Salmonella_enterica_SRR38360442_example
General Summary
General Summary PASS
| Metric | Value |
|---|---|
| Top species (Kraken2) | Salmonella enterica (83.0%) |
| Carbapenemase | Absent |
| BUSCO | C 99.4% · S 99.3% · D 0.1% · F 0.1% · M 0.5% · n=874 (ENTEROBACTERIACEAE) |
| MLST | ST13 (senterica_achtman_2) |
| QC Check | Value | Status |
|---|---|---|
| BUSCO Complete ≥ 90% | 99.4% | PASS |
| Total contigs | 1 | — |
| Largest contig | 4938406 bp | — |
MLST Typing
MLST Typing
| Scheme | senterica_achtman_2 |
| Sequence Type | ST13 |
Allele calls
| aroC | dnaN | hemD | hisD | purE | sucA | thrA | |
|---|---|---|---|---|---|---|---|
| Allele | 3 | 3 | 7 | 4 | 3 | 3 | 7 |
Serotyping (Salmonella)
Serotyping (Salmonella)
| Serotype | Antigenic profile | Notes |
|---|---|---|
| Agona | 4:f,g,s:- | — |
AMR Genes (ABRicate)
AMR Genes (ABRicate)
| Gene | Accession | Class | Coverage | Plasmid |
|---|---|---|---|---|
| fosA7.2 | NG_067228.1 | FOSFOMYCIN | 100.0% | |
| dfrA14 | NG_056035.1 | TRIMETHOPRIM | 100.0% | |
| arr-2 | NG_048580.1 | RIFAMYCIN | 100.0% | |
| aadA22 | NG_047346.1 | STREPTOMYCIN | 100.0% | |
| lnu(F) | NG_047927.1 | LINCOSAMIDE | 100.0% | |
| sul3 | NG_048120.1 | SULFONAMIDE | 100.0% | |
| tet(A) | NG_048154.1 | TETRACYCLINE | 100.0% | |
| blaTEM-1 | NG_050145.1 | BETA-LACTAM | 100.0% | |
| floR | NG_047862.1 | CHLORAMPHENICOL;FLORFENICOL | 100.0% | |
| aph(3')-Ia | NG_056047.1 | KANAMYCIN | 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 | 74,684 | 73,113 |
| Total bases | 281.5 Mbp | 277.0 Mbp |
| Q30 rate | 89.8% | 91.1% |
| Q20 rate | 94.3% | 95.5% |
| Mean read length | 3,769 bp | 3,789 bp |
| GC content | 52.2% | 52.2% |
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).
Salmonella enterica
83.03%
60,706 reads
Escherichia coli
0.20%
144 reads
Salmonella bongori
0.12%
86 reads
Klebsiella pneumoniae
0.08%
60 reads
Shigella dysenteriae
0.05%
36 reads
Escherichia albertii
0.03%
23 reads
Salmonella sp. SA14318
0.01%
4 reads
Klebsiella variicola
0.01%
9 reads
Enterobacter roggenkampii
0.01%
6 reads
Salmonella sp. HY31
0.00%
3 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) | 99.3% |
| Complete (duplicated) | 0.1% |
| Complete (total) | 99.4% |
| Fragmented | 0.1% |
| Missing | 0.5% |
| Total markers (n) | 874 |
| Lineage | ENTEROBACTERIACEAE |
Gene Annotation (Bakta)
Gene Annotation (Bakta)
Genome Statistics
| Genome size | 4,938,271 bp |
| GC content | 52.00% |
| N50 | 4,938,271 bp |
| Coding ratio | 88.6% |
Annotated Features
| Feature type | Count |
|---|---|
| CDS (protein-coding genes) | 4,643 |
| ncRNA | 129 |
| tRNA | 90 |
| ncRNA region | 61 |
| rRNA | 22 |
| sORF | 22 |
| crispr | 2 |
| oriC | 2 |
| tmRNA | 1 |
| oriT | 1 |