Table 3. Accuracy of GINDEL trained by combination of different features.
Length | Gntps | D. C. | S. F. | R. | D. S. | D. C. R. | R. S. F. | D. C. S. F. | All |
50–75 | 294 | 0.8844 | 0.9218 | 0.7721 | 0.9252 | 0.8844 | 0.9082 | 0.9388 | 0.9592 |
75–100 | 294 | 0.8878 | 0.9728 | 0.8844 | 0.9490 | 0.9354 | 0.9728 | 0.9762 | 0.9796 |
100–150 | 238 | 0.8866 | 0.9958 | 0.8277 | 0.9454 | 0.9664 | 0.9874 | 1.0000 | 1.0000 |
150–200 | 154 | 0.9351 | 0.9610 | 0.9351 | 0.9870 | 0.9870 | 0.9545 | 0.9870 | 0.9870 |
200–300 | 224 | 0.9420 | 0.9200 | 0.8259 | 0.9464 | 0.9688 | 0.9375 | 0.9643 | 0.9688 |
300–400 | 420 | 0.9262 | 0.9333 | 0.8262 | 0.9381 | 0.9619 | 0.9405 | 0.9643 | 0.9667 |
400–500 | 182 | 0.9615 | 0.9670 | 0.8736 | 0.9560 | 1.0000 | 0.9780 | 1.0000 | 1.0000 |
500–800 | 140 | 0.9929 | 0.9714 | 0.9214 | 0.9929 | 1.0000 | 0.9714 | 1.0000 | 1.0000 |
800–1100 | 168 | 1.0000 | 0.9464 | 0.8929 | 1.0000 | 1.0000 | 0.9583 | 1.0000 | 1.0000 |
1100–1500 | 168 | 0.9702 | 0.9643 | 0.9226 | 0.9702 | 1.0000 | 0.9702 | 0.9940 | 1.0000 |
1500–2000 | 210 | 0.9714 | 0.9762 | 0.9476 | 0.9857 | 1.0000 | 0.9762 | 0.9952 | 0.9952 |
2000–4000 | 252 | 0.9762 | 0.9444 | 0.9246 | 0.9722 | 0.9960 | 0.9841 | 0.9881 | 0.9960 |
4000–9000 | 238 | 0.9748 | 0.9500 | 0.8277 | 0.9706 | 0.9748 | 0.9538 | 0.9832 | 0.9874 |
>9000 | 112 | 0.9821 | 0.9821 | 0.8660 | 0.9821 | 1.0000 | 0.9821 | 1.0000 | 1.0000 |
Results on the percentage of correctly called genotypes are given for deletions with different lengths. Gntps represents the total number of genotypes in specific length. D., C., S., F., and R. represents # of discordant read-pairs, # of concordant read-pairs, # of split-mapped reads, # of fully mapped reads, and read depth. All means using all the five features.