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TPA_asm: Salmonella enterica subsp. enterica serovar Paratyphi A strain AUSMDU00102552, whole genome shotgun sequencing project

GenBank: DBCNXF000000000.1

  • This entry is the master record for a whole genome shotgun sequencing project and contains no sequence data.

LOCUS       DBCNXF010000000          113 rc    DNA     linear   BCT 26-NOV-2024
DEFINITION  TPA_asm: Salmonella enterica subsp. enterica serovar Paratyphi A
            strain AUSMDU00102552, whole genome shotgun sequencing project.
ACCESSION   DBCNXF000000000
VERSION     DBCNXF000000000.1
DBLINK      BioProject: PRJNA514245
            BioSample: SAMN44863422
            Sequence Read Archive: SRR31507155
KEYWORDS    WGS; Third Party Data; TPA; TPA:assembly.
SOURCE      Salmonella enterica subsp. enterica serovar Paratyphi A (Salmonella
            paratyphi)
  ORGANISM  Salmonella enterica subsp. enterica serovar Paratyphi A
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 113)
  AUTHORS   Souvorov,A., Agarwala,R. and Lipman,D.J.
  TITLE     SKESA: strategic k-mer extension for scrupulous assemblies
  JOURNAL   Genome Biol 19 (1), 153 (2018)
   PUBMED   30286803
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 113)
  CONSRTM   NCBI Pathogen Detection Project
  TITLE     Direct Submission
  JOURNAL   Submitted (26-NOV-2024) National Center for Biotechnology
            Information, National Library of Medicine, National Institutes of
            Health, Bldg 45, Center Drive, Bethesda, MD, USA
COMMENT     The Salmonella enterica subsp. enterica serovar Paratyphi A whole
            genome shotgun (WGS) project has the project accession
            DBCNXF000000000.  This version of the project (01) has the
            accession number DBCNXF010000000, and consists of sequences
            DBCNXF010000001-DBCNXF010000113.
            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'.
            
            ##Genome-Assembly-Data-START##
            Assembly Date         :: 26-NOV-2024
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT002495626.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT002495626.1
            Genome Coverage       :: 115x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 11/26/2024 11:32:33
            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
            Annotation Software revision      :: 2024-07-18.build7555
            Genes (total)                     :: 4,611
            CDSs (total)                      :: 4,523
            Genes (coding)                    :: 4,270
            CDSs (with protein)               :: 4,270
            Genes (RNA)                       :: 88
            rRNAs                             :: 1, 2, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 1 (5S)
            partial rRNAs                     :: 2, 4 (16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 253
            CDSs (without protein)            :: 253
            Pseudo Genes (ambiguous residues) :: 0 of 253
            Pseudo Genes (frameshifted)       :: 110 of 253
            Pseudo Genes (incomplete)         :: 96 of 253
            Pseudo Genes (internal stop)      :: 90 of 253
            Pseudo Genes (multiple problems)  :: 37 of 253
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..113
                     /organism="Salmonella enterica subsp. enterica serovar
                     Paratyphi A"
                     /mol_type="genomic DNA"
                     /strain="AUSMDU00102552"
                     /serovar="Paratyphi A"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:54388"
                     /geo_loc_name="Australia: Victoria"
                     /collection_date="2024-05-31"
                     /collected_by="MDU-PHL"
                     /note="genotype: ST85"
WGS         DBCNXF010000001-DBCNXF010000113
//
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