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Source database (GenBank or RefSeq) File type

ASM180143v1

Organism name:

Gammaproteobacteria bacterium RIFCSPHIGHO2_12_38_15 (g-proteobacteria)

Taxonomy check:

Inconclusive

BioSample:

SAMN04313768

BioProject:

PRJNA288027

Submitter:

Banfield Lab, University of California, Berkeley

Date:

2016/10/20

Assembly type:

Assembly level:

Scaffold

Genome representation:

full

Excluded from RefSeq:

derived from metagenome
genus undefined

GenBank assembly accession:

GCA_001801435.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

MGXS01

Assembly method:

IDBA_UD v. 06.01.2014s

Genome coverage:

10x

Sequencing technology:

Illumina HiSeq2000

IDs: 833631 [UID] 3557948 [GenBank]

See Genome Information for Gammaproteobacteria bacterium RIFCSPHIGHO2_12_38_15

Pathogen Detection Resources

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_001801435.1	n/a	n/a	ASM180143v1	Scaffold	Latest GenBank

Comment

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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Provider::NCBI
Annotation Date::09/08/2016 13:08:06
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::3.3
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::1,533
CDS (total)::1,495
Genes (coding)::1,412
CDS (coding)::1,412
Genes (RNA)::38
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1 (5S)
partial rRNAs::1, 1 (16S, 23S)
tRNAs::32
ncRNAs::3
Pseudo Genes (total)::83
Pseudo Genes (ambiguous residues)::7 of 83
Pseudo Genes (frameshifted)::3 of 83
Pseudo Genes (incomplete)::75 of 83
Pseudo Genes (internal stop)::2 of 83
Pseudo Genes (multiple problems)::4 of 83
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	1,562,040
Total ungapped length	1,561,918
Gaps between scaffolds	0
Number of scaffolds	88
Scaffold N50	23,423
Scaffold L50	21
Number of contigs	94
Contig N50	23,423
Contig L50	21
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	88

	ANI	Query coverage	Subject coverage
Declared type	na	na	na
Best-match type	83.87	0.04	0.02

Assembly

Genome Assembly

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ASM180143v1

See Genome Information for Gammaproteobacteria bacterium RIFCSPHIGHO2_12_38_15

Pathogen Detection Resources

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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Assembly Information

Related Information

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Global assembly definition

Assembly statistics

Assembly QA

Taxonomy Check Data

Declared organism

Best-matching type-strain assembly for declared species

Best-matching type-strain assembly

Average Nucleotide Identity (ANI) data

ANI result