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Salmonella enterica subsp. enterica serovar Saintpaul strain SENASICA_Sa_BQ63, whole genome shotgun sequencing project

GenBank: ABRTTC000000000.1

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

LOCUS       ABRTTC010000000           37 rc    DNA     linear   BCT 18-APR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Saintpaul strain
            SENASICA_Sa_BQ63, whole genome shotgun sequencing project.
ACCESSION   ABRTTC000000000
VERSION     ABRTTC000000000.1
DBLINK      BioProject: PRJNA480281
            BioSample: SAMN40973939
            Sequence Read Archive: SRR28724137
KEYWORDS    WGS.
SOURCE      Salmonella enterica subsp. enterica serovar Saintpaul
  ORGANISM  Salmonella enterica subsp. enterica serovar Saintpaul
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 37)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (17-APR-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 subsp. enterica serovar Saintpaul whole
            genome shotgun (WGS) project has the project accession
            ABRTTC000000000.  This version of the project (01) has the
            accession number ABRTTC010000000, and consists of sequences
            ABRTTC010000001-ABRTTC010000037.
            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         :: 17-APR-2024
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT002140562.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT002140562.1
            Genome Coverage       :: 157x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 04/18/2024 03:35:52
            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      :: 2021-01-11.build5132
            Genes (total)                     :: 4,797
            CDSs (total)                      :: 4,703
            Genes (coding)                    :: 4,625
            CDSs (with protein)               :: 4,625
            Genes (RNA)                       :: 94
            rRNAs                             :: 4, 2, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 4 (5S)
            partial rRNAs                     :: 2, 3 (16S, 23S)
            tRNAs                             :: 74
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 78
            CDSs (without protein)            :: 78
            Pseudo Genes (ambiguous residues) :: 0 of 78
            Pseudo Genes (frameshifted)       :: 25 of 78
            Pseudo Genes (incomplete)         :: 49 of 78
            Pseudo Genes (internal stop)      :: 21 of 78
            Pseudo Genes (multiple problems)  :: 14 of 78
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..37
                     /organism="Salmonella enterica subsp. enterica serovar
                     Saintpaul"
                     /mol_type="genomic DNA"
                     /strain="SENASICA_Sa_BQ63"
                     /serovar="Saintpaul"
                     /isolation_source="Poultry"
                     /sub_species="enterica"
                     /db_xref="taxon:90105"
                     /geo_loc_name="Mexico"
                     /collection_date="2023-08-06"
                     /collected_by="INSP-FMVZ"
WGS         ABRTTC010000001-ABRTTC010000037
//
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