Table 4 Precision and recall values of PSE-HMM are compared to m-HMM, Pindel, CNV-seq, and Delly
| Â | Coverage | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
1× | 5× | 10× | ||||||||
Precision mean/std | Recall mean/std | F-measure | Precision mean/std | Recall mean/std | F-measure | Precision mean/std | Recall mean/std | F-measure | ||
Duplications | PSE-HMM | 0.91/0.03 | 0.79/0.02 | 0.85 | 0.92/0.02 | 0.95/0.01 | 0.93 | 0.88/0.01 | 0.97/0.02 | 0.92 |
m-HMM | 0.95/0.01 | 0.21/0.02 | 0.35 | 1.00/0.02 | 0.64/0.02 | 0.78 | 1.00/0.01 | 0.71/0.01 | 0.83 | |
Pindel | 1.00/0.00 | 0.11/0.04 | 0.20 | 1.00/0.00 | 0.67/0.03 | 0.80 | 1.00/0.01 | 0.81/0.03 | 0.90 | |
CNV-seq | 0.55/0.03 | 0.41/0.03 | 0.47 | 0.98/0.00 | 0.54/0.03 | 0.70 | 0.99/0.00 | 0.57/0.03 | 0.72 | |
Delly | 1.00/0.00 | 0.80/0.05 | 0.89 | 1.00/0.00 | 0.99/0.05 | 0.99 | 1.00/0.00 | 1.00/0.00 | 1.00 | |
Deletions | PSE-HMM (heterozygous) | 0.43/0.03 | 0.37/0.03 | 0.40 | 0.54/0.04 | 0.97/0.01 | 0.69 | 0.60/0.02 | 1.00/0.02 | 0.75 |
PSE-HMM (homozygous) | 0.20/0.03 | 0.92/0.05 | 0.33 | 0.73/0.03 | 0.97/0.02 | 0.83 | 0.81/0.02 | 0.93/0.03 | 0.87 | |
PSE-HMM (hetero + homo)a | 0.31/0.03 | 0.86/0.02 | 0.46 | 0.63/0.02 | 0.99/0.01 | 0.77 | 0.72/0.03 | 1.00/0.03 | 0.84 | |
m-HMM (heterozygous) | 0.67/0.02 | 0.16/0.04 | 0.25 | 0.93/0.03 | 0.88/0.03 | 0.91 | 0.93/0.03 | 0.92/0.02 | 0.93 | |
m-HMM (homozygous) | 0.95/0.02 | 0.65/0.02 | 0.77 | 0.99/0.02 | 0.62/0.02 | 0.77 | 0.99/0.01 | 0.62/0.03 | 0.77 | |
m-HMM (hetero + homo)a | 0.93/0.02 | 0.43/0.03 | 0.59 | 0.99/0.01 | 0.78/0.02 | 0.87 | 0.99/0.02 | 0.80/0.03 | 0.88 | |
Pindel | 0.93/0.15 | 0.02/0.01 | 0.04 | 0.91/0.03 | 0.36/0.02 | 0.52 | 0.87/0.06 | 0.45/0.05 | 0.59 | |
CNV-seq | 0.72/0.05 | 0.75/0.02 | 0.73 | 0.98/0.00 | 0.91/0.01 | 0.94 | 0.98/0.00 | 0.95/0.01 | 0.96 | |
Delly | 0.98/0.00 | 0.32/0.04 | 0.48 | 0.99/0.00 | 0.48/0.03 | 0.65 | 0.99/0.00 | 0.49/0.04 | 0.66 | |
Diploid | PSE-HMM | 0.96/0.00 | 0.79/0.01 | 0.87 | 0.99/0.00 | 0.93/0.00 | 0.96 | 1.00/0.00 | 0.96/0.00 | 0.98 |
m-HMM | 0.87/0.01 | 1.00/0.01 | 0.93 | 0.94/0.00 | 1.00/0.00 | 0.97 | 0.95/0.00 | 1.00/0.00 | 0.97 | |
Pindel | 0.82/0.01 | 1.00/0.00 | 0.90 | 0.90/0.01 | 1.00/0.00 | 0.95 | 0.93/0.01 | 1.00/0.00 | 0.96 | |
CNV-seq | 0.91/0.00 | 0.93/0.00 | 0.92 | 0.94/0.00 | 1.00/0.00 | 0.97 | 0.95/0.00 | 1.00/0.00 | 0.97 | |
Delly | 0.91/0.01 | 1.00/0.00 | 0.95 | 0.94/0.01 | 1.00/0.00 | 0.97 | 0.94/0.01 | 1.00/0.00 | 0.97 | |