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Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain SAL-19-VL-SD-IA-0016, whole genome shotgun sequencing project

GenBank: AAPEIG000000000.1

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

LOCUS       AAPEIG010000000          175 rc    DNA     linear   BCT 24-FEB-2020
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            SAL-19-VL-SD-IA-0016, whole genome shotgun sequencing project.
ACCESSION   AAPEIG000000000
VERSION     AAPEIG000000000.1
DBLINK      BioProject: PRJNA316457
            BioSample: SAMN14125565
            Sequence Read Archive: SRR11101202
KEYWORDS    WGS.
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 175)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (19-FEB-2020) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Salmonella enterica subsp. enterica serovar 4,[5],12:i:- whole
            genome shotgun (WGS) project has the project accession
            AAPEIG000000000.  This version of the project (01) has the
            accession number AAPEIG010000000, and consists of sequences
            AAPEIG010000001-AAPEIG010000175.
            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         :: 19-FEB-2020
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT000687794.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000687794.1
            Genome Coverage       :: 71x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 02/20/2020 14:35:48
            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      :: 2020-02-06.build4373
            Genes (total)                     :: 5,301
            CDSs (total)                      :: 5,200
            Genes (coding)                    :: 5,117
            CDSs (with protein)               :: 5,117
            Genes (RNA)                       :: 101
            rRNAs                             :: 3, 1, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 3 (5S)
            partial rRNAs                     :: 1, 3 (16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 83
            CDSs (without protein)            :: 83
            Pseudo Genes (ambiguous residues) :: 0 of 83
            Pseudo Genes (frameshifted)       :: 29 of 83
            Pseudo Genes (incomplete)         :: 59 of 83
            Pseudo Genes (internal stop)      :: 16 of 83
            Pseudo Genes (multiple problems)  :: 18 of 83
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..175
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="SAL-19-VL-SD-IA-0016"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="Feces (Sus scrofa domesticus)"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /geo_loc_name="USA: IA"
                     /collection_date="2019-04-04"
                     /collected_by="ISUVDL"
WGS         AAPEIG010000001-AAPEIG010000175
//
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