Staphylococcus_aureus_ERR14835505_example
General Summary
General Summary PASS
| Metric | Value |
|---|---|
| Top species (Kraken2) | Staphylococcus aureus (69.0%) |
| Carbapenemase | Absent |
| BUSCO | C 97.6% · S 97.3% · D 0.4% · F 0.6% · M 1.7% · n=1317 (STAPHYLOCOCCUS) |
| MLST | ST22 (saureus) |
| QC Check | Value | Status |
|---|---|---|
| BUSCO Complete ≥ 90% | 97.6% | PASS |
| Total contigs | 2 | — |
| Largest contig | 2886754 bp | — |
MLST Typing
MLST Typing
| Scheme | saureus |
| Sequence Type | ST22 |
Allele calls
| arcC | aroE | glpF | gmk | pta | tpi | yqiL | |
|---|---|---|---|---|---|---|---|
| Allele | 7 | 6 | 1 | 5 | 8 | 8 | 6 |
SCCmec Typing (S. aureus)
SCCmec Typing (S. aureus)
| SCCmec Type | Subtype | Targets | Schema | Version | Comment |
|---|---|---|---|---|---|
| IV | IVa | ccrA2,ccrB2,IS431,IS431_1,IS431_2,IS1272,mecA,mecR1 | sccmec_targets | 1.2.0 | Coverage based on 25 hits;There were one or more overlapping hits |
AMR Genes (ABRicate)
AMR Genes (ABRicate)
| Gene | Accession | Class | Coverage | Plasmid |
|---|---|---|---|---|
| dfrC | NG_047752.1 | TRIMETHOPRIM | 100.0% | |
| mecA | NG_047937.1 | METHICILLIN | 100.0% | |
| tet(38) | NG_055983.1 | TETRACYCLINE | 100.0% | |
| blaI_of_Z | NG_047499.1 | BETA-LACTAM | 100.0% | |
| blaR1 | NG_047539.1 | BETA-LACTAM | 99.9% | |
| blaZ | NG_055999.1 | BETA-LACTAM | 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 | 101,506 | 91,081 |
| Total bases | 498.3 Mbp | 456.4 Mbp |
| Q30 rate | 35.8% | 37.5% |
| Q20 rate | 73.5% | 76.1% |
| Mean read length | 4,908 bp | 5,010 bp |
| GC content | 33.2% | 33.0% |
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).
Staphylococcus aureus
68.98%
62,826 reads
Homo sapiens
0.35%
322 reads
Staphylococcus argenteus
0.13%
122 reads
Staphylococcus epidermidis
0.09%
84 reads
Staphylococcus haemolyticus
0.07%
66 reads
Staphylococcus schweitzeri
0.05%
43 reads
Staphylococcus felis
0.04%
34 reads
Staphylococcus sp. MZ8
0.03%
25 reads
Staphylococcus simiae
0.03%
31 reads
Macrococcoides caseolyticum
0.03%
23 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) | 97.3% |
| Complete (duplicated) | 0.4% |
| Complete (total) | 97.6% |
| Fragmented | 0.6% |
| Missing | 1.7% |
| Total markers (n) | 1317 |
| Lineage | STAPHYLOCOCCUS |
Gene Annotation (Bakta)
Gene Annotation (Bakta)
Genome Statistics
| Genome size | 2,928,885 bp |
| GC content | 32.85% |
| N50 | 2,891,023 bp |
| Coding ratio | 85.4% |
Annotated Features
| Feature type | Count |
|---|---|
| CDS (protein-coding genes) | 2,792 |
| ncRNA | 79 |
| tRNA | 61 |
| ncRNA region | 23 |
| rRNA | 19 |
| sORF | 6 |
| oriC | 2 |
| tmRNA | 1 |