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ASM842067v1

  • Anomalous assembly.
Organism name:
Alistipes onderdonkii (CFB group bacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: BIOML-A28
BioSample:
SAMN11943143
BioProject:
PRJNA544527
Submitter:
Massachusetts Institute of Technology
Date:
2019/09/16
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
Assembly anomaly:
contaminated
Excluded from RefSeq:
  • contaminated
  • from large multi-isolate project
  • genome length too large
GenBank assembly accession:
GCA_008420675.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
VVOG01
Assembly method:
SPAdes v. 3.9.1
Expected final version:
no
Genome coverage:
86.157x
Sequencing technology:
Illumina NextSeq

IDs: 4584061 [UID] 13769518 [GenBank]

See Genome Information for Alistipes onderdonkii

There are 401 assemblies for this organism

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History (Show revision history)

Comment

The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP 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::09/12/2019 15:44:06
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.9
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::4,196
CDSs (total)::4,127
Genes (coding)::3,907
CDSs (with protein)::3,907
Genes (RNA)::69
rRNAs::2, 3, 2 (5S, 16S, 23S)
complete rRNAs::2, 2, 2 (5S, 16S, 23S)
partial rRNAs::1 (16S)
tRNAs::58
ncRNAs::4
Pseudo Genes (total)::220
CDSs (without protein)::220
Pseudo Genes (ambiguous residues)::0 of 220
Pseudo Genes (frameshifted)::89 of 220
Pseudo Genes (incomplete)::132 of 220
Pseudo Genes (internal stop)::34 of 220
Pseudo Genes (multiple problems)::28 of 220
##Genome-Annotation-Data-END##

Global statistics

Total sequence length4,421,502
Total ungapped length4,415,973
Gaps between scaffolds0
Number of scaffolds242
Scaffold N50175,318
Scaffold L507
Number of contigs258
Contig N50130,869
Contig L5010
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)242

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
unplaced4,421,5022424,415,973175,318160

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Alistipes onderdonkiiAlistipes onderdonkii

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_006542645.1Alistipes onderdonkii subsp. vulgaristype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_006542645.1Alistipes onderdonkiitype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type97.9565.2382.13
Best-match type97.9565.2382.13

ANI result

Taxonomy check statusBest match statusComment
OKderived-species-matchna