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Source database (GenBank or RefSeq) File type

PDT000364506.1

Description:

NCBI Pathogen Detection Assembly PDT000364506.1

Organism name:

Listeria monocytogenes (firmicutes)

Taxonomy check:

Infraspecific name:

Strain: FSIS31800910

BioSample:

SAMN09852795

BioProject:

PRJNA215355

Submitter:

FDA/CFSAN

Date:

2018/10/23

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_003685035.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

REWJ01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

97x

Sequencing technology:

ILLUMINA

IDs: 2031911 [UID] 7630228 [GenBank]

See Genome Information for Listeria monocytogenes

Pathogen Detection Resources

There are 60478 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_003685035.1	n/a	n/a	PDT000364506.1	Contig	Latest GenBank

Comment

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'.
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Date::08/17/2018 21:52:26
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::4.5
Genes (total)::3,030
CDS (total)::2,977
Genes (coding)::2,957
CDS (coding)::2,957
Genes (RNA)::53
rRNAs::2, 2, 2 (5S, 16S, 23S)
complete rRNAs::2 (5S)
partial rRNAs::2, 2 (16S, 23S)
tRNAs::43
ncRNAs::4
Pseudo Genes (total)::20
Pseudo Genes (ambiguous residues)::0 of 20
Pseudo Genes (frameshifted)::12 of 20
Pseudo Genes (incomplete)::6 of 20
Pseudo Genes (internal stop)::4 of 20
Pseudo Genes (multiple problems)::2 of 20
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	3,014,954
Total ungapped length	3,014,954
Number of contigs	29
Contig N50	212,449
Contig L50	5
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	29

	ANI	Query coverage	Subject coverage
Declared type	99.49	91.43	92.49
Best-match type	99.49	91.43	92.49

Assembly

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Download Assembly

PDT000364506.1

See Genome Information for Listeria monocytogenes

Pathogen Detection Resources

There are 60478 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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Declared organism

Best-matching type-strain assembly for declared species

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Average Nucleotide Identity (ANI) data

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