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Table 2 Improved mutation calling in higher coverage.

From: Virmid: accurate detection of somatic mutations with sample impurity inference

αa n.Answerb Coverage = 40 × Coverage = 100 ×
   n.Predictc n.Correctd Precision Recall F-score n.Predictc n.Correctd Precision Recall F-score
70%   1999 1976 0.98 0.87 0.93 2208 2198 1.00e 0.97 0.98
80% 2265 1551 1516 0.98 0.67 0.79 2142 2133 1.00f 0.94 0.97
90%   638 611 0.96 0.27 0.42 1572 1545 0.98 0.68 0.81
  1. Precision and recall values are compared between two different coverages (40 × and 100 ×) at highly contaminated data (α = 70%, 80%, and 90%). Much deeper coverage is required when severe contamination is expected.
  2. aα is the proportion of the control sample in the disease sample (contamination level).
  3. bn.Answer is the number of true somatic mutations.
  4. cn.Predict is the number of mutations predicted by Virmid.
  5. dn.Correct is the number of correct mutations in the prediction.
  6. eRounded up from 0.9954.
  7. fRounded up from 0.9958.