Escherichia_coli_SRR38074175_example

NS Bio Bacterial Analysis · Generated 2026-05-11

General Summary

General Summary PASS

Metric	Value
Top species (Kraken2)	Escherichia coli (71.5%)
Carbapenemase	Absent
BUSCO	C 99.5% · S 99.4% · D 0.1% · F 0.3% · M 0.1% · n=874 (ENTEROBACTERIACEAE)
MLST	ST73 (ecoli_achtman_4)

QC Check	Value	Status
BUSCO Complete ≥ 90%	99.5%	PASS
Total contigs	5	—
Largest contig	5131858 bp	—

MLST Typing

Scheme	ecoli_achtman_4
Sequence Type	ST73

Allele calls

	adk	fumC	gyrB	icd	mdh	purA	recA
Allele	36	24	9	13	17	11	25

Serotyping (E. coli)

Name	Species	Serotype	O type	H type	QC	Warnings
contigs	Escherichia coli	O6:H1	O6	H1	-	-

AMR Genes (ABRicate)

Gene	Accession	Class	Coverage	Plasmid
blaEC-5	NG_049085.1	CEPHALOSPORIN	100.0%

Quality Filtering (fastp)

Filtering Summary

Passed: 91,007

Low quality: 5,978

Too short: 1,368

Too long: 0

Passed Low quality Too short Too long

Read Statistics

Metric	Before filtering	After filtering
Total reads	98,331	91,007
Total bases	366.6 Mbp	357.6 Mbp
Q30 rate	72.5%	73.9%
Q20 rate	85.4%	86.6%
Mean read length	3,728 bp	3,929 bp
GC content	50.5%	50.5%

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).

Escherichia coli

71.46%

65,031 reads

Klebsiella pneumoniae

1.01%

917 reads

Escherichia albertii

0.18%

163 reads

Shigella dysenteriae

0.12%

106 reads

Escherichia fergusonii

0.09%

78 reads

Shigella flexneri

0.09%

85 reads

Escherichia marmotae

0.08%

74 reads

Salmonella enterica

0.07%

68 reads

Klebsiella grimontii

0.06%

51 reads

Escherichia sp. E4742

0.05%

42 reads

Top 10 species-level hits. Bar width scaled to highest-abundance species.

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.

Complete (single): 99.4%

Complete (duplicated): 0.1%

Fragmented: 0.3%

Missing: 0.1%

Single Duplicated Fragmented Missing

Complete (single-copy)	99.4%
Complete (duplicated)	0.1%
Complete (total)	99.5%
Fragmented	0.3%
Missing	0.1%
Total markers (n)	874
Lineage	ENTEROBACTERIACEAE

Gene Annotation (Bakta)

Genome Statistics

Genome size	5,208,221 bp
GC content	50.42%
N50	5,132,192 bp
Coding ratio	88.9%

Annotated Features

Feature type	Count
CDS (protein-coding genes)	4,824
ncRNA	195
tRNA	88
sORF	75
ncRNA region	55
rRNA	22
oriC	3
tmRNA	1
oriT	1