Streptococcus parasanguinis QC Overview

Streptococcus parasanguinis is a Gram-positive, alpha-haemolytic coccus of the family Streptococcaceae, belonging to the mitis group of viridans streptococci. It is one of the early colonisers of the oral cavity and dental plaque, but can enter the bloodstream and cause infective endocarditis, particularly in individuals with predisposing cardiac conditions. Genomically, S. parasanguinis is naturally competent for transformation and carries fimbria-associated genes (fap1 and related loci) that mediate adhesion to saliva-coated surfaces and are important for biofilm initiation.

Preferred scheme: qualibact-v1.0

Engine quality flag: warn

The engine flagged the reference dataset for this species — review the signals below before relying on these thresholds.

Low genome count (warn)Only 108 genomes survived Isolation-Forest outlier filtering — the engine flags reference pools below 500 as warn, below 100 as error, because percentile-based bounds become unreliable at low n.
FAIL band dragged beyond WARN band by outliers (warn)FINAL band is dragged far beyond the species WARN band by a small number of extreme outliers (either in the submitted species data, or in the RefSeq reference set).

Derived from 114 genomes: 6 from RefSeq and 108 from other sources. For the derivation pipeline and the PASS / WARN / FAIL verdict model, see the methods page for qualibact-v1.0.

Applied to the full All-The-Bacteria dataset, these thresholds place 114 genomes at PASS, 9 at WARN, and 11 at FAIL (134 assessed in total). The per-tier genome lists can be downloaded below in .csv.gz format; the FAIL list also records the reason each assembly was rejected.

Summary table

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.

summary.csv

Show summary statistics inline

Metric	Distribution	n	Mean	SD	Min	Q1	Median	Q3	Max
N50	non-normal	108	213,701	146,564	55,164	114,024	163,151	274,815	644,915
no_of_contigs	normal	108	40.34	16.86	11	28	40	53	85
longest	non-normal	108	463,027	192,706	169,026	317,417	457,567	553,993	1,014,293
GC_Content	non-normal	108	41.75	0.24	41.29	41.53	41.79	41.97	42.2
Completeness_Specific	non-normal	108	100	0	99.99	100	100	100	100
Contamination	non-normal	108	0.02	0.02	0	0	0.01	0.02	0.09
Total_Coding_Sequences	non-normal	108	2,043	65.33	1,902	1,998	2,033	2,090	2,169
Genome_Size	normal	108	2,158,269	61,359	2,002,655	2,114,868	2,157,231	2,205,896	2,271,871

Full statistics including KS test vs RefSeq and Wasserstein distance are in the downloadable summary.csv.

Suggested thresholds for Streptococcus parasanguinis (qualibact-v1.0)

Derived from 114 genomes including 6 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	2,000,000	2,000,000	2,300,000	2,300,000
GC_Content	41.2	41.3	42.1	42.2
Total_Coding_Sequences	1,900	1,900	2,200	2,200
Completeness_Specific	97	99	-	-
Contamination	-	-	1	2
N50	59,000	71,000	-	-
no_of_contigs	-	-	80	90
longest	-	-	-	-

How to read this: a value between the two warn columns is typical for this species and passes QC. A value between a warn column and the corresponding fail column is borderline — worth a manual look but not an outright failure. A value outside the fail columns is unusual enough to fail QC.

Download CSV

All-The-Bacteria — PASS / WARN / FAIL genome lists

The published rounded thresholds (the values in the table above) were applied to the full AllTheBacteria-2024-08 set for this species. Each row carries the per-metric verdict and, where applicable, the reason a genome was demoted to WARN or FAIL. Files are gzipped CSV.

PASS genomes WARN genomes FAIL genomes

CDS vs Genome Size

This plot shows the relationship between the number of coding sequences (CDS) and genome size — how the number of genes scales with assembly length. The relationship should be roughly linear: as genome size increases, the number of coding sequences should rise proportionally. A secondary trend line or non-linear behaviour can indicate either bona fide sub-populations within the retained genomes (e.g. distinct sub-clades) or residual contamination that survived filtering.

RefSeq distributions

GC Content (RefSeq)

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Histogram (SRA vs RefSeq)

Histogram comparing SRA to RefSeq; each bar shows genome density across value ranges to highlight shifts, peaks, or outliers.

QQ plot (SRA vs RefSeq)

QQ (quantile-quantile) plot comparing SRA and RefSeq. Points along the diagonal follow the expected distribution; deviations indicate skew, outliers, or other systematic differences.

Table of included RefSeq complete genomes

A table of complete RefSeq genomes for Streptococcus parasanguinis used to calibrate this scheme. The file includes accessions, some sample information, genome size, GC content, and other key metrics.

Download table

Filtered plots

Longest contig vs Completeness

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These plots show genomes before and after filtering to highlight the outliers removed:

Left: heatmap of all genomes in the dataset.
Middle: a representative sample of genomes, with anomalies highlighted in purple.
Right: the filtered distribution after applying the thresholds.

The filtered distribution shown here may not exactly match the published thresholds because additional rounding and curator adjustments are applied on top.

All

Streptococcus_parasanguinis_all_longest_Completeness_Specific.pngDownload

Sample

Streptococcus_parasanguinis_sample_longest_Completeness_Specific.pngDownload

Filtered

Streptococcus_parasanguinis_filt_longest_Completeness_Specific.pngDownload

All QC schemes for this species

qualibact-v1.0 (preferred)enterobase-v2.3

Preferred scheme: qualibact-v1.0