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Salmonella enterica subsp. enterica serovar Typhimurium strain SAL-22-VL-ON-ON-0037, whole genome shotgun sequencing project

GenBank: ABODYB000000000.1

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

LOCUS       ABODYB010000000          104 rc    DNA     linear   BCT 20-OCT-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            SAL-22-VL-ON-ON-0037, whole genome shotgun sequencing project.
ACCESSION   ABODYB000000000
VERSION     ABODYB000000000.1
DBLINK      BioProject: PRJNA503850
            BioSample: SAMN35724178
            Sequence Read Archive: SRR24907588
KEYWORDS    WGS.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 104)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2023) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Salmonella enterica subsp. enterica serovar Typhimurium whole
            genome shotgun (WGS) project has the project accession
            ABODYB000000000.  This version of the project (01) has the
            accession number ABODYB010000000, and consists of sequences
            ABODYB010000001-ABODYB010000104.
            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         :: 13-JUN-2023
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT001778342.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT001778342.1
            Genome Coverage       :: 49x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 06/13/2023 23:08:48
            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)                     :: 4,916
            CDSs (total)                      :: 4,821
            Genes (coding)                    :: 4,711
            CDSs (with protein)               :: 4,711
            Genes (RNA)                       :: 95
            rRNAs                             :: 5, 1, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 5 (5S)
            partial rRNAs                     :: 1, 3 (16S, 23S)
            tRNAs                             :: 73
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 44 of 110
            Pseudo Genes (incomplete)         :: 59 of 110
            Pseudo Genes (internal stop)      :: 28 of 110
            Pseudo Genes (multiple problems)  :: 18 of 110
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..104
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="SAL-22-VL-ON-ON-0037"
                     /serovar="Typhimurium"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /geo_loc_name="Canada: Ontario"
                     /collection_date="2022-10-06"
                     /collected_by="University of Guelph Animal Health
                     Laboratory. Canada, Guelph"
WGS         ABODYB010000001-ABODYB010000104
//
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