NPM1-mutated AML samples that were correctly identified by the model (true positives) had a significantly higher median VAF than NPM1-mutated AML samples that were misclassified (false negatives) (true positives: 0.41 [95% CI: 0.39–0.42] vs. false negatives: 0.31 [95% CI: 0.1–0.42], p = 0.018, Fig. 5). The gene discussed is NPM1; the disease is acute myeloid leukemia.