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Escherichia coli strain CVM N18EC1294, whole genome shotgun sequencing project

GenBank: AASFXP000000000.1

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

LOCUS       AASFXP010000000          113 rc    DNA     linear   BCT 15-APR-2020
DEFINITION  Escherichia coli strain CVM N18EC1294, whole genome shotgun
            sequencing project.
ACCESSION   AASFXP000000000
VERSION     AASFXP000000000.1
DBLINK      BioProject: PRJNA292663
            BioSample: SAMN12359564
            Sequence Read Archive: SRR9852771
KEYWORDS    WGS.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 113)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUL-2019) 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 AASFXP000000000.  This version of the project
            (01) has the accession number AASFXP010000000, and consists of
            sequences AASFXP010000001-AASFXP010000113.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            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         :: 29-JUL-2019
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT000550330.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000550330.1
            Genome Coverage       :: 89x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 07/29/2019 21:44:14
            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      :: 4.8
            Genes (total)                     :: 5,251
            CDSs (total)                      :: 5,154
            Genes (coding)                    :: 4,925
            CDSs (with protein)               :: 4,925
            Genes (RNA)                       :: 97
            rRNAs                             :: 3, 2, 3 (5S, 16S, 23S)
            complete rRNAs                    :: 3 (5S)
            partial rRNAs                     :: 2, 3 (16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 117 of 229
            Pseudo Genes (incomplete)         :: 92 of 229
            Pseudo Genes (internal stop)      :: 57 of 229
            Pseudo Genes (multiple problems)  :: 36 of 229
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CVM N18EC1294"
                     /isolation_source="Chicken Thighs"
                     /db_xref="taxon:562"
                     /geo_loc_name="USA: SC"
                     /collection_date="2018"
                     /collected_by="FDA"
WGS         AASFXP010000001-AASFXP010000113
//
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