Figure 2From: RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencingMeasuring sensitivity, specificity, and Matthews correlation coefficient (MCC) for optimal choice of resolution threshold and base quality threshold. Analysis was done averaging sensitivity, specificity, and MCC across three 0.1% synthetic mixture DNA replicates sequenced on a GAIIx platform. (A) With a base quality threshold of 30, the specificity increases slightly from 0.999 to 1 as the resolution threshold is increased from 0.01% to 0.1%. More drastically, the sensitivity decreases at a threshold greater than 0.05% from near 1 to 0.857 at 0.1%. The MCC statistic that combines these two measures and adjusts for unequal distribution of true positives and true negatives peaks a range of 0.02% - 0.07%, indicating an optimal resolution threshold. (B) As the base quality threshold is increased from 0 to 30, RVD sensitivity becomes less dependent on resolution threshold. Thus, a higher base quality threshold may improve resolution of the algorithm.Back to article page