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Escherichia coli O157:H7 strain CFSAN077274, whole genome shotgun sequencing project

GenBank: AARFTO000000000.1

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

LOCUS       AARFTO010000000          194 rc    DNA     linear   BCT 02-APR-2020
DEFINITION  Escherichia coli O157:H7 strain CFSAN077274, whole genome shotgun
            sequencing project.
ACCESSION   AARFTO000000000
VERSION     AARFTO000000000.1
DBLINK      BioProject: PRJNA230969
            BioSample: SAMN11942990
            Sequence Read Archive: SRR9188684
KEYWORDS    WGS; GMI.
SOURCE      Escherichia coli O157:H7
  ORGANISM  Escherichia coli O157:H7
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 194)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (19-FEB-2020) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administration, 5100 Paint Branch Pkwy,
            College Park, MD, USA
COMMENT     The Escherichia coli O157:H7 whole genome shotgun (WGS) project has
            the project accession AARFTO000000000.  This version of the project
            (01) has the accession number AARFTO010000000, and consists of
            sequences AARFTO010000001-AARFTO010000194.
            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         :: PDT000517894.2
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000517894.2
            Genome Coverage       :: 60x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 02/20/2020 16:36:04
            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)                     :: 5,618
            CDSs (total)                      :: 5,522
            Genes (coding)                    :: 5,324
            CDSs (with protein)               :: 5,324
            Genes (RNA)                       :: 96
            rRNAs                             :: 1, 1, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 1 (5S)
            partial rRNAs                     :: 1, 2 (16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 96 of 198
            Pseudo Genes (incomplete)         :: 77 of 198
            Pseudo Genes (internal stop)      :: 55 of 198
            Pseudo Genes (multiple problems)  :: 24 of 198
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..194
                     /organism="Escherichia coli O157:H7"
                     /mol_type="genomic DNA"
                     /strain="CFSAN077274"
                     /isolation_source="cattle manure"
                     /db_xref="taxon:83334"
                     /geo_loc_name="USA: CA"
                     /collection_date="2017-07-10"
                     /collected_by="FDA"
WGS         AARFTO010000001-AARFTO010000194
//
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