{ "type": "genome", "identifier": "GCF_023284005.1", "organism": "Shewanella surugensis", "title": "Shewanella surugensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Karolinska Institutet", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023284005.1", "bioproject": "PRJNA224116", "biosample": "SAMN24537866", "wgs_master": "JAKIKS000000000.1", "refseq_category": "reference genome", "taxid": "212020", "species_taxid": "212020", "organism_name": "Shewanella surugensis", "infraspecific_name": "strain=DSM 17177", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/05/09", "asm_name": "ASM2328400v1", "asm_submitter": "Karolinska Institutet", "gbrs_paired_asm": "GCA_023284005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/284/005/GCF_023284005.1_ASM2328400v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6083073", "genome_size_ungapped": "6083073", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "384", "contig_count": "384", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023284005.1-RS_2024_09_27", "annotation_date": "2024-09-27", "total_gene_count": "5595", "protein_coding_gene_count": "5188", "non_coding_gene_count": "118", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-05-09", "dateModified": "2022-05-09", "datePublished": "2022-05-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella surugensis" ], "sample_taxid": [ "212020" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Suruga Bay" ], "sample_host_location_id": [], "data_size": "1.739 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6083073", "Number of Sequences": "384", "Longest Sequences (bp)": "170676", "N50 (bp)": "37187", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.6", "Number of CDSs": "5384", "Average Protein Length": "300.5", "Coding Ratio (%)": "79.8", "Number of rRNAs": "3", "Number of tRNAs": "96", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella surugensis", "strain": "strain=DSM 17177", "accession": "GCA_023284005.1", "taxid": 212020, "species_taxid": 212020, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1823, "total_fragments": 1840, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella atlantica", "strain": "strain=HAW-EB5", "accession": "GCA_003966265.1", "taxid": 271099, "species_taxid": 271099, "relation_to_type": "type", "validated": true, "ani": 78.8228, "matched_fragments": 157, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella schlegeliana", "strain": "strain=JCM 11561", "accession": "GCA_016765635.1", "taxid": 190308, "species_taxid": 190308, "relation_to_type": "type", "validated": true, "ani": 78.5766, "matched_fragments": 182, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella schlegeliana", "strain": "strain=LMG 21406", "accession": "GCA_023283605.1", "taxid": 190308, "species_taxid": 190308, "relation_to_type": "type", "validated": true, "ani": 78.5102, "matched_fragments": 178, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella schlegeliana", "strain": "strain=JCM 11561", "accession": "GCA_019654995.1", "taxid": 190308, "species_taxid": 190308, "relation_to_type": "type", "validated": true, "ani": 78.4812, "matched_fragments": 183, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella piezotolerans", "strain": "strain=WP3", "accession": "GCA_000014885.1", "taxid": 404011, "species_taxid": 404011, "relation_to_type": "type", "validated": true, "ani": 78.4384, "matched_fragments": 192, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella psychrophila", "strain": "strain=WP2", "accession": "GCA_002005305.1", "taxid": 225848, "species_taxid": 225848, "relation_to_type": "type", "validated": true, "ani": 78.4369, "matched_fragments": 182, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella marinintestina", "strain": "strain=LMG 21403", "accession": "GCA_023283845.1", "taxid": 190305, "species_taxid": 190305, "relation_to_type": "type", "validated": true, "ani": 78.4082, "matched_fragments": 186, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella kaireitica", "strain": "strain=DSM 17170", "accession": "GCA_023284045.1", "taxid": 212021, "species_taxid": 212021, "relation_to_type": "type", "validated": true, "ani": 78.338, "matched_fragments": 183, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella colwelliana", "strain": "strain=ATCC 39565", "accession": "GCA_000518705.1", "taxid": 23, "species_taxid": 23, "relation_to_type": "type", "validated": true, "ani": 78.3331, "matched_fragments": 186, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sairae", "strain": "strain=LMG 21408", "accession": "GCA_023283535.1", "taxid": 190310, "species_taxid": 190310, "relation_to_type": "type", "validated": true, "ani": 78.1929, "matched_fragments": 193, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sairae", "strain": "strain=JCM 11563", "accession": "GCA_019655015.1", "taxid": 190310, "species_taxid": 190310, "relation_to_type": "type", "validated": true, "ani": 78.1887, "matched_fragments": 191, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella oncorhynchi", "strain": "strain=S-1", "accession": "GCA_012584455.1", "taxid": 2726434, "species_taxid": 2726434, "relation_to_type": "type", "validated": true, "ani": 77.9577, "matched_fragments": 159, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella baltica", "strain": "strain=NCTC10735", "accession": "GCA_900456975.1", "taxid": 62322, "species_taxid": 62322, "relation_to_type": "type", "validated": true, "ani": 77.9482, "matched_fragments": 156, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella glacialimarina", "strain": "strain=TZS-4", "accession": "GCA_020511155.1", "taxid": 2590884, "species_taxid": 2590884, "relation_to_type": "type", "validated": true, "ani": 