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Salmonella enterica strain SAL-18-VL-SD-OK-0002, whole genome shotgun sequencing project

GenBank: AAFPJP000000000.1

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

LOCUS       AAFPJP010000000           34 rc    DNA     linear   BCT 03-JUL-2019
DEFINITION  Salmonella enterica strain SAL-18-VL-SD-OK-0002, whole genome
            shotgun sequencing project.
ACCESSION   AAFPJP000000000
VERSION     AAFPJP000000000.1
DBLINK      BioProject: PRJNA316457
            BioSample: SAMN09951524
            Sequence Read Archive: SRR7799339
KEYWORDS    WGS.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 34)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (07-SEP-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Salmonella enterica whole genome shotgun (WGS) project has the
            project accession AAFPJP000000000.  This version of the project
            (01) has the accession number AAFPJP010000000, and consists of
            sequences AAFPJP010000001-AAFPJP010000034.
            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'.
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Assembly-Data-START##
            Assembly Date         :: 07-SEP-2018
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT000372802.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000372802.1
            Genome Coverage       :: 141x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 09/07/2018 04:15:02
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS+
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline
            Annotation Provider               :: NCBI
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Annotation Software revision      :: 4.5
            Genes (total)                     :: 5,164
            CDS (total)                       :: 5,065
            Genes (coding)                    :: 4,897
            CDS (coding)                      :: 4,897
            Genes (RNA)                       :: 99
            rRNAs                             :: 5, 2, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 5 (5S)
            partial rRNAs                     :: 2, 2 (16S, 23S)
            tRNAs                             :: 77
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 90 of 168
            Pseudo Genes (incomplete)         :: 63 of 168
            Pseudo Genes (internal stop)      :: 54 of 168
            Pseudo Genes (multiple problems)  :: 36 of 168
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..34
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="SAL-18-VL-SD-OK-0002"
                     /isolation_source="Bovine Intestines (Bovine)"
                     /db_xref="taxon:28901"
                     /geo_loc_name="USA: OK"
                     /collection_date="2018-02"
                     /collected_by="OADDL - OK"
WGS         AAFPJP010000001-AAFPJP010000034
//
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