Table 2.
Comparison of 2SNV and PredictHaplo on Full and Subsampled Data
| Clones | Clone 1 | Clone 2 | Clone 3 | Clone 4 | Clone 5 | Clone 6 | Clone 7 | Clone 8 | Clone 9 | Clone 10 | FP | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of reads | Method | True frequency, % | 50 | 25 | 12.5 | 6.25 | 3.125 | 1.56 | 0.78 | 0.39 | 0.19 | 0.097 | 0 |
| 33.5K (all) | 2SNV | Match | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | × | 1 |
| Frequency (%) | 51.8 | 23.7 | 12.5 | 6.4 | 2.3 | 1.2 | 0.7 | 0.3 | 0.1 | 0 | 1.0 | ||
| PH | Match | ✓ | ✓ | ✓ | × | ✓ | × | ✓ | ✓ | × | × | 0 | |
| Frequency (%) | 56.7 | 23.8 | 13.7 | 0 | 3.1 | 0 | 1.5 | 1.2 | 0 | 0 | 0 | ||
| 16K | 2SNV | Match (%) | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 0 | 0 | 0.2 |
| Frequency (%) | 52.4 | 23.7 | 12.5 | 6.4 | 2.3 | 1.1 | 0.7 | 0.3 | 0 | 0 | 0.6 | ||
| PH | Match | 100 | 100 | 100 | 70 | 100 | 0 | 100 | 40 | 0 | 0 | 0.3 | |
| Frequency (%) | 54.2 | 23.5 | 13.1 | 6.0 | 2.9 | 0 | 1.4 | 1.0 | 0 | 0 | 0.5 | ||
| 8K | 2SNV | Match (%) | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 0 | 0 | 0 | 0 |
| Frequency (%) | 53.1 | 23.7 | 12.5 | 6.5 | 2.3 | 1.25 | 0.7 | 0 | 0 | 0 | 0 | ||
| PH | Match (%) | 100 | 100 | 100 | 0 | 100 | 0 | 100 | 20 | 0 | 0 | 0.2 | |
| Frequency (%) | 58.1 | 24.0 | 12.7 | 0 | 3.1 | 0 | 1.6 | 1.3 | 0 | 0 | 0.5 | ||
| 4K | 2SNV | Match (%) | 100 | 100 | 100 | 100 | 100 | 100 | 20 | 0 | 0 | 0 | 0 |
| Frequency (%) | 53.7 | 23.7 | 12.3 | 6.5 | 2.4 | 1.2 | 0.9 | 0 | 0 | 0 | 0 | ||
| PH | Match (%) | 100 | 100 | 100 | 0 | 70 | 0 | 10 | 0 | 0 | 0 | 0.3 | |
| Frequency (%) | 60.1 | 23.9 | 12.8 | 0 | 3.5 | 0 | 2.5 | 0 | 0 | 0 | 0.5 | ||
| 2K | 2SNV | Match (%) | 100 | 100 | 100 | 100 | 100 | 0 | 0 | 0 | 0 | 0 | 0 |
| Frequency (%) | 55.2 | 23.4 | 12.5 | 6.9 | 2.0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| PH | Match (%) | 100 | 100 | 90 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.3 | |
| Frequency (%) | 60.4 | 24.3 | 15.6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.4 | ||
| 1K | 2SNV | Match (%) | 100 | 100 | 100 | 100 | 10 | 0 | 0 | 0 | 0 | 0 | 0 |
| Frequency (%) | 56.7 | 23.7 | 12.7 | 6.6 | 3.2 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| PH | Match (%) | 90 | 90 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.1 | |
| Frequency (%) | 72.8 | 26.8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.4 | ||
| 0.5K | 2SNV | Match (%) | 100 | 100 | 100 | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Frequency (%) | 62.0 | 23.7 | 12.8 | 7.6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| PH | Match (%) | 50* | 50* | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Frequency (%) | 69.9 | 30.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
For all 33.5K reads, the sign “✓” (respectively, “ × ”) denotes fully matched (respectively, unmatched) true variant and the column FP reports the number of incorrectly predicted variants (false positives) and their total frequency. For each subsample size (16K, …, 0.5K), the table reports the percent of runs when a variant is completely matched and its average frequency. Similarly, the column FP reports the average number of false-positive variants and their average total frequency.