) as a measure of low technical performance for samples flagged by any of the 17 Illumina control metrics and samples passing all of them. Metrics are ordered by median O n with the number of samples in each non-exclusive category indicated on the right. Flagged samples have in general higher values of O n than samples that passed all checks, indicating that flagged samples are more likely to have poor performance characteristics