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Source database (GenBank or RefSeq) File type

PDT001264418.1

Description:

NCBI Pathogen Detection Assembly PDT001264418.1

Organism name:

Enterococcus faecalis (firmicutes)

Taxonomy check:

Infraspecific name:

Strain: FSIS12209740

BioSample:

SAMN26514278

BioProject:

PRJNA292669

Submitter:

FDA

Date:

2022/03/16

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_022591535.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

ABFJOG01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

124x

Sequencing technology:

ILLUMINA

IDs: 12330131 [UID] 32301658 [GenBank]

See Genome Information for Enterococcus faecalis

Pathogen Detection Resources

There are 8807 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_022591535.1	n/a	n/a	PDT001264418.1	Contig	Latest GenBank

Comment

The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/
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::03/16/2022 07:41:18
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::2021-01-11.build5132
Genes (total)::2,888
CDSs (total)::2,827
Genes (coding)::2,784
CDSs (with protein)::2,784
Genes (RNA)::61
rRNAs::2, 1, 2 (5S, 16S, 23S)
complete rRNAs::2, 1 (5S, 16S)
partial rRNAs::2 (23S)
tRNAs::52
ncRNAs::4
Pseudo Genes (total)::43
CDSs (without protein)::43
Pseudo Genes (ambiguous residues)::0 of 43
Pseudo Genes (frameshifted)::18 of 43
Pseudo Genes (incomplete)::23 of 43
Pseudo Genes (internal stop)::6 of 43
Pseudo Genes (multiple problems)::4 of 43
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	2,943,814
Total ungapped length	2,943,814
Number of contigs	133
Contig N50	60,944
Contig L50	19
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	133

	ANI	Query coverage	Subject coverage
Declared type	99.04	85.71	87.72
Best-match type	99.04	85.71	87.72

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PDT001264418.1

See Genome Information for Enterococcus faecalis

Pathogen Detection Resources

There are 8807 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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Best-matching type-strain assembly for declared species

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