Treponema pallidum is a Gram-negative, spirochete bacterium of the family Treponemataceae, obligately parasitic and not cultivable on artificial media. Subspecies pallidum is the causative agent of syphilis, a sexually transmitted infection with multistage clinical manifestations that remains a major global public health concern. Genomically, T. pallidum has a highly reduced genome (~1.14 Mb) with minimal metabolic capacity, extensive reliance on host-derived nutrients, and remarkably low genetic diversity, though recombination at the tprK locus enables antigenic variation and immune evasion.
Derived from 571 genomes: 18 from RefSeq and 553 from other sources. For the derivation pipeline and the PASS / WARN / FAIL verdict model, see the methods page for qualibact-v1.0.
This table summarises the distribution of each metric, including standard deviation, mean, median, and percentiles.
A combined summary table across all species is available on the summary page.
| Metric | Distribution | n | Mean | SD | Min | Q1 | Median | Q3 | Max |
|---|---|---|---|---|---|---|---|---|---|
| N50 | non-normal | 553 | 193,558 | 167,156 | 4,818 | 98,374 | 170,676 | 173,295 | 599,061 |
| no_of_contigs | non-normal | 553 | 106.11 | 94.95 | 20 | 42 | 74 | 137 | 750 |
| longest | non-normal | 553 | 328,623 | 175,142 | 20,644 | 175,854 | 299,421 | 438,606 | 611,947 |
| GC_Content | non-normal | 553 | 52.59 | 0.23 | 50.71 | 52.51 | 52.68 | 52.73 | 53.23 |
| Completeness_Specific | non-normal | 553 | 96.96 | 3.14 | 71.69 | 97.3 | 97.75 | 98.53 | 99.73 |
| Contamination | non-normal | 553 | 0.21 | 0.34 | 0 | 0.08 | 0.09 | 0.1 | 2.75 |
| Total_Coding_Sequences | non-normal | 553 | 1,078 | 94.89 | 981 | 1,023 | 1,048 | 1,102 | 2,237 |
| Genome_Size | non-normal | 553 | 1,177,747 | 62,509 | 961,410 | 1,139,173 | 1,158,184 | 1,200,797 | 1,532,205 |
Full statistics including KS test vs RefSeq and Wasserstein distance are in the downloadable summary.csv.
Derived from 571 genomes including 18 RefSeq references
Both Fail and Warn bands shown as the published rounded values — easier to cite and consistent across the species page, CSV downloads, and downstream QC tools.
| Metric | Fail below | Warn below | Warn above | Fail above |
|---|---|---|---|---|
| Genome_Size | - | - | - | - |
| GC_Content | - | - | - | - |
| Total_Coding_Sequences | - | - | - | - |
| Completeness_Specific | - | - | - | - |
| Contamination | - | - | - | - |
| N50 | - | - | - | - |
| no_of_contigs | - | - | - | - |
| longest | - | - | - | - |
How to read this: A value outside a failure limit fails QC. Within the failure limits, values beyond a warning limit are borderline and worth a manual look; values within the warning limits pass that criterion. A dash means that no bound is defined on that side.