Table 4.
Predicted prophages identified in genome projects
| GenomeIDa | SRA | PATRIC speciesb | #contigs | %GCc | Size (Mbp)d | # Prophagese | Prophage contig matchf |
|---|---|---|---|---|---|---|---|
| 1733.4750 | ERR2514035 | M. tuberculosis | 1047 | 55.0 | 8.03 | 1 | Enterococcus casseliflavus |
| 1733.8175 | ERR2517475 | M. tuberculosis | 11,273 | 59.1 | 13.1 | 1 | M. abscessus |
| 1733.8957 | SRR5709926 | M. tuberculosis | 2074 | 67.2 | 11.5 | 2 | Actinomycetales |
| 1733.10987 | SRR6153015 | M. tuberculosis | 1025 | 53.2 | 8.99 | 1 | Clostridium; Bacillus ssp. |
| 1765.193 | n/a | M. bovis | 576 | 59.4 | 11.95 | 1 | Bacillus ssp. |
| 1773.5318 | SRR2101661 | M. tuberculosis | 635 | 21.1 | 5.29 | 1 | Bacillus licheniformis |
| 1773.13291 | n/a | M. tuberculosis | 650 | 67.3 | 10.38 | 1 | M. avium |
| 1773.13467 | n/a | M. tuberculosis | 1683 | 53.3 | 6.99 | 1 | Staphylococcus epidermitis |
| 1773.13508 | n/a | M. tuberculosis | 2572 | 53.6 | 7.31 | 1 | Staphylococcus epidermitis |
| 1773.13517 | n/a | M. tuberculosis | 5330 | 52.5 | 7.39 | 1 | Staphylococcus epidermitis |
| 1773.14094 | n/a | M. tuberculosis | 1025 | 53.2 | 8.99 | 1 | Clostridium; Bacillus ssp. |
| 1773.14969 | SRR6397654 | M. tuberculosis | 390 | 67.3 | 10.35 | 1 | M. avium |
| 1773.15146 | SRR6397396 | M. tuberculosis | 330 | 53.4 | 6.86 | 1 | Staphylococcus epidermitis |
| 1773.15187 | SRR6397568 | M. tuberculosis | 334 | 53.4 | 6.86 | 1 | Staphylococcus epidermitis |
| 1773.15196 | SRR6397721 | M. tuberculosis | 363 | 53.2 | 6.92 | 1 | Staphylococcus epidermitis |
| 1773.15773 | SRR6153015 | M. tuberculosis | 308 | 53.2 | 8.89 | 1 | Clostridium; Bacillus ssp. |
| 1773.17698 | ERR751414 | M. tuberculosis | 167 | 58.6 | 8.40 | 1 | Morganella morganii |
| 1773.18195 | ERR1873557 | M. tuberculosis | 199 | 62.3 | 10.36 | 1 | Pseudomonas ssp. |
| 1773.18223 | ERR1873445 | M. tuberculosis | 214 | 62.2 | 10.34 | 1 | Pseudomonas ssp. |
| 1773.18344 | ERR1035327 | M. tuberculosis | 177 | 56.2 | 6.26 | 1 | Lactobacillus |
| 1773.18754 | ERR036242 | M. tuberculosis | 385 | 59.2 | 9.62 | 2 | Paenibacillus |
| 1773.18812 | ERR037510 | M. tuberculosis | 1051 | 50.5 | 8.78 | 1 | Clostridium |
| 1773.19498 | ERR181684 | M. tuberculosis | 87 | 65.7 | 4.42 | 1* | M. tuberculosis |
| 1773.20520 | ERR1035082 | M. tuberculosis | 746 | 50.3 | 9.44 | 1 | Bacillus ssp. |
| 1773.25614 | n/a | M. tuberculosis | 1 | 65.6 | 4.46 | 1** | M. tuberculosis |
aPATRIC GenomeID.
bSpecies designated in PATRIC.
cAverage GC% M. tuberculosis GC% is 65.52 ± 0.39%, and values outside this suggest non-M. tuberculosis or mixed assemblies.
dAverage M. tuberculosis genome size is 4.41± 0.4 Mb. Projects outside this likely reflect mixed assemblies.
eNumber of prophages predicted using DEPhT in fast mode. *, phage virion DNA, probably not M. tuberculosis; **, scrambled prophage in phage resistant mutant.
fClosest genome(s) to prophage-containing contig by BLASTN.