Pseudomonas_aeruginosa_SRR38324899_example
General Summary
General Summary PASS
| Metric | Value |
|---|---|
| Top species (Kraken2) | Pseudomonas aeruginosa (78.9%) |
| Carbapenemase | Present |
| BUSCO | C 99.4% · S 98.4% · D 1.0% · F 0.3% · M 0.3% · n=704 (PSEUDOMONADALES) |
| MLST | ST308 (paeruginosa) |
| QC Check | Value | Status |
|---|---|---|
| BUSCO Complete ≥ 90% | 99.4% | PASS |
| Total contigs | 5 | — |
| Largest contig | 7182721 bp | — |
MLST Typing
MLST Typing
| Scheme | paeruginosa |
| Sequence Type | ST308 |
Allele calls
| acsA | aroE | guaA | mutL | nuoD | ppsA | trpE | |
|---|---|---|---|---|---|---|---|
| Allele | 13 | 4 | 5 | 5 | 12 | 7 | 15 |
Serogroup (P. aeruginosa)
Serogroup (P. aeruginosa)
| Serogroup | Targets | Coverage | Hits | Schema | Version | Comment |
|---|---|---|---|---|---|---|
| O11 | O11 | 100.00 | 1 | pasty | 2.2.1 | — |
AMR Genes (ABRicate)
AMR Genes (ABRicate)
| Gene | Accession | Class | Coverage | Plasmid |
|---|---|---|---|---|
| blaOXA-488 | NG_049768.1 | BETA-LACTAM | 100.0% | |
| aph(3')-IIb | NG_047423.1 | KANAMYCIN | 100.0% | |
| blaPDC-19a | NG_049889.1 | CEPHALOSPORIN | 100.0% | |
| aadA6 | NG_047359.1 | STREPTOMYCIN | 100.0% | |
| sul1 | NG_048082.1 | SULFONAMIDE | 100.0% | |
| blaVIM-2 | NG_050347.1 | CARBAPENEM | 100.0% | |
| aac(6')-Ib4 | NG_051844.1 | GENTAMICIN | 100.0% | |
| aadA1 | NG_047326.1 | STREPTOMYCIN | 100.0% | |
| blaOXA-2 | NG_049496.1 | BETA-LACTAM | 100.0% | |
| fosA-354827590 | NG_047883.1 | FOSFOMYCIN | 100.0% | |
| crpP | NG_062203.1 | FLUOROQUINOLONE | 100.0% | |
| catB7 | NG_047614.1 | CHLORAMPHENICOL | 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 | 49,447 | 47,270 |
| Total bases | 207.5 Mbp | 194.8 Mbp |
| Q30 rate | 72.2% | 76.1% |
| Q20 rate | 82.5% | 86.4% |
| Mean read length | 4,197 bp | 4,122 bp |
| GC content | 63.2% | 64.7% |
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).
Pseudomonas aeruginosa
78.92%
37,305 reads
Klebsiella pneumoniae
0.42%
199 reads
Enterobacter hormaechei
0.23%
107 reads
Klebsiella oxytoca
0.22%
103 reads
Acinetobacter baumannii
0.22%
106 reads
Pseudomonas sp. QE6
0.12%
56 reads
Casadabanvirus LPB1
0.09%
41 reads
Pseudomonas paraeruginosa
0.04%
20 reads
Pseudomonas citronellolis
0.03%
13 reads
Pseudomonas putida
0.03%
13 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) | 98.4% |
| Complete (duplicated) | 1.0% |
| Complete (total) | 99.4% |
| Fragmented | 0.3% |
| Missing | 0.3% |
| Total markers (n) | 704 |
| Lineage | PSEUDOMONADALES |
Gene Annotation (Bakta)
Gene Annotation (Bakta)
Genome Statistics
| Genome size | 7,186,843 bp |
| GC content | 65.83% |
| N50 | 7,182,182 bp |
| Coding ratio | 89.8% |
Annotated Features
| Feature type | Count |
|---|---|
| CDS (protein-coding genes) | 6,685 |
| tRNA | 68 |
| ncRNA | 55 |
| ncRNA region | 44 |
| rRNA | 12 |
| sORF | 3 |
| oriC | 3 |
| crispr | 1 |
| tmRNA | 1 |