Table 4.
Sequencing coverage and read-mapping quality features for true-positive and false-positive predictions
| Feature | All TPs a | All FPs b | DNV c | Germline d |
|---|---|---|---|---|
| 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 |
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.
a'Includes all SNVs that validated in the tumor sample.
bCombined value for these two categories of FPs.
c Indicates SNVs that were not confirmed in the tumor sample.
dIndicates SNVs that were also detected in the matched germline.
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.