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GenBank: DBDJSG000000000.1
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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