{ "type": "genome", "identifier": "GCF_015069875.1", "organism": "Shewanella benthica", "title": "Shewanella benthica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography, Ministry of Natural Resources", "publication": [ {} ], "properties": { "assembly_accession": "GCF_015069875.1", "bioproject": "PRJNA224116", "biosample": "SAMN16273954", "wgs_master": "JADDKM000000000.1", "refseq_category": "reference genome", "taxid": "43661", "species_taxid": "43661", "organism_name": "Shewanella benthica", "infraspecific_name": "strain=DSM 8812", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/10/28", "asm_name": "ASM1506987v1", "asm_submitter": "Third Institute of Oceanography, Ministry of Natural Resources", "gbrs_paired_asm": "GCA_015069875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/069/875/GCF_015069875.1_ASM1506987v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4034511", "genome_size_ungapped": "4034411", "gc_percent": "46.000000", "replicon_count": "0", "scaffold_count": "46", "contig_count": "46", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_015069875.1-RS_2024_11_26", "annotation_date": "2024-11-26", "total_gene_count": "3434", "protein_coding_gene_count": "3317", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-10-28", "dateModified": "2020-10-28", "datePublished": "2020-10-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella benthica" ], "sample_taxid": [ "43661" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Atlantic Ocean" ], "sample_host_location_id": [], "data_size": "1.157 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4034511", "Number of Sequences": "46", "Longest Sequences (bp)": "339269", "N50 (bp)": "156363", "Gap Ratio (%)": "0.002479", "GCcontent (%)": "45.8", "Number of CDSs": "3358", "Average Protein Length": "336.0", "Coding Ratio (%)": "83.9", "Number of rRNAs": "4", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella benthica", "strain": "strain=DSM 8812", "accession": "GCA_015069875.1", "taxid": 43661, "species_taxid": 43661, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1321, "total_fragments": 1321, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella psychropiezotolerans", "strain": "strain=YLB-06", "accession": "GCA_007197555.1", "taxid": 2593655, "species_taxid": 2593655, "relation_to_type": "type", "validated": true, "ani": 92.0712, "matched_fragments": 1078, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella violacea", "strain": "strain=DSS12", "accession": "GCA_000091325.1", "taxid": 60217, "species_taxid": 60217, "relation_to_type": "type", "validated": true, "ani": 86.6932, "matched_fragments": 922, "total_fragments": 1321, "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