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TPA_asm: Stenotrophomonas maltophilia strain STEN00738, whole genome shotgun sequencing project

GenBank: DBDJSG000000000.1

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

LOCUS       DBDJSG010000000          312 rc    DNA     linear   BCT 10-DEC-2024
DEFINITION  TPA_asm: Stenotrophomonas maltophilia strain STEN00738, whole
            genome shotgun sequencing project.
ACCESSION   DBDJSG000000000
VERSION     DBDJSG000000000.1
DBLINK      BioProject: PRJNA514245
            BioSample: SAMN45299400
            Sequence Read Archive: SRR31655274
KEYWORDS    WGS; Third Party Data; TPA; TPA:assembly.
SOURCE      Stenotrophomonas maltophilia
  ORGANISM  Stenotrophomonas maltophilia
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Lysobacterales; Lysobacteraceae; Stenotrophomonas; Stenotrophomonas
            maltophilia group.
REFERENCE   1  (bases 1 to 312)
  AUTHORS   Souvorov,A., Agarwala,R. and Lipman,D.J.
  TITLE     SKESA: strategic k-mer extension for scrupulous assemblies
  JOURNAL   Genome Biol 19 (1), 153 (2018)
   PUBMED   30286803
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 312)
  CONSRTM   NCBI Pathogen Detection Project
  TITLE     Direct Submission
  JOURNAL   Submitted (10-DEC-2024) National Center for Biotechnology
            Information, National Library of Medicine, National Institutes of
            Health, Bldg 45, Center Drive, Bethesda, MD, USA
COMMENT     The Stenotrophomonas maltophilia whole genome shotgun (WGS) project
            has the project accession DBDJSG000000000.  This version of the
            project (01) has the accession number DBDJSG010000000, and consists
            of sequences DBDJSG010000001-DBDJSG010000312.
            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         :: 10-DEC-2024
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT002523904.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT002523904.1
            Genome Coverage       :: 53x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 12/10/2024 11:02:25
            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
            Annotation Software revision      :: 2024-07-18.build7555
            Genes (total)                     :: 4,523
            CDSs (total)                      :: 4,452
            Genes (coding)                    :: 4,413
            CDSs (with protein)               :: 4,413
            Genes (RNA)                       :: 71
            rRNAs                             :: 1, 2 (16S, 23S)
            partial rRNAs                     :: 1, 2 (16S, 23S)
            tRNAs                             :: 64
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 39
            CDSs (without protein)            :: 39
            Pseudo Genes (ambiguous residues) :: 0 of 39
            Pseudo Genes (frameshifted)       :: 13 of 39
            Pseudo Genes (incomplete)         :: 27 of 39
            Pseudo Genes (internal stop)      :: 9 of 39
            Pseudo Genes (multiple problems)  :: 9 of 39
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..312
                     /organism="Stenotrophomonas maltophilia"
                     /mol_type="genomic DNA"
                     /strain="STEN00738"
                     /isolation_source="Tissue"
                     /host="Homo sapiens"
                     /db_xref="taxon:40324"
                     /geo_loc_name="USA: Pittsburgh, Pennsylvania"
                     /lat_lon="40.44 N 79.97 W"
                     /collection_date="2023"
                     /collected_by="University of Pittsburgh Medical Center"
WGS         DBDJSG010000001-DBDJSG010000312
//
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