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Source database (GenBank or RefSeq) File type

PDT000626001.1

Description:

NCBI Pathogen Detection Assembly PDT000626001.1

Organism name:

Escherichia coli (E. coli)

Taxonomy check:

Infraspecific name:

Strain: MA_289

BioSample:

SAMN13245785

BioProject:

PRJNA293225

Submitter:

US Food and Drug Administration

Date:

2020/04/21

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_012618445.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

AASXAF01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

52x

Sequencing technology:

ILLUMINA

IDs: 6889731 [UID] 19024888 [GenBank]

See Genome Information for Escherichia coli

Pathogen Detection Resources

There are 266204 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_012618445.1	n/a	n/a	PDT000626001.1	Contig	Latest GenBank

Comment

The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/genome/annotation_prok/
This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated ... with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Date::11/20/2019 19:37:12
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::4.10
Genes (total)::5,289
CDSs (total)::5,188
Genes (coding)::5,057
CDSs (with protein)::5,057
Genes (RNA)::101
rRNAs::6, 4, 3 (5S, 16S, 23S)
complete rRNAs::6 (5S)
partial rRNAs::4, 3 (16S, 23S)
tRNAs::80
ncRNAs::8
Pseudo Genes (total)::131
CDSs (without protein)::131
Pseudo Genes (ambiguous residues)::0 of 131
Pseudo Genes (frameshifted)::57 of 131
Pseudo Genes (incomplete)::69 of 131
Pseudo Genes (internal stop)::25 of 131
Pseudo Genes (multiple problems)::17 of 131
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	5,322,815
Total ungapped length	5,322,815
Number of contigs	155
Contig N50	161,225
Contig L50	10
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	155

	ANI	Query coverage	Subject coverage
Declared type	99.10	84.04	86.76
Best-match type	99.10	84.04	86.76

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PDT000626001.1

See Genome Information for Escherichia coli

Pathogen Detection Resources

There are 266204 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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