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Salmonella sp. WGH-01 chromosome, complete genome

发布时间：2026/4/10 15:52:52 阅读次数：23

Salmonella sp. WGH-01 chromosome, complete genome
GenBank: CP096171.1
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LOCUS       CP096171                1001 bp    DNA     linear   BCT 16-MAY-2022
DEFINITION Salmonella sp. WGH-01 chromosome, complete genome.
ACCESSION   CP096171 REGION: 3643480..3644480
VERSION     CP096171.1
DBLINK      BioProject: PRJNA827233
            BioSample: SAMN27606337
KEYWORDS    .
SOURCE      Salmonella sp. WGH-01
ORGANISM Salmonella sp. WGH-01
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1 (bases 1 to 1001)
AUTHORS   Zhao,J., Lu,X., Tie,A., Ngegba,E., Wang,L., Sun,L., Liang,Y.,
            Abdulai,M.K., Bah,S., Wang,G., Dong,X., Harding,D. and Kan,B.
TITLE     Molecular diagnostics and next-generation sequencing reveal real
            etiological characteristics of invasive Salmonella infection in
            febrile illness in Freetown, Sierra Leone
JOURNAL   Emerg Microbes Infect, 1-20 (2022) In press
   PUBMED   35537043
REMARK    Publication Status: Available-Online prior to print
REFERENCE   2 (bases 1 to 1001)
AUTHORS   Liu,J.
TITLE     Direct Submission
JOURNAL   Submitted (19-APR-2022) Chinese Center for Disease Control and
            Prevention, Chinese Center for Disease Control and Prevention, 155
            Changbai Road, Changping District, Beijing 102200, China
COMMENT     The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.

            ##Genome-Assembly-Data-START##
            Assembly Method        :: SPAdes v. V3
            Genome Representation :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 100.0x
            Sequencing Technology :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##

            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/21/2022 12:52:20
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.1
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Genes (total)                     :: 5,597
            CDSs (total)                      :: 5,483
            Genes (coding)                    :: 1,476
            CDSs (with protein)               :: 1,476
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 4,007
            CDSs (without protein)            :: 4,007
            Pseudo Genes (ambiguous residues) :: 0 of 4,007
            Pseudo Genes (frameshifted)       :: 3,826 of 4,007
            Pseudo Genes (incomplete)         :: 402 of 4,007
            Pseudo Genes (internal stop)      :: 493 of 4,007
            Pseudo Genes (multiple problems) :: 651 of 4,007
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..1001
                     /organism="Salmonella sp. WGH-01"
                     /mol_type="genomic DNA"
                     /strain="WGH-01"
                     /isolation_source="blood samples from outpatients"
                     /host="Homo sapiens"
                     /db_xref="taxon:2935857"
                     /country="Sierra Leone"
                     /collection_date="2019"
     gene            <1..>1001
                     /gene="invA"
                     /locus_tag="MYA98_21175"
                     /pseudo
     CDS             <1..>1001
                     /gene="invA"
                     /locus_tag="MYA98_21175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_461817.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=3
                     /transl_table=11
                     /product="type III secretion system export apparatus
                     protein InvA"
ORIGIN
        1 caacgtttcc tgcggtactg ttaattacca cgctctttcg tctggcatta tcgatcagta
       61 ccagccgtct tatcttgatt gaagccgatg ccggtgaaat tatcgccacg ttcgggcaat
      121 tcgttattgg cgatagcccg gcggtgggtt ttgttgtctt ctctattgtc accgtggtcc
      181 agtttatcgt tattaccaaa ggttcagaac gcgtcgcgga agtcgcggcc cgattttctc
      241 tggatggtat gcccggtaaa cagatgagta ttgatgccga tttgaaggcc ggtattattg
      301 atgcggatgc tgcgcgcgaa cggcgaagcg tactggaaag ggaaagccag ctttacggtt
      361 cctttgacgg tgcgatgaag tttatcaaag gtgacgctat tgccggcatc attatcatct
      421 ttgtgaactt tattggcggt atttcggtgg ggatgacccg ccatggtatg gatttgtcct
      481 ccgctctgtc tacttatacc atgctgacca ttggtgatgg tcttgtcgcc cagatccccg
      541 cattgttgat tgcgattagt gccggtttta tcgtgactcg cgtaaatggc gatagcgata
      601 atatggggcg gaatatcatg acgcagctgt tgaacaaccc atttgtattg gttgttacgg
      661 ctattttgac catttcaatg ggaactctgc cgggattccc gctgccggta tttgttattt
      721 tatcggtggt tttaagcgta ctcttctatt ttaaattccg tgaagcaaaa cgtagcgccg
      781 ccaaacctaa aaccagcaaa ggcgagcagc cgctcagtat tgaggaaaag aagggtcgtc
      841 gttaggactg attggcgatc tcgataaagt ctctacagag actgtaccgt tgatattact
      901 tgtgccgaag agccggcgtg aagatctgga aaaagctcaa cttgcggagc gcctacgtag
      961 tcagttcttt attgattatg gcgtgcgcct gccggaagta t

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