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Organism name:
Lachnoclostridium phytofermentans ISDg (firmicutes)
Taxonomy check:
Infraspecific name:
Strain: ISDg
US DOE Joint Genome Institute
Assembly type:
Assembly level:
Complete Genome
Genome representation:
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000018685.1 (latest)
RefSeq assembly accession:
GCF_000018685.1 (latest)
RefSeq assembly and GenBank assembly identical:

IDs: 39748 [UID] 19488 [GenBank] 39748 [RefSeq]

See Genome Information for Lachnoclostridium phytofermentans

There are 5 assemblies for this organism

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History (Show revision history)


URL -- http://www.jgi.doe.gov
JGI Project ID: 3634491
Source DNA and bacteria available from Susan Leschine (suel@microbio.umass.edu)
Contacts: Susan Leschine (suel@microbio.umass.edu)
 Paul Richardson (microbes@cuba.jgi-psf.org)
Quality assurance done by JGI-Stanford
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LANL
Finished microbial genomes have been curated to close ... all gaps with greater than 98% coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000.
The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. it is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis.
The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/  more


Annotation Provider::NCBI RefSeq
Annotation Date::03/30/2022 01:27:19
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.1
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::4,112
CDSs (total)::4,023
Genes (coding)::3,976
CDSs (with protein)::3,976
Genes (RNA)::89
rRNAs::8, 8, 8 (5S, 16S, 23S)
complete rRNAs::8, 8, 8 (5S, 16S, 23S)
Pseudo Genes (total)::47
CDSs (without protein)::47
Pseudo Genes (ambiguous residues)::0 of 47
Pseudo Genes (frameshifted)::13 of 47
Pseudo Genes (incomplete)::35 of 47
Pseudo Genes (internal stop)::6 of 47
Pseudo Genes (multiple problems)::6 of 47

Global statistics

Total sequence length4,847,594
Total ungapped length4,847,594
Total number of chromosomes and plasmids1

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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
Assembly Unit: Primary Assembly (GCF_000018695.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP000885.1=NC_010001.1

Assembly statistics

Chromosome 4,847,594

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Lachnoclostridium phytofermentans ISDgLachnoclostridium phytofermentans

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001403615.1Desnuesiella massiliensistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type90.010.520.46

ANI result

Taxonomy check statusBest match statusComment
OKlow-coverageAssembly is the type-strain, no match is expected
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