Mycobacterium_avium_SRR34136513_example
General Summary
General Summary PASS
| Metric | Value |
|---|---|
| Top species (Kraken2) | Mycobacterium avium (97.5%) |
| Carbapenemase | Absent |
| BUSCO | C 98.9% · S 98.7% · D 0.2% · F 0.5% · M 0.6% · n=1512 (MYCOBACTERIUM) |
| MLST | ST141 (mycobacteria_2) |
| QC Check | Value | Status |
|---|---|---|
| BUSCO Complete ≥ 90% | 98.9% | PASS |
| Total contigs | 6 | — |
| Largest contig | 2774829 bp | — |
MLST Typing
MLST Typing
| Scheme | mycobacteria_2 |
| Sequence Type | ST141 |
Allele calls
| L16 | L19 | L35 | S12 | S14Z | S19 | S7 | S8 | |
|---|---|---|---|---|---|---|---|---|
| Allele | 128 | 110 | 103 | 107 | 102 | 98 | 125 | 120 |
NTM-Profiler
NTM-Profiler
Species Identification
| Species | Mycobacterium avium (99.80% ANI) 100.0% abundance |
| Subspecies | subsp. hominissuis (100.0%) |
| Prediction method | sourmash |
Resistance Genes
No resistance-associated genes detected.
Resistance Variants
| Gene | Nucleotide | Protein | Type | Drug(s) |
|---|---|---|---|---|
| rrs | n.1388A>G | — | non_coding_transcript_exon_variant | amikacin |
| rrl | n.2279A>G | — | non_coding_transcript_exon_variant | macrolides |
AMR Genes (ABRicate)
AMR Genes (ABRicate)
No resistance genes detected.
Quality Filtering (fastp)
Quality Filtering (fastp)
Filtering Summary
Passed Low quality Too short Too long
Read Statistics
| Metric | Before filtering | After filtering |
|---|---|---|
| Total reads | 43,054 | 42,715 |
| Total bases | 333.5 Mbp | 330.8 Mbp |
| Q30 rate | 86.6% | 87.1% |
| Q20 rate | 92.5% | 92.9% |
| Mean read length | 7,744 bp | 7,745 bp |
| GC content | 69.0% | 69.0% |
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).
Mycobacterium avium
97.47%
41,634 reads
Mycobacterium heckeshornense
0.29%
122 reads
Mycobacterium sp. SMC-4
0.12%
50 reads
Streptomyces niveus
0.07%
30 reads
Frankia sp. ArI3
0.07%
31 reads
Achromobacter spanius
0.06%
26 reads
Mycobacteroides abscessus
0.05%
22 reads
Mycobacterium intracellulare
0.04%
18 reads
Mycobacterium paraintracellulare
0.04%
18 reads
Mycolicibacterium phocaicum
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) | 98.7% |
| Complete (duplicated) | 0.2% |
| Complete (total) | 98.9% |
| Fragmented | 0.5% |
| Missing | 0.6% |
| Total markers (n) | 1512 |
| Lineage | MYCOBACTERIUM |
Gene Annotation (Bakta)
Gene Annotation (Bakta)
Genome Statistics
| Genome size | 5,296,601 bp |
| GC content | 69.04% |
| N50 | 2,775,499 bp |
| Coding ratio | 91.3% |
Annotated Features
| Feature type | Count |
|---|---|
| CDS (protein-coding genes) | 4,898 |
| tRNA | 48 |
| ncRNA | 15 |
| ncRNA region | 15 |
| rRNA | 3 |
| sORF | 2 |
| oriC | 2 |
| tmRNA | 1 |