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GenBank: AAFPJP000000000.1
LOCUS AAFPJP010000000 34 rc DNA linear BCT 03-JUL-2019 DEFINITION Salmonella enterica strain SAL-18-VL-SD-OK-0002, whole genome shotgun sequencing project. ACCESSION AAFPJP000000000 VERSION AAFPJP000000000.1 DBLINK BioProject: PRJNA316457 BioSample: SAMN09951524 Sequence Read Archive: SRR7799339 KEYWORDS WGS. SOURCE Salmonella enterica ORGANISM Salmonella enterica Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella. REFERENCE 1 (bases 1 to 34) CONSRTM Veterinary Laboratory Investigation and Response Network TITLE Direct Submission JOURNAL Submitted (07-SEP-2018) Center for Veterinary Medicine, US Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA COMMENT The Salmonella enterica whole genome shotgun (WGS) project has the project accession AAFPJP000000000. This version of the project (01) has the accession number AAFPJP010000000, and consists of sequences AAFPJP010000001-AAFPJP010000034. 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 :: 07-SEP-2018 Assembly Method :: SKESA v. 2.2 Assembly Name :: PDT000372802.1 Long Assembly Name :: NCBI Pathogen Detection Assembly PDT000372802.1 Genome Coverage :: 141x Sequencing Technology :: ILLUMINA ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Date :: 09/07/2018 04:15:02 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) :: 5,164 CDS (total) :: 5,065 Genes (coding) :: 4,897 CDS (coding) :: 4,897 Genes (RNA) :: 99 rRNAs :: 5, 2, 2 (5S, 16S, 23S) complete rRNAs :: 5 (5S) partial rRNAs :: 2, 2 (16S, 23S) tRNAs :: 77 ncRNAs :: 13 Pseudo Genes (total) :: 168 Pseudo Genes (ambiguous residues) :: 0 of 168 Pseudo Genes (frameshifted) :: 90 of 168 Pseudo Genes (incomplete) :: 63 of 168 Pseudo Genes (internal stop) :: 54 of 168 Pseudo Genes (multiple problems) :: 36 of 168 CRISPR Arrays :: 3 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..34 /organism="Salmonella enterica" /mol_type="genomic DNA" /strain="SAL-18-VL-SD-OK-0002" /isolation_source="Bovine Intestines (Bovine)" /db_xref="taxon:28901" /geo_loc_name="USA: OK" /collection_date="2018-02" /collected_by="OADDL - OK" WGS AAFPJP010000001-AAFPJP010000034 //
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