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Salmonella enterica subsp. enterica serovar Infantis strain MOD1_Per71, whole genome shotgun sequencing project

GenBank: AAEWXB000000000.1

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

LOCUS       AAEWXB010000000           67 rc    DNA     linear   BCT 10-JUN-2019
DEFINITION  Salmonella enterica subsp. enterica serovar Infantis strain
            MOD1_Per71, whole genome shotgun sequencing project.
ACCESSION   AAEWXB000000000
VERSION     AAEWXB000000000.1
DBLINK      BioProject: PRJNA378379
            BioSample: SAMN07246713
            Sequence Read Archive: SRR7456254
KEYWORDS    WGS; GMI.
SOURCE      Salmonella enterica subsp. enterica serovar Infantis
  ORGANISM  Salmonella enterica subsp. enterica serovar Infantis
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 67)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUN-2018) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administraion, 5100 Paint Branch Pkwy,
            College Park, MD, USA
COMMENT     The Salmonella enterica subsp. enterica serovar Infantis whole
            genome shotgun (WGS) project has the project accession
            AAEWXB000000000.  This version of the project (01) has the
            accession number AAEWXB010000000, and consists of sequences
            AAEWXB010000001-AAEWXB010000067.
            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'.
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Assembly-Data-START##
            Assembly Date         :: 29-JUN-2018
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT000338764.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000338764.1
            Genome Coverage       :: 212x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 06/30/2018 01:03:12
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS+
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline
            Annotation Provider               :: NCBI
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Annotation Software revision      :: 4.5
            Genes (total)                     :: 5,182
            CDS (total)                       :: 5,077
            Genes (coding)                    :: 4,851
            CDS (coding)                      :: 4,851
            Genes (RNA)                       :: 105
            rRNAs                             :: 8, 3, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6 (5S)
            partial rRNAs                     :: 2, 3, 6 (5S, 16S, 23S)
            tRNAs                             :: 75
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 226
            Pseudo Genes (ambiguous residues) :: 0 of 226
            Pseudo Genes (frameshifted)       :: 120 of 226
            Pseudo Genes (incomplete)         :: 110 of 226
            Pseudo Genes (internal stop)      :: 73 of 226
            Pseudo Genes (multiple problems)  :: 66 of 226
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..67
                     /organism="Salmonella enterica subsp. enterica serovar
                     Infantis"
                     /mol_type="genomic DNA"
                     /strain="MOD1_Per71"
                     /serovar="Infantis"
                     /isolation_source="biological fluid or tissue"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:595"
                     /geo_loc_name="Peru"
                     /collection_date="2010-03-21"
                     /collected_by="MOD1"
WGS         AAEWXB010000001-AAEWXB010000067
//
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