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ASM967801v1

Organism name:
Ligilactobacillus ruminis (firmicutes)
Taxonomy check:
OK
Infraspecific name:
Strain: BIOML-A19
BioSample:
SAMN11946146
BioProject:
PRJNA544527
Submitter:
Massachusetts Institute of Technology
Date:
2019/11/20
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_009678015.1 (latest)
RefSeq assembly accession:
GCF_009678015.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
WKOC01
Assembly method:
SPAdes v. 3.9.1
Expected final version:
yes
Genome coverage:
69.422x
Sequencing technology:
Illumina NextSeq

IDs: 5342381 [UID] 15463478 [GenBank] 15483248 [RefSeq]

See Genome Information for Ligilactobacillus ruminis

There are 115 assemblies for this organism

See more

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://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::11/15/2019 19:06:40
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.10
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::2,142
CDSs (total)::2,070
Genes (coding)::1,979
CDSs (with protein)::1,979
Genes (RNA)::72
rRNAs::2, 1, 2 (5S, 16S, 23S)
complete rRNAs::2, 1, 1 (5S, 16S, 23S)
partial rRNAs::1 (23S)
tRNAs::64
ncRNAs::3
Pseudo Genes (total)::91
CDSs (without protein)::91
Pseudo Genes (ambiguous residues)::1 of 91
Pseudo Genes (frameshifted)::35 of 91
Pseudo Genes (incomplete)::50 of 91
Pseudo Genes (internal stop)::25 of 91
Pseudo Genes (multiple problems)::19 of 91
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length2,157,177
Total ungapped length2,157,118
Gaps between scaffolds0
Number of scaffolds69
Scaffold N5060,394
Scaffold L5011
Number of contigs71
Contig N5060,394
Contig L5011
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)69

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
unplaced2,157,177692,157,11860,39420

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Ligilactobacillus ruminisLigilactobacillus ruminis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_001591905.1Ligilactobacillus ruminis DSM 20403 = NBRC 102161type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001591905.1Ligilactobacillus ruministype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type97.5080.1486.69
Best-match type97.5080.1486.69

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna