Klebsiella_pneumoniae_SRR38388358_example
General Summary
General Summary PASS
| Metric | Value |
|---|---|
| Top species (Kraken2) | Klebsiella pneumoniae (68.1%) |
| Carbapenemase | Absent |
| BUSCO | C 95.4% Β· S 95.4% Β· D 0.0% Β· F 2.5% Β· M 2.1% Β· n=874 (ENTEROBACTERIACEAE) |
| MLST | ST277 (klebsiella) |
| QC Check | Value | Status |
|---|---|---|
| BUSCO Complete β₯ 90% | 95.4% | PASS |
| Total contigs | 5 | β |
| Largest contig | 5344382 bp | β |
MLST Typing
MLST Typing
| Scheme | klebsiella |
| Sequence Type | ST277 |
Allele calls
| gapA | infB | mdh | pgi | phoE | rpoB | tonB | |
|---|---|---|---|---|---|---|---|
| Allele | 3 | 1 | 1 | 1 | 1 | 1 | 43 |
Kleborate (Klebsiella spp.)
Kleborate (Klebsiella spp.)
| Species | ST | K locus | O locus | Virulence score | Resistance score | Ybt | Clb | Iuc | Iro | RmpA | RmpA2 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Klebsiella pneumoniae | ST277 | KL46 | OL3Ξ³ | 0 | 0 | NA | NA | NA | NA | - | - |
AMR Genes (ABRicate)
AMR Genes (ABRicate)
| Gene | Accession | Class | Coverage | Plasmid |
|---|---|---|---|---|
| fosA6 | NG_051497.1 | FOSFOMYCIN | 100.0% | |
| blaSHV-27 | NG_050064.1 | CEPHALOSPORIN | 100.0% | |
| oqxA9 | NG_050427.1 | PHENICOL;QUINOLONE | 100.0% | |
| oqxB26 | NG_050445.1 | PHENICOL;QUINOLONE | 100.0% |
Quality Filtering (fastp)
Quality Filtering (fastp)
Filtering Summary
Passed Low quality Too short Too long
Read Statistics
| Metric | Before filtering | After filtering |
|---|---|---|
| Total reads | 43,893 | 37,000 |
| Total bases | 236.3 Mbp | 201.9 Mbp |
| Q30 rate | 27.3% | 29.5% |
| Q20 rate | 57.3% | 60.3% |
| Mean read length | 5,383 bp | 5,455 bp |
| GC content | 56.4% | 56.4% |
Taxonomic Classification (Kraken2)
Taxonomic Classification (Kraken2)
What is Kraken2? Kraken2 classifies sequencing reads by matching k-mers against a reference database. The percentage shown is the proportion of all reads assigned to each species and its sub-taxa (clade abundance).
Klebsiella pneumoniae
68.14%
25,212 reads
Klebsiella quasipneumoniae
3.03%
1,120 reads
Klebsiella variicola
2.35%
870 reads
Enterobacter hormaechei
1.34%
497 reads
Escherichia coli
0.69%
257 reads
Klebsiella africana
0.51%
190 reads
Klebsiella aerogenes
0.42%
154 reads
Klebsiella quasivariicola
0.32%
120 reads
Salmonella enterica
0.32%
118 reads
Klebsiella michiganensis
0.27%
100 reads
Top 10 species-level hits. Bar width scaled to highest-abundance species.
Genome Completeness (BUSCO)
Genome Completeness (BUSCO)
What is BUSCO? BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome
completeness by searching for conserved genes expected in the organism's lineage. A high
"Complete" score indicates a near-complete assembly; "Fragmented" and "Missing" suggest gaps.
Single
Duplicated
Fragmented
Missing
| Complete (single-copy) | 95.4% |
| Complete (duplicated) | 0.0% |
| Complete (total) | 95.4% |
| Fragmented | 2.5% |
| Missing | 2.1% |
| Total markers (n) | 874 |
| Lineage | ENTEROBACTERIACEAE |
Gene Annotation (Bakta)
Gene Annotation (Bakta)
Genome Statistics
| Genome size | 5,554,826 bp |
| GC content | 57.19% |
| N50 | 5,347,937 bp |
| Coding ratio | 88.1% |
Annotated Features
| Feature type | Count |
|---|---|
| CDS (protein-coding genes) | 5,480 |
| tRNA | 86 |
| ncRNA | 84 |
| ncRNA region | 52 |
| rRNA | 25 |
| sORF | 18 |
| oriC | 5 |
| oriT | 3 |
| tmRNA | 1 |
| crispr | 1 |