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Salmonella enterica subsp. enterica serovar Chailey strain SAL-18-VL-SD-IA-0048, whole genome shotgun sequencing project

GenBank: AAFJRA000000000.1

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

LOCUS       AAFJRA010000000           94 rc    DNA     linear   BCT 25-JUN-2019
DEFINITION  Salmonella enterica subsp. enterica serovar Chailey strain
            SAL-18-VL-SD-IA-0048, whole genome shotgun sequencing project.
ACCESSION   AAFJRA000000000
VERSION     AAFJRA000000000.1
DBLINK      BioProject: PRJNA316457
            BioSample: SAMN12056351
            Sequence Read Archive: SRR9301061
KEYWORDS    WGS.
SOURCE      Salmonella enterica subsp. enterica serovar Chailey
  ORGANISM  Salmonella enterica subsp. enterica serovar Chailey
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 94)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Salmonella enterica subsp. enterica serovar Chailey whole
            genome shotgun (WGS) project has the project accession
            AAFJRA000000000.  This version of the project (01) has the
            accession number AAFJRA010000000, and consists of sequences
            AAFJRA010000001-AAFJRA010000094.
            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         :: 13-JUN-2019
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT000522674.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000522674.1
            Genome Coverage       :: 87x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 06/14/2019 20:49:12
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline
            Annotation Provider               :: NCBI
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Annotation Software revision      :: 4.8
            Genes (total)                     :: 4,641
            CDSs (total)                      :: 4,542
            Genes (coding)                    :: 4,454
            CDSs (with protein)               :: 4,454
            Genes (RNA)                       :: 99
            rRNAs                             :: 6, 1, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 6 (5S)
            partial rRNAs                     :: 1, 3 (16S, 23S)
            tRNAs                             :: 73
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 88
            CDSs (without protein)            :: 88
            Pseudo Genes (ambiguous residues) :: 0 of 88
            Pseudo Genes (frameshifted)       :: 40 of 88
            Pseudo Genes (incomplete)         :: 50 of 88
            Pseudo Genes (internal stop)      :: 19 of 88
            Pseudo Genes (multiple problems)  :: 20 of 88
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..94
                     /organism="Salmonella enterica subsp. enterica serovar
                     Chailey"
                     /mol_type="genomic DNA"
                     /strain="SAL-18-VL-SD-IA-0048"
                     /serovar="Chailey"
                     /isolation_source="Porcine Enteric (Sus scrofa
                     domesticus)"
                     /sub_species="enterica"
                     /db_xref="taxon:2564322"
                     /geo_loc_name="USA: NC"
                     /collection_date="2018-11-29"
                     /collected_by="ISUVDL"
WGS         AAFJRA010000001-AAFJRA010000094
//
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