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ASM346802v1

Organism name:
Holdemanella biformis (firmicutes)
Taxonomy check:
OK
Infraspecific name:
Strain: AM42-13AC
BioSample:
SAMN09736541
BioProject:
PRJNA482748
Submitter:
BGI
Date:
2018/09/06
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_003468025.1 (latest)
RefSeq assembly accession:
GCF_003468025.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
QSGD01
Assembly method:
SOAPdenovo v. 2
Expected final version:
yes
Genome coverage:
100x
Sequencing technology:
Illumina Hiseq

IDs: 1924391 [UID] 7297818 [GenBank] 7350698 [RefSeq]

See Genome Information for Holdemanella biformis

There are 61 assemblies for this organism

See more

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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/genome/annotation_prok/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::08/04/2018 06:50:28
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::4.6
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::2,603
CDS (total)::2,543
Genes (coding)::2,453
CDS (coding)::2,453
Genes (RNA)::60
rRNAs::2, 1, 2 (5S, 16S, 23S)
complete rRNAs::2, 1, 1 (5S, 16S, 23S)
partial rRNAs::1 (23S)
tRNAs::52
ncRNAs::3
Pseudo Genes (total)::90
Pseudo Genes (ambiguous residues)::17 of 90
Pseudo Genes (frameshifted)::34 of 90
Pseudo Genes (incomplete)::42 of 90
Pseudo Genes (internal stop)::16 of 90
Pseudo Genes (multiple problems)::17 of 90
CRISPR Arrays::1
##Genome-Annotation-Data-END##

Global statistics

Total sequence length2,560,346
Total ungapped length2,560,026
Gaps between scaffolds0
Number of scaffolds145
Scaffold N5034,549
Scaffold L5020
Number of contigs177
Contig N5034,303
Contig L5023
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)145

Supplemental Content

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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
unplaced2,560,3461452,560,02634,549320

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Holdemanella biformisHoldemanella biformis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000156655.1Holdemanella biformis DSM 3989suspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000156655.1Holdemanella biformissuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type97.2870.8175.05
Best-match type97.2870.8175.05

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna