LOCUS AAPEIG010000000 175 rc DNA linear BCT 24-FEB-2020
DEFINITION Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
SAL-19-VL-SD-IA-0016, whole genome shotgun sequencing project.
ACCESSION AAPEIG000000000
VERSION AAPEIG000000000.1
DBLINK BioProject: PRJNA316457
BioSample: SAMN14125565
Sequence Read Archive: SRR11101202
KEYWORDS WGS.
SOURCE Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
ORGANISM Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE 1 (bases 1 to 175)
CONSRTM Veterinary Laboratory Investigation and Response Network
TITLE Direct Submission
JOURNAL Submitted (19-FEB-2020) Center for Veterinary Medicine, US Food and
Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT The Salmonella enterica subsp. enterica serovar 4,[5],12:i:- whole
genome shotgun (WGS) project has the project accession
AAPEIG000000000. This version of the project (01) has the
accession number AAPEIG010000000, and consists of sequences
AAPEIG010000001-AAPEIG010000175.
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 :: 19-FEB-2020
Assembly Method :: SKESA v. 2.2
Assembly Name :: PDT000687794.1
Long Assembly Name :: NCBI Pathogen Detection Assembly
PDT000687794.1
Genome Coverage :: 71x
Sequencing Technology :: ILLUMINA
##Genome-Assembly-Data-END##
##Genome-Annotation-Data-START##
Annotation Date :: 02/20/2020 14:35:48
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 :: 2020-02-06.build4373
Genes (total) :: 5,301
CDSs (total) :: 5,200
Genes (coding) :: 5,117
CDSs (with protein) :: 5,117
Genes (RNA) :: 101
rRNAs :: 3, 1, 3 (5S, 16S, 23S)
complete rRNAs :: 3 (5S)
partial rRNAs :: 1, 3 (16S, 23S)
tRNAs :: 79
ncRNAs :: 15
Pseudo Genes (total) :: 83
CDSs (without protein) :: 83
Pseudo Genes (ambiguous residues) :: 0 of 83
Pseudo Genes (frameshifted) :: 29 of 83
Pseudo Genes (incomplete) :: 59 of 83
Pseudo Genes (internal stop) :: 16 of 83
Pseudo Genes (multiple problems) :: 18 of 83
CRISPR Arrays :: 2
##Genome-Annotation-Data-END##
FEATURES Location/Qualifiers
source 1..175
/organism="Salmonella enterica subsp. enterica serovar
4,[5],12:i:-"
/mol_type="genomic DNA"
/strain="SAL-19-VL-SD-IA-0016"
/serovar="4,[5],12:i:-"
/isolation_source="Feces (Sus scrofa domesticus)"
/sub_species="enterica"
/db_xref="taxon:440524"
/geo_loc_name="USA: IA"
/collection_date="2019-04-04"
/collected_by="ISUVDL"
WGS AAPEIG010000001-AAPEIG010000175
//