Analysis Report · Bacterial WGS · v1.0.0

Sample: sample1

Complete end-to-end analysis of assembly_contigs.fasta — assembly QC, gene annotation, AMR screening, and MLST typing. Putative organism: Bacillus velezensis (based on AMR gene homology and genome characteristics).

Run date 2026-04-19

Input assembly_contigs.fasta

Genome size 3.97 Mb

QC status PASS

AMR genes 5 detected

Pipeline BacTrack-NF v1.0.0

Module 1 · Assembly QC

High-quality assembly — N50 = 1.01 Mb

De novo assembly evaluated from contig length distribution and per-contig coverage metrics embedded in the FASTA headers. All quality thresholds passed.

Total contigs

24 ≥ 1 kb

3.97 Mb

Assembly size

3,966,013 bp

192.8×

Mean coverage

Weighted by contig length

1.01 Mb

N50

1,013,119 bp

Contig Statistics

Largest contig1,074,607 bp

Smallest contig325 bp

N501,013,119 bp

Contigs ≥ 1 kb24 / 36

Contigs < 500 bp6

Total assembly size3,966,013 bp

GC content (est.)~46.5%

QC statusPASS ✓

Coverage Metrics

Weighted mean cov.

192.8×

Contig 1 coverage

180.5×

Contig 2 coverage

198.3×

Contig 3 coverage

182.3×

Contig 4 coverage

201.7×

Contig 5 coverage

203.1×

Contig length distribution (top 24 contigs)

16121824

Module 2 · AMR Screening

5 AMR genes detected across 4 drug classes

Resistance genes identified using NCBI AMRFinder+ (nucleotide BLAST) and Abricate against the ResFinder and CARD databases. Results below are merged and deduplicated.

Tetracycline resistance

Lincosamide / Macrolide / Streptogramin

Phenicol / Oxazolidinone resistance

Streptothricin resistance

Rifamycin (lower confidence)

Gene	Contig	Drug Class	% Identity	% Coverage	Database	Confidence
clbA	assembly_contig_8	Lincosamide · Macrolide · Streptogramin · Oxazolidinone · Phenicol	92.55%	100%	AMRFinder+	HIGH
cfr(B)_3	assembly_contig_8	Chloramphenicol · Florfenicol · Linezolid · Clindamycin · Tiamulin	88.67%	100%	ResFinder	HIGH
tet(L)_5	assembly_contig_3	Tetracycline · Doxycycline	87.29%	100%	ResFinder	HIGH
satA	assembly_contig_8	Streptothricin	84.39%	100%	AMRFinder+	HIGH
rphB	assembly_contig_1	Rifamycin (phosphotransferase)	80.95%	97.7%	CARD	MOD

Note: Three AMR genes (clbA, cfr(B), satA) co-localise on assembly_contig_8, suggesting a mobile genetic element (plasmid or integrative conjugative element). The rphB hit at 80.95% identity may reflect a chromosomally-encoded homologue rather than an acquired resistance gene — interpret with caution.

Module 3 · Gene Annotation

3,925 coding sequences — Prokka annotation

Genome annotated using Prokka v1.14.6 against the Bacteria kingdom database with BLAST-based homology search. All rRNA operons detected.

3,925

Coding sequences (CDS)

protein-coding genes

Transfer RNAs (tRNA)

all 20 amino acids covered

Ribosomal RNAs (rRNA)

5S · 16S · 23S detected

Feature Summary

CDS (protein-coding)3,925

tRNA genes74

rRNA genes4

tmRNA1

Total annotated features4,004

Gene density~990 genes/Mb

Annotation toolProkka 1.14.6

DatabaseBacteria (BLAST)

Functional COG Categories (selected)

Metabolism

~910

Information storage

~600

Cell processes

~470

Signalling / regulation

~355

Hypothetical proteins

~700

COG assignments estimated from Prokka functional annotations. Hypothetical proteins represent ~18% of CDS.

Notable Annotated Functions

Gene / Product	Function	Relevance
rlmA, rlmCD, rlhA	23S rRNA methyltransferases	Ribosome modification; potential intrinsic antibiotic tolerance
nupG	Purine nucleoside transport protein	Nucleoside salvage pathway
yrrK	Putative pre-16S rRNA nuclease	rRNA processing
Multiple tRNA synthetases	Aminoacyl-tRNA biosynthesis	All 20 amino acids represented in tRNA complement

Module 4 · MLST & Organism Identification

Putative Bacillus velezensis — MLST not applicable

Organism identification inferred from AMR gene homology (CARD) and genome size. No standardised MLST scheme is available in PubMLST for this species.

Organism Identification Evidence

Putative speciesBacillus velezensis

Evidence sourceCARD AMR homology

Key hitclbA from B. velezensis (93% id)

Expected genome size3.8–4.2 Mb ✓

16S rRNA genes4 detected

ConfidencePutative — confirm with 16S BLAST

MLST schemeNone in PubMLST

ℹ️

MLST Not Available for This Organism

Bacillus velezensis (syn. B. amyloliquefaciens subsp. plantarum) does not have an established MLST scheme in the PubMLST database. For strain typing, consider:

Whole-genome ANI comparison against type strains
Core-genome phylogeny with reference B. velezensis genomes
16S rRNA BLAST against NCBI nr (AGCGGCGGACGGGTGAGT...)
GBDP / TYGS web service for digital DNA-DNA hybridisation

To run MLST for other species: mlst --scheme <species> assembly.fasta

Methods

Tools and databases used

Prokka

v1.14.6 · Seemann et al. 2014

Rapid prokaryotic genome annotation. BLAST-based search against Bacteria kingdom database. Identifies CDS, rRNA, tRNA, tmRNA, and regulatory features.

DB: UniProtKB/Swiss-Prot · HAMAP · Pfam

NCBI AMRFinder+

v4.0.23 · DB: 2025-07-16.1

Identifies AMR genes via BLASTX protein alignment against the NCBI Reference Gene Catalog. Nucleotide mode used on assembly contigs.

DB: NCBI Reference Gene Catalog 2025-07-16

Abricate

v1.0.1 · Seemann

Mass screening of contigs against multiple resistance databases using BLAST. Run against ResFinder (acquired resistance genes) and CARD (comprehensive AMR).

DB: ResFinder · CARD · VFDB (2025-Jan-14)

Assembly QC

Custom Python · coverage from headers

N50, total length, contig count, and coverage statistics calculated directly from FASTA contig headers (Flye/SPAdes format with embedded coverage values).

Input: assembly_contigs.fasta (36 contigs)

MLST

Not run — no scheme available

Multi-locus sequence typing not performed. No established MLST scheme exists for Bacillus velezensis in PubMLST or Enterobase.

Recommended: ANI-based typing via pyANI

BacTrack-NF

v1.0.0-beta · Nextflow DSL2

End-to-end bacterial WGS analysis pipeline. Modular Nextflow architecture with Docker/Singularity containers. Report generated 2026-04-19.

Platform: macOS Darwin 22.6.0 · local profile