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Table 4 Sequencing coverage and read-mapping quality features for true-positive and false-positive predictions

From: A simple consensus approach improves somatic mutation prediction accuracy

Feature All TPsa All FPsb DNVc Germlined
Median read depth     
 Germline 105 25h 28h 12g
 Tumor 94 20h 21g 19g
Mean non-reference allele frequency     
 Germline 0.08% 1.4%g 1.27%g 1.77%g
 Tumor 43.10% 30.9%h 27.3%h 39.80%
Mean percentage uniquely mapped reads 97.10% 85.3%f 83.7%f 89.30%
Fraction of SNVs with <95% reads mapping uniquely 8.3% (19/229) 52.2%h (71/136) 57.7%h (56/97) 38.4%f (15/39)
Fraction of predicted SNVs with >5% of reads mate-rescued 4.4% (10/229) 39.7%h (54/136) 46.3%h (45/97) 23.1%e (9/39)
Mean percentage of reads mapped to multiple locations 1.90% 4.7%e 4.40% 5.5%f
  1. Abbreviations: DNV, Did not validate; FP, false positive; J, JointSNVMix2; JS, JointSNVMix2 + SomaticSniper; M, MuTect, MJ, MuTect + JointSNVMix2; MJS, MuTect + JointSNVMix2; + SomaticSniper; MS, MuTect + SomaticSniper; NRAF, non-reference allele frequency; S, SomaticSniper; SNV, single nucleotide variant.; TP, true positive.
  2. a'Includes all SNVs that validated in the tumor sample.
  3. bCombined value for these two categories of FPs.
  4. c Indicates SNVs that were not confirmed in the tumor sample.
  5. dIndicates SNVs that were also detected in the matched germline.
  6. Significance was tested using Wilcoxon rank-sum test for continuous variables and Fisher’s exact test for fraction of reads mapping uniquely/by mate-pair rescue/to multiple locations: :eP<0.05; fP<1 × 10-5; gP<1 × 10-10;,,hP<1 × 10-15.