Streptococcus pneumoniae is a Gram-positive, alpha-haemolytic, lancet-shaped diplococcus of the family Streptococcaceae, commonly carried asymptomatically in the human nasopharynx. It is a major cause of community-acquired pneumonia, bacterial meningitis, otitis media, and sepsis worldwide, with the polysaccharide capsule being its principal virulence determinant and the basis for over 100 known serotypes. Genomically, S. pneumoniae is naturally transformable and highly recombinogenic, with an open pangenome that facilitates capsule switching, acquisition of antibiotic resistance, and vaccine escape.
Derived from 111,922 genomes: 275 from RefSeq and 111,647 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 | 111,647 | 94,682 | 44,187 | 14,538 | 62,038 | 85,519 | 120,234 | 379,395 |
| no_of_contigs | non-normal | 111,647 | 83.89 | 34.07 | 16 | 59 | 78 | 102 | 343 |
| longest | non-normal | 111,647 | 247,058 | 104,590 | 43,742 | 172,435 | 226,655 | 304,131 | 774,669 |
| GC_Content | non-normal | 111,647 | 39.61 | 0.09 | 39.19 | 39.55 | 39.61 | 39.68 | 40.25 |
| Completeness_Specific | non-normal | 111,647 | 100 | 0 | 99.99 | 100 | 100 | 100 | 100 |
| Contamination | non-normal | 111,647 | 0.21 | 0.17 | 0 | 0.1 | 0.16 | 0.24 | 2.59 |
| Total_Coding_Sequences | non-normal | 111,647 | 2,109 | 77.67 | 1,893 | 2,057 | 2,101 | 2,155 | 2,495 |
| Genome_Size | non-normal | 111,647 | 2,082,331 | 55,618 | 1,903,720 | 2,046,550 | 2,081,261 | 2,117,622 | 2,327,908 |
Full statistics including KS test vs RefSeq and Wasserstein distance are in the downloadable summary.csv.
Derived from 111,922 genomes including 275 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.