Lactococcus lactis QC Overview

Lactococcus lactis is a non-motile, Gram-positive coccus in the family Streptococcaceae, best known as the principal starter organism in the production of cheese, buttermilk, and other fermented dairy products. It is generally recognised as safe (GRAS) and is widely used as a model organism for lactic acid bacteria research and as a chassis for recombinant protein expression. The genome of L. lactis (~2.3-2.6 Mb) varies considerably between dairy and plant-associated strains, with the dairy lineages showing genome decay driven by adaptation to milk.

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 228 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.

Derived from 339 genomes: 111 from RefSeq and 228 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 213 genomes at PASS, 19 at WARN, and 16 at FAIL (248 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	228	179,465	107,331	14,158	84,229	168,048	227,458	458,242
no_of_contigs	non-normal	228	104.13	56.79	21	71	82	120	331
longest	normal	228	376,616	132,732	70,530	243,077	399,916	465,450	746,529
GC_Content	non-normal	228	35.09	0.17	34.66	34.96	35.11	35.24	35.43
Completeness_Specific	non-normal	228	100	0	99.98	100	100	100	100
Contamination	non-normal	228	0.51	0.34	0.05	0.35	0.44	0.54	1.88
Total_Coding_Sequences	normal	228	2,565	151.71	2,102	2,489	2,576	2,625	2,941
Genome_Size	normal	228	2,516,310	117,455	2,150,170	2,458,829	2,531,169	2,559,889	2,836,550

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

Suggested thresholds for Lactococcus lactis (qualibact-v1.0)

Derived from 339 genomes including 111 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	2,200,000	2,200,000	2,800,000	3,000,000
GC_Content	34.6	34.7	35.3	35.5
Total_Coding_Sequences	2,100	2,200	2,900	3,100
Completeness_Specific	94	100	-	-
Contamination	-	-	2	5
N50	15,000	42,000	-	-
no_of_contigs	-	-	250	280
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 Lactococcus lactis 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

Lactococcus_lactis_all_longest_Completeness_Specific.pngDownload

Sample

Lactococcus_lactis_sample_longest_Completeness_Specific.pngDownload

Filtered

Lactococcus_lactis_filt_longest_Completeness_Specific.pngDownload

All QC schemes for this species

qualibact-v1.0 (preferred)

Preferred scheme: qualibact-v1.0