Specificity as a function of total paired-end read counts at different coverage thresholds for the sets of 48 multiplexed samples. Coverage has little impact on specificity, which starts at ≥99.8% for most individuals with >1.25 million reads. Specificity is defined as the percentage of homozygous wild type genotypes as seen by the array called correctly as homozygous wild type by sequencing. Red symbols: ≥3x coverage. Green symbols: ≥5x coverage. Blue symbols: ≥10x coverage. Brown symbols: ≥15x coverage. Black symbols: ≥20x coverage. Trend lines were generated using the “lowess” function in R with default parameters. The dip in specificity at around 2.25 million reads is likely due to noise as a single extra false positive can cause the observed shift downward. PE = paired-end.