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GenBank: ABDFGC000000000.1
LOCUS ABDFGC010000000 43 rc DNA linear BCT 13-OCT-2021 DEFINITION Staphylococcus pseudintermedius strain SPSE-20-VL-SD-IA-0038 isolate Canis lupus familiaris, whole genome shotgun sequencing project. ACCESSION ABDFGC000000000 VERSION ABDFGC000000000.1 DBLINK BioProject: PRJNA318594 BioSample: SAMN22184040 Sequence Read Archive: SRR16298890 KEYWORDS WGS. SOURCE Staphylococcus pseudintermedius ORGANISM Staphylococcus pseudintermedius Bacteria; Bacillati; Bacillota; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus; Staphylococcus intermedius group. REFERENCE 1 (bases 1 to 43) CONSRTM Veterinary Laboratory Investigation and Response Network TITLE Direct Submission JOURNAL Submitted (12-OCT-2021) Center for Veterinary Medicine, US Food and Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA COMMENT The Staphylococcus pseudintermedius whole genome shotgun (WGS) project has the project accession ABDFGC000000000. This version of the project (01) has the accession number ABDFGC010000000, and consists of sequences ABDFGC010000001-ABDFGC010000043. 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 :: 12-OCT-2021 Assembly Method :: SKESA v. 2.2 Assembly Name :: PDT001149398.1 Long Assembly Name :: NCBI Pathogen Detection Assembly PDT001149398.1 Genome Coverage :: 371x Sequencing Technology :: ILLUMINA ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Date :: 10/13/2021 04:19:12 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) :: 2,594 CDSs (total) :: 2,525 Genes (coding) :: 2,475 CDSs (with protein) :: 2,475 Genes (RNA) :: 69 rRNAs :: 3, 3, 1 (5S, 16S, 23S) complete rRNAs :: 3 (5S) partial rRNAs :: 3, 1 (16S, 23S) tRNAs :: 57 ncRNAs :: 5 Pseudo Genes (total) :: 50 CDSs (without protein) :: 50 Pseudo Genes (ambiguous residues) :: 0 of 50 Pseudo Genes (frameshifted) :: 17 of 50 Pseudo Genes (incomplete) :: 31 of 50 Pseudo Genes (internal stop) :: 16 of 50 Pseudo Genes (multiple problems) :: 14 of 50 CRISPR Arrays :: 1 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..43 /organism="Staphylococcus pseudintermedius" /mol_type="genomic DNA" /strain="SPSE-20-VL-SD-IA-0038" /isolate="Canis lupus familiaris" /isolation_source="urine" /db_xref="taxon:283734" /geo_loc_name="USA: IA" /collection_date="2020-10-05" /collected_by="ISUVDL" WGS ABDFGC010000001-ABDFGC010000043 //
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