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Source database (GenBank or RefSeq) File type

PDT000262053.2

Description:

NCBI Pathogen Detection Assembly PDT000262053.2

Organism name:

Campylobacter coli (e-proteobacteria)

Taxonomy check:

Infraspecific name:

Strain: NC_C3424

BioSample:

SAMN07982457

BioProject:

PRJNA293228

Submitter:

US Food and Drug Administration

Date:

2019/05/06

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_005186925.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

AACGKY01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

160x

Sequencing technology:

ILLUMINA

IDs: 2772971 [UID] 9789918 [GenBank]

See Genome Information for Campylobacter coli

Pathogen Detection Resources

There are 32822 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_005186925.1	n/a	n/a	PDT000262053.2	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::04/28/2019 10:15:30
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::4.8
Genes (total)::1,858
CDSs (total)::1,813
Genes (coding)::1,758
CDSs (with protein)::1,758
Genes (RNA)::45
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1, 1 (5S, 16S, 23S)
tRNAs::39
ncRNAs::3
Pseudo Genes (total)::55
CDSs (without protein)::55
Pseudo Genes (ambiguous residues)::0 of 55
Pseudo Genes (frameshifted)::29 of 55
Pseudo Genes (incomplete)::20 of 55
Pseudo Genes (internal stop)::10 of 55
Pseudo Genes (multiple problems)::4 of 55
CRISPR Arrays::1
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	1,778,809
Total ungapped length	1,778,809
Number of contigs	19
Contig N50	133,232
Contig L50	5
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	19

	ANI	Query coverage	Subject coverage
Declared type	98.72	91.47	83.93
Best-match type	98.72	91.47	83.93

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PDT000262053.2

See Genome Information for Campylobacter coli

Pathogen Detection Resources

There are 32822 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

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Average Nucleotide Identity (ANI) data

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