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ASM172559v1

Organism name:
Xanthomonadaceae bacterium SCN 69-25 (g-proteobacteria)
Taxonomy check:
Inconclusive
BioSample:
SAMN03652523
BioProject:
PRJNA279279
Submitter:
Banfield Lab, University of California, Berkeley
Date:
2016/09/13
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
Excluded from RefSeq:
  • derived from metagenome
  • genus undefined
GenBank assembly accession:
GCA_001725595.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
MEGS01
Assembly method:
idba_ud v. 1.1
Genome coverage:
25.24x
Sequencing technology:
Illumina HiSeq2000

IDs: 793881 [UID] 3444198 [GenBank]

See Genome Information for Xanthomonadaceae bacterium SCN 69-25

History (Show revision history)

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::08/31/2016 18:29:59
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)::4,724
CDS (total)::4,670
Genes (coding)::4,572
CDS (coding)::4,572
Genes (RNA)::54
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1 (5S)
partial rRNAs::1, 1 (16S, 23S)
tRNAs::47
ncRNAs::4
Pseudo Genes (total)::98
Pseudo Genes (ambiguous residues)::6 of 98
Pseudo Genes (frameshifted)::15 of 98
Pseudo Genes (incomplete)::78 of 98
Pseudo Genes (internal stop)::3 of 98
Pseudo Genes (multiple problems)::4 of 98
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,711,127
Total ungapped length5,710,785
Gaps between scaffolds0
Number of scaffolds68
Scaffold N50128,536
Scaffold L5016
Number of contigs79
Contig N50117,640
Contig L5017
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)68

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced5,711,127685,710,785128,536110

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Xanthomonadaceae bacterium SCN 69-25Xanthomonadaceae bacterium SCN 69-25

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
no-typeno-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_024609805.1Tahibacter caenitype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type89.9269.1172.22

ANI result

Taxonomy check statusBest match statusComment
Inconclusivebelow-threshold-mismatchna