77.8613, "matched_fragments": 156, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella polaris", "strain": "strain=SM1901", "accession": "GCA_006385555.1", "taxid": 2588449, "species_taxid": 2588449, "relation_to_type": "type", "validated": true, "ani": 77.7291, "matched_fragments": 174, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella inventionis", "strain": "strain=KCTC 42807", "accession": "GCA_023283595.1", "taxid": 1738770, "species_taxid": 1738770, "relation_to_type": "type", "validated": true, "ani": 77.6419, "matched_fragments": 158, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella morhuae", "strain": "strain=ATCC BAA-1205", "accession": "GCA_900156405.1", "taxid": 365591, "species_taxid": 365591, "relation_to_type": "type", "validated": true, "ani": 77.6371, "matched_fragments": 169, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella aestuarii", "strain": "strain=JCM 17801", "accession": "GCA_023283685.1", "taxid": 1028752, "species_taxid": 1028752, "relation_to_type": "type", "validated": true, "ani": 77.6366, "matched_fragments": 151, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella ulleungensis", "strain": "strain=KCTC 62130", "accession": "GCA_023283965.1", "taxid": 2282699, "species_taxid": 2282699, "relation_to_type": "type", "validated": true, "ani": 77.632, "matched_fragments": 168, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella algicola", "strain": "strain=JCM 31091", "accession": "GCA_014648035.1", "taxid": 640633, "species_taxid": 640633, "relation_to_type": "type", "validated": true, "ani": 77.5815, "matched_fragments": 160, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella ulleungensis", "strain": "strain=JCM 32305", "accession": "GCA_014648315.1", "taxid": 2282699, "species_taxid": 2282699, "relation_to_type": "type", "validated": true, "ani": 77.5735, "matched_fragments": 171, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella intestini", "strain": "strain=MCCC 1A01895", "accession": "GCA_018221465.1", "taxid": 2017544, "species_taxid": 2017544, "relation_to_type": "type", "validated": true, "ani": 77.4934, "matched_fragments": 133, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella marina", "strain": "strain=JCM 15074", "accession": "GCA_000614975.1", "taxid": 487319, "species_taxid": 487319, "relation_to_type": "type", "validated": true, "ani": 77.3629, "matched_fragments": 149, "total_fragments": 1840, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003966265.1", "gtdb_species": "s__Shewanella atlantica", "ani": 78.7681, "matched_fragments": 159, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_016757755.1", "gtdb_species": "s__Shewanella sp016757755", "ani": 78.5772, "matched_fragments": 193, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_016765635.1", "gtdb_species": "s__Shewanella schlegeliana", "ani": 78.5732, "matched_fragments": 183, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003605125.1", "gtdb_species": "s__Shewanella algidipiscicola", "ani": 78.4756, "matched_fragments": 178, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "98.64", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000014885.1", "gtdb_species": "s__Shewanella piezotolerans", "ani": 78.4589, "matched_fragments": 192, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002005305.1", "gtdb_species": "s__Shewanella psychrophila", "ani": 78.4216, "matched_fragments": 180, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002836205.1", "gtdb_species": "s__Shewanella sp002836205", "ani": 78.3486, "matched_fragments": 197, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000018285.1", "gtdb_species": "s__Shewanella pealeana", "ani": 78.345, "matched_fragments": 178, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000518705.1", "gtdb_species": "s__Shewanella colwelliana", "ani": 78.3216, "matched_fragments": 186, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007197645.1", "gtdb_species": "s__Shewanella hanedai", "ani": 78.3153, "matched_fragments": 192, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007004545.2", "gtdb_species": "s__Shewanella sp007004545", "ani": 78.2996, "matched_fragments": 185, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000518605.1", "gtdb_species": "s__Shewanella fidelis", "ani": 78.0864, "matched_fragments": 201, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "97.11", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900456975.1", "gtdb_species": "s__Shewanella baltica", "ani": 77.9409, "matched_fragments": 157, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.88", "min_intra_species_ani": "96.32", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_000172075.1", "gtdb_species": "s__Shewanella benthica_A", "ani": 77.8667, "matched_fragments": 157, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.25", "min_intra_species_ani": "96.25", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002873135.1", "gtdb_species": "s__Shewanella sp002873135", "ani": 77.8412, "matched_fragments": 158, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.82", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003797125.1", "gtdb_species": "s__Shewanella frigidimarina", "ani": 77.7847, "matched_fragments": 157, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "96.12", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001957135.1", "gtdb_species": "s__Shewanella sp001957135", "ani": 77.7574, "matched_fragments": 170, "total_fragments": 1840, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_006385555.1", "gtdb_species": "s__Shewanella polaris", "ani": 77.7239, "matched_fragments": 175, "total_fragments": 1840, "gtdb_taxonomy": 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