Table 2.
Single-nucleotide error rate comparison of prophage detection programs
| Program | True positive (bp)a | False positive (bp)b | True negative (bp)c | False negative (bp)d |
|---|---|---|---|---|
| PhageBoost | 628256 | 240902 | 44072113 | 896160 |
| VirSorter2 + CheckV | 1391420 | 908285 | 43404730 | 132996 |
| PHASTER | 1382161 | 253163 | 44059852 | 142255 |
| DEPhT (fast) | 1524416 | 864719 | 43320915 | 0 |
| DEPhT (normal) | 1524415 | 156 | 44312859 | 1 |
aTrue positive values are determined as the number of nucleotides in each prophage prediction that are within a manually validated prophage.
bFalse positive values are determined as the number of nucleotides in each prophage prediction that are not within a manually validated prophage.
cTrue negative values are determined as the number of nucleotides that are not within a manually validated prophage and are not part of a prophage prediction.
dFalse negative values are determined as the number of nucleotides that are within a manually validated prophage, and are not part of a prophage prediction.