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GenBank: DBCNXF000000000.1
LOCUS DBCNXF010000000 113 rc DNA linear BCT 26-NOV-2024 DEFINITION TPA_asm: Salmonella enterica subsp. enterica serovar Paratyphi A strain AUSMDU00102552, whole genome shotgun sequencing project. ACCESSION DBCNXF000000000 VERSION DBCNXF000000000.1 DBLINK BioProject: PRJNA514245 BioSample: SAMN44863422 Sequence Read Archive: SRR31507155 KEYWORDS WGS; Third Party Data; TPA; TPA:assembly. SOURCE Salmonella enterica subsp. enterica serovar Paratyphi A (Salmonella paratyphi) ORGANISM Salmonella enterica subsp. enterica serovar Paratyphi A Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella. REFERENCE 1 (bases 1 to 113) 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 113) CONSRTM NCBI Pathogen Detection Project TITLE Direct Submission JOURNAL Submitted (26-NOV-2024) National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 45, Center Drive, Bethesda, MD, USA COMMENT The Salmonella enterica subsp. enterica serovar Paratyphi A whole genome shotgun (WGS) project has the project accession DBCNXF000000000. This version of the project (01) has the accession number DBCNXF010000000, and consists of sequences DBCNXF010000001-DBCNXF010000113. 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 :: 26-NOV-2024 Assembly Method :: SKESA v. 2.2 Assembly Name :: PDT002495626.1 Long Assembly Name :: NCBI Pathogen Detection Assembly PDT002495626.1 Genome Coverage :: 115x Sequencing Technology :: ILLUMINA ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Date :: 11/26/2024 11:32:33 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) :: 4,611 CDSs (total) :: 4,523 Genes (coding) :: 4,270 CDSs (with protein) :: 4,270 Genes (RNA) :: 88 rRNAs :: 1, 2, 4 (5S, 16S, 23S) complete rRNAs :: 1 (5S) partial rRNAs :: 2, 4 (16S, 23S) tRNAs :: 71 ncRNAs :: 10 Pseudo Genes (total) :: 253 CDSs (without protein) :: 253 Pseudo Genes (ambiguous residues) :: 0 of 253 Pseudo Genes (frameshifted) :: 110 of 253 Pseudo Genes (incomplete) :: 96 of 253 Pseudo Genes (internal stop) :: 90 of 253 Pseudo Genes (multiple problems) :: 37 of 253 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..113 /organism="Salmonella enterica subsp. enterica serovar Paratyphi A" /mol_type="genomic DNA" /strain="AUSMDU00102552" /serovar="Paratyphi A" /host="Homo sapiens" /sub_species="enterica" /db_xref="taxon:54388" /geo_loc_name="Australia: Victoria" /collection_date="2024-05-31" /collected_by="MDU-PHL" /note="genotype: ST85" WGS DBCNXF010000001-DBCNXF010000113 //
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