Renibacterium salmoninarum is a Gram-positive, non-motile, slow-growing coccobacillus and the sole species of the genus Renibacterium within the family Micrococcaceae. It is the causative agent of bacterial kidney disease (BKD), a chronic and often fatal systemic infection of salmonid fish that represents a major concern in aquaculture worldwide. R. salmoninarum has a reduced genome (approximately 3.2 Mb) with a high proportion of insertion sequences, reflecting its obligate intracellular lifestyle and limited metabolic independence.
For detailed methods on how these thresholds were calculated, please see Methods. The suggested thresholds are in the table below. These thresholds are based on 6 genomes from RefSeq and 0 genomes from other sources.
These tables provide a summary of the distribution of each metric, including SDeviation, Mean, Median, and Percentiles.
| Metric | Lower bound | Upper bound |
|---|---|---|
| Genome_Size | 3,000,000 | 3,100,000 |
| GC_Content | 56.00 | 57.00 |
| Total_Coding_Sequences | 3,400 | 3,500 |
| Completeness_Specific | 99.00 | - |
| Contamination | - | 2.000 |
| no_of_contigs | - | 90.00 |
| N50 | 68,000 | - |
This plot shows the relationship between the number of coding sequences (CDS) and genome size. It helps to visualize how genome size correlates with the number of genes. This should be linear – as genome size increases, the number of coding sequences should also increase. Any secondary trend lines or non-linear behaviour indicates bona fide separate populations within the retained genomes or some remaining contaminant.
Histogram comparing SRA to RefSeq; each bar shows genome density across value ranges to highlight shifts, peaks, or outliers.
QQ (quantile-quantile) plot comparing SRA and RefSeq. Points along the diagonal follow the expected distribution; deviations indicate skew, outliers, or other systematic differences.
A table of complete RefSeq genomes for Renibacterium salmoninarum used to calibrate this scheme. The file includes accessions, some sample information, genome size, GC content, and other key metrics.