{ "type": "genome", "identifier": "GCF_000614975.1", "organism": "Shewanella marina JCM 15074", "title": "Shewanella marina JCM 15074", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000614975.1", "bioproject": "PRJNA224116", "biosample": "SAMD00011086", "wgs_master": "BALM00000000.1", "refseq_category": "reference genome", "taxid": "1236542", "species_taxid": "487319", "organism_name": "Shewanella marina JCM 15074", "infraspecific_name": "strain=JCM 15074", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/03/31", "asm_name": "ASM61497v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_000614975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/614/975/GCF_000614975.1_ASM61497v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4424648", "genome_size_ungapped": "4424648", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "75", "contig_count": "75", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000614975.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "4084", "protein_coding_gene_count": "3658", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-03-31", "dateModified": "2014-03-31", "datePublished": "2014-03-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella marina JCM 15074" ], "sample_taxid": [ "1236542" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.256 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)": "4424648", "Number of Sequences": "75", "Longest Sequences (bp)": "419977", "N50 (bp)": "142156", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.4", "Number of CDSs": "4215", "Average Protein Length": "302.9", "Coding Ratio (%)": "86.6", "Number of rRNAs": "3", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella marina", "strain": "strain=JCM 15074", "accession": "GCA_000614975.1", "taxid": 487319, "species_taxid": 487319, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1432, "total_fragments": 1440, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella loihica", "strain": "strain=PV-4", "accession": "GCA_000016065.1", "taxid": 359303, "species_taxid": 359303, "relation_to_type": "type", "validated": true, "ani": 78.8377, "matched_fragments": 115, "total_fragments": 1440, "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": 78.5126, "matched_fragments": 188, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella oneidensis", "strain": "strain=MR-1", "accession": "GCA_013267215.1", "taxid": 70863, "species_taxid": 70863, "relation_to_type": "type", "validated": true, "ani": 78.4738, "matched_fragments": 171, "total_fragments": 1440, "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": 78.4331, "matched_fragments": 179, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella oneidensis", "strain": "strain=MR-1", "accession": "GCA_000146165.2", "taxid": 70863, "species_taxid": 70863, "relation_to_type": "type", "validated": true, "ani": 78.4076, "matched_fragments": 176, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella psychromarinicola", "strain": "strain=M2", "accession": "GCA_003855155.1", "taxid": 2487742, "species_taxid": 2487742, "relation_to_type": "type", "validated": true, "ani": 78.3493, "matched_fragments": 191, "total_fragments": 1440, "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": 78.2856, "matched_fragments": 253, "total_fragments": 1440, "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": 78.2802, "matched_fragments": 256, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella woodyi", "strain": "strain=ATCC 51908", "accession": "GCA_000019525.1", "taxid": 60961, "species_taxid": 60961, "relation_to_type": "type", "validated": true, "ani": 78.1983, "matched_fragments": 192, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella vesiculosa", "strain": "strain=M7", "accession": "GCA_021560015.1", "taxid": 518738, "species_taxid": 518738, "relation_to_type": "type", "validated": true, "ani": 78.1824, "matched_fragments": 188, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella xiamenensis", "strain": "strain=JCM 16212", "accession": "GCA_014647135.1", "taxid": 332186, "species_taxid": 332186, "relation_to_type": "type", "validated": true, "ani": 78.1123, "matched_fragments": 176, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella hafniensis", "strain": "strain=ATCC BAA-1207", "accession": "GCA_019655335.1", "taxid": 365590, "species_taxid": 365590, "relation_to_type": "type", "validated": true, "ani": 78.0895, "matched_fragments": 189, "total_fragments": 1440, "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": 78.0704, "matched_fragments": 206, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella basaltis", "strain": "strain=KCTC 22121", "accession": "GCA_023283885.1", "taxid": 472183, "species_taxid": 472183, "relation_to_type": "type", "validated": true, "ani": 78.0162, "matched_fragments": 193, "total_fragments": 1440, "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": 78.0007, "matched_fragments": 196, "total_fragments": 1440, "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": 77.9739, "matched_fragments": 194, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella fidelis", "strain": "strain=ATCC BAA-318", "accession": "GCA_000518605.1", "taxid": 173509, "species_taxid": 173509, "relation_to_type": "type", "validated": true, "ani": 77.9588, "matched_fragments": 261, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella algidipiscicola", "strain": "strain=LMG 23746", "accession": "GCA_019655175.1", "taxid": 614070, "species_taxid": 614070, "relation_to_type": "type", "validated": true, "ani": 77.9543, "matched_fragments": 176, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella inventionis", "strain": "strain=CGMCC 1.15339", "accession": "GCA_014641855.1", "taxid": 1738770, "species_taxid": 1738770, "relation_to_type": "type", "validated": true, "ani": 77.897, "matched_fragments": 205, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella litoralis", "strain": "strain=JCM 32306", "accession": "GCA_009828585.1", "taxid": 2282700, "species_taxid": 2282700, "relation_to_type": "type", "validated": true, "ani": 77.8679, "matched_fragments": 216, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella algidipiscicola", "strain": "strain=LMG 23746", "accession": "GCA_003605125.1", "taxid": 614070, "species_taxid": 614070, "relation_to_type": "type", "validated": true, "ani": 77.8613, "matched_fragments": 177, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella litoralis", "strain": "strain=JCM 32306", "accession": "GCA_014648335.1", "taxid": 2282700, "species_taxid": 2282700, "relation_to_type": "type", "validated": true, "ani": 77.8489, "matched_fragments": 212, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella abyssi", "strain": "strain=DSM 17171", "accession": "GCA_023284025.1", "taxid": 311789, "species_taxid": 311789, "relation_to_type": "type", "validated": true, "ani": 77.8343, "matched_fragments": 186, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella gelidimarina", "strain": "strain=ATCC 700752", "accession": "GCA_023283945.1", "taxid": 56813, "species_taxid": 56813, "relation_to_type": "type", "validated": true, "ani": 77.6958, "matched_fragments": 194, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella donghaensis", "strain": "strain=LT17", "accession": "GCA_007567505.1", "taxid": 238836, "species_taxid": 238836, "relation_to_type": "type", "validated": true, "ani": 77.6325, "matched_fragments": 211, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Motilimonas cestriensis", "strain": "strain=MKS20", "accession": "GCA_021295315.1", "taxid": 2742685, "species_taxid": 2742685, "relation_to_type": "type", "validated": true, "ani": 76.4342, "matched_fragments": 50, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000614975.1", "gtdb_species": "s__Shewanella marina", "ani": 100.0, "matched_fragments": 1432, "total_fragments": 1440, "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": "conclusive" }, { "accession": "GCF_000016065.1", "gtdb_species": "s__Shewanella loihica", "ani": 78.8011, "matched_fragments": 116, "total_fragments": 1440, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.22", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016765635.1", "gtdb_species": "s__Shewanella schlegeliana", "ani": 78.5279, "matched_fragments": 209, "total_fragments": 1440, "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_000019185.1", "gtdb_species": "s__Shewanella halifaxensis", "ani": 78.5268, "matched_fragments": 211, "total_fragments": 1440, "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_900456975.1", "gtdb_species": "s__Shewanella baltica", "ani": 78.4494, "matched_fragments": 191, "total_fragments": 1440, "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_000203935.1", "gtdb_species": "s__Shewanella sp000203935", "ani": 78.4108, "matched_fragments": 175, "total_fragments": 1440, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.76", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003797125.1", "gtdb_species": "s__Shewanella frigidimarina", "ani": 78.4069, "matched_fragments": 200, "total_fragments": 1440, "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_014164505.1", "gtdb_species": "s__Shewanella sp014164505", "ani": 78.386, "matched_fragments": 160, "total_fragments": 1440, "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_009831655.1", "gtdb_species": "s__Shewanella insulae", "ani": 78.3533, "matched_fragments": 119, "total_fragments": 1440, "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_000146165.2", "gtdb_species": "s__Shewanella oneidensis", "ani": 78.3427, "matched_fragments": 179, "total_fragments": 1440, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011765625.1", "gtdb_species": "s__Shewanella aestuarii_A", "ani": 78.298, "matched_fragments": 197, "total_fragments": 1440, "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_000019525.1", "gtdb_species": "s__Shewanella woodyi", "ani": 78.1787, "matched_fragments": 193, "total_fragments": 1440, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002838165.1", "gtdb_species": "s__Shewanella sp002838165", "ani": 78.1575, "matched_fragments": 207, "total_fragments": 1440, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.37", "min_intra_species_ani": "97.32", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_014648035.1", "gtdb_species": "s__Shewanella algicola", "ani": 78.12, "matched_fragments": 206, "total_fragments": 1440, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.1181, "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_014647135.1", "gtdb_species": "s__Shewanella xiamenensis", "ani": 78.1123, "matched_fragments": 176, "total_fragments": 1440, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.56", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_006385555.1", "gtdb_species": "s__Shewanella polaris", "ani": 78.0562, "matched_fragments": 208, "total_fragments": 1440, "gtdb_taxonomy": 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