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PDT000943603.1

Description:
NCBI Pathogen Detection Assembly PDT000943603.1
Organism name:
Shigella flexneri 5b (enterobacteria)
Taxonomy check:
OK
Isolate:
MH170031
BioSample:
SAMEA104168633
BioProject:
PRJNA514245
Submitter:
National Center for Biotechnology Information
Date:
2021/03/05
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
Excluded from RefSeq:
  • from large multi-isolate project
GenBank assembly accession:
GCA_017187835.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
DADLCP01
Assembly method:
SKESA v. 2.2
Expected final version:
no
Genome coverage:
84x
Sequencing technology:
ILLUMINA

IDs: 9442321 [UID] 25354148 [GenBank]

See Genome Information for Shigella flexneri

There are 14734 assemblies for this organism

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History (Show revision history)

Comment

The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/
This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The ... de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Date::01/29/2021 18:35:11
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::2020-02-06.build4373
Genes (total)::4,412
CDSs (total)::4,332
Genes (coding)::3,964
CDSs (with protein)::3,964
Genes (RNA)::80
rRNAs::1, 4, 2 (5S, 16S, 23S)
partial rRNAs::1, 4, 2 (5S, 16S, 23S)
tRNAs::68
ncRNAs::5
Pseudo Genes (total)::368
CDSs (without protein)::368
Pseudo Genes (ambiguous residues)::0 of 368
Pseudo Genes (frameshifted)::166 of 368
Pseudo Genes (incomplete)::87 of 368
Pseudo Genes (internal stop)::149 of 368
Pseudo Genes (multiple problems)::32 of 368
##Genome-Annotation-Data-END##

Global statistics

Total sequence length4,351,835
Total ungapped length4,351,835
Number of contigs372
Contig N5029,799
Contig L5046
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)372

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
Contig
Count
Ungapped
Length
Contig
N50
Spanned
Gaps
Unspanned
Gaps
unplaced4,351,8353724,351,83529,79900

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Shigella flexneri 5bShigella flexneri

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_001078805.1Shigella flexneri 2atype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001078805.1Shigella flexneritype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.9096.8889.35
Best-match type99.9096.8889.35

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna