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Escherichia coli strain ECOL-20-VL-NY-FL-0025, whole genome shotgun sequencing project

GenBank: ABCEGO000000000.1

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

LOCUS       ABCEGO010000000           50 rc    DNA     linear   BCT 30-AUG-2021
DEFINITION  Escherichia coli strain ECOL-20-VL-NY-FL-0025, whole genome shotgun
            sequencing project.
ACCESSION   ABCEGO000000000
VERSION     ABCEGO000000000.1
DBLINK      BioProject: PRJNA324565
            BioSample: SAMN21038398
            Sequence Read Archive: SRR15668799
KEYWORDS    WGS.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 50)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (30-AUG-2021) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Escherichia coli whole genome shotgun (WGS) project has the
            project accession ABCEGO000000000.  This version of the project
            (01) has the accession number ABCEGO010000000, and consists of
            sequences ABCEGO010000001-ABCEGO010000050.
            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         :: 30-AUG-2021
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT001119212.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT001119212.1
            Genome Coverage       :: 53x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 08/30/2021 19:54:55
            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)                     :: 5,091
            CDSs (total)                      :: 5,002
            Genes (coding)                    :: 4,835
            CDSs (with protein)               :: 4,835
            Genes (RNA)                       :: 89
            rRNAs                             :: 1, 3, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 1 (5S)
            partial rRNAs                     :: 3, 3 (16S, 23S)
            tRNAs                             :: 76
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 91 of 167
            Pseudo Genes (incomplete)         :: 91 of 167
            Pseudo Genes (internal stop)      :: 45 of 167
            Pseudo Genes (multiple problems)  :: 55 of 167
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..50
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ECOL-20-VL-NY-FL-0025"
                     /isolation_source="Urine (Canis lupus familiaris)"
                     /host="Canis lupus familiaris"
                     /db_xref="taxon:562"
                     /geo_loc_name="USA: FL"
                     /collection_date="2020-08-26"
                     /collected_by="Florida Department of Agriculture and
                     Consumer Services, Bronson Animal Disease Diagnostic
                     Laboratory"
WGS         ABCEGO010000001-ABCEGO010000050
//
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