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GenBank: ABODYB000000000.1
LOCUS ABODYB010000000 104 rc DNA linear BCT 20-OCT-2023 DEFINITION Salmonella enterica subsp. enterica serovar Typhimurium strain SAL-22-VL-ON-ON-0037, whole genome shotgun sequencing project. ACCESSION ABODYB000000000 VERSION ABODYB000000000.1 DBLINK BioProject: PRJNA503850 BioSample: SAMN35724178 Sequence Read Archive: SRR24907588 KEYWORDS WGS. SOURCE Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium) ORGANISM Salmonella enterica subsp. enterica serovar Typhimurium Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella. REFERENCE 1 (bases 1 to 104) CONSRTM Veterinary Laboratory Investigation and Response Network TITLE Direct Submission JOURNAL Submitted (13-JUN-2023) Center for Veterinary Medicine, US Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA COMMENT The Salmonella enterica subsp. enterica serovar Typhimurium whole genome shotgun (WGS) project has the project accession ABODYB000000000. This version of the project (01) has the accession number ABODYB010000000, and consists of sequences ABODYB010000001-ABODYB010000104. 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 :: 13-JUN-2023 Assembly Method :: SKESA v. 2.2 Assembly Name :: PDT001778342.1 Long Assembly Name :: NCBI Pathogen Detection Assembly PDT001778342.1 Genome Coverage :: 49x Sequencing Technology :: ILLUMINA ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Date :: 06/13/2023 23:08:48 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 :: 2021-01-11.build5132 Genes (total) :: 4,916 CDSs (total) :: 4,821 Genes (coding) :: 4,711 CDSs (with protein) :: 4,711 Genes (RNA) :: 95 rRNAs :: 5, 1, 3 (5S, 16S, 23S) complete rRNAs :: 5 (5S) partial rRNAs :: 1, 3 (16S, 23S) tRNAs :: 73 ncRNAs :: 13 Pseudo Genes (total) :: 110 CDSs (without protein) :: 110 Pseudo Genes (ambiguous residues) :: 0 of 110 Pseudo Genes (frameshifted) :: 44 of 110 Pseudo Genes (incomplete) :: 59 of 110 Pseudo Genes (internal stop) :: 28 of 110 Pseudo Genes (multiple problems) :: 18 of 110 CRISPR Arrays :: 2 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..104 /organism="Salmonella enterica subsp. enterica serovar Typhimurium" /mol_type="genomic DNA" /strain="SAL-22-VL-ON-ON-0037" /serovar="Typhimurium" /isolation_source="feces" /host="Sus scrofa domesticus" /sub_species="enterica" /db_xref="taxon:90371" /geo_loc_name="Canada: Ontario" /collection_date="2022-10-06" /collected_by="University of Guelph Animal Health Laboratory. Canada, Guelph" WGS ABODYB010000001-ABODYB010000104 //
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