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Staphylococcus pseudintermedius strain SPSE-20-VL-SD-IA-0038 isolate Canis lupus familiaris, whole genome shotgun sequencing project

GenBank: ABDFGC000000000.1

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

LOCUS       ABDFGC010000000           43 rc    DNA     linear   BCT 13-OCT-2021
DEFINITION  Staphylococcus pseudintermedius strain SPSE-20-VL-SD-IA-0038
            isolate Canis lupus familiaris, whole genome shotgun sequencing
            project.
ACCESSION   ABDFGC000000000
VERSION     ABDFGC000000000.1
DBLINK      BioProject: PRJNA318594
            BioSample: SAMN22184040
            Sequence Read Archive: SRR16298890
KEYWORDS    WGS.
SOURCE      Staphylococcus pseudintermedius
  ORGANISM  Staphylococcus pseudintermedius
            Bacteria; Bacillati; Bacillota; Bacilli; Bacillales;
            Staphylococcaceae; Staphylococcus; Staphylococcus intermedius
            group.
REFERENCE   1  (bases 1 to 43)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (12-OCT-2021) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Staphylococcus pseudintermedius whole genome shotgun (WGS)
            project has the project accession ABDFGC000000000.  This version of
            the project (01) has the accession number ABDFGC010000000, and
            consists of sequences ABDFGC010000001-ABDFGC010000043.
            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         :: 12-OCT-2021
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT001149398.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT001149398.1
            Genome Coverage       :: 371x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 10/13/2021 04:19:12
            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)                     :: 2,594
            CDSs (total)                      :: 2,525
            Genes (coding)                    :: 2,475
            CDSs (with protein)               :: 2,475
            Genes (RNA)                       :: 69
            rRNAs                             :: 3, 3, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 3 (5S)
            partial rRNAs                     :: 3, 1 (16S, 23S)
            tRNAs                             :: 57
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 50
            CDSs (without protein)            :: 50
            Pseudo Genes (ambiguous residues) :: 0 of 50
            Pseudo Genes (frameshifted)       :: 17 of 50
            Pseudo Genes (incomplete)         :: 31 of 50
            Pseudo Genes (internal stop)      :: 16 of 50
            Pseudo Genes (multiple problems)  :: 14 of 50
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..43
                     /organism="Staphylococcus pseudintermedius"
                     /mol_type="genomic DNA"
                     /strain="SPSE-20-VL-SD-IA-0038"
                     /isolate="Canis lupus familiaris"
                     /isolation_source="urine"
                     /db_xref="taxon:283734"
                     /geo_loc_name="USA: IA"
                     /collection_date="2020-10-05"
                     /collected_by="ISUVDL"
WGS         ABDFGC010000001-ABDFGC010000043
//
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