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Salmonella enterica strain IDR2400055918-02-10, whole genome shotgun sequencing project

GenBank: ABWONP000000000.1

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

LOCUS       ABWONP010000000           43 rc    DNA     linear   BCT 03-DEC-2024
DEFINITION  Salmonella enterica strain IDR2400055918-02-10, whole genome
            shotgun sequencing project.
ACCESSION   ABWONP000000000
VERSION     ABWONP000000000.1
DBLINK      BioProject: PRJNA183850
            BioSample: SAMN45144333
            Sequence Read Archive: SRR31583884
KEYWORDS    WGS.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 43)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (03-DEC-2024) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administration, 5100 Paint Branch Pkwy,
            College Park, MD, USA
COMMENT     The Salmonella enterica whole genome shotgun (WGS) project has the
            project accession ABWONP000000000.  This version of the project
            (01) has the accession number ABWONP010000000, and consists of
            sequences ABWONP010000001-ABWONP010000043.
            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         :: 03-DEC-2024
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT002505599.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT002505599.1
            Genome Coverage       :: 62x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 12/03/2024 18:06:40
            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)                     :: 4,805
            CDSs (total)                      :: 4,718
            Genes (coding)                    :: 4,588
            CDSs (with protein)               :: 4,588
            Genes (RNA)                       :: 87
            rRNAs                             :: 3, 4, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 3 (5S)
            partial rRNAs                     :: 4, 2 (16S, 23S)
            tRNAs                             :: 66
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 130
            CDSs (without protein)            :: 130
            Pseudo Genes (ambiguous residues) :: 0 of 130
            Pseudo Genes (frameshifted)       :: 61 of 130
            Pseudo Genes (incomplete)         :: 95 of 130
            Pseudo Genes (internal stop)      :: 27 of 130
            Pseudo Genes (multiple problems)  :: 47 of 130
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..43
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="IDR2400055918-02-10"
                     /isolation_source="Wastewater influent"
                     /db_xref="taxon:28901"
                     /geo_loc_name="USA: NY"
                     /collection_date="2024-08-15"
                     /collected_by="New York State Department of Health"
WGS         ABWONP010000001-ABWONP010000043
//
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