Table 1.
Performance over 50 down-sampling experiments at 10X, and 20X coverage
|
Coverage |
10x |
20x |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Params | "c5 e5" | "c7 e5" | "c5 e7" | "c3 e5" | "c5 e3" | "c5 e5" | "c7 e5" | "c5 e7" | "c3 e5" | "c5 e3" |
| TP |
210 |
182 |
187 |
217 |
210 |
234 |
239 |
228 |
237 |
236 |
| FP |
25 |
0 |
7 |
55 |
302 |
1 |
0 |
1 |
3 |
46 |
| FN |
40 |
68 |
63 |
40 |
38 |
16 |
11 |
22 |
13 |
14 |
| Sensitivity |
84.00% |
72.80% |
74.80% |
86.80% |
84.00% |
93.60% |
95.60% |
91.20% |
94.80% |
94.40% |
| PPV | 89.36% | 100.00% | 96.39% | 79.78% | 41.02% | 99.57% | 100.00% | 99.56% | 98.75% | 83.69% |
True Positive (TP) False Positive (FP) False Negative (FN) counts, Sensitivity, and Positive Predictive Value (PPV). PPV is the probability any given variant call is true (TP/(TP+FP)). Parameters changed are Coverage (c) and Standard-deviation Threshold (e) for spots signal processing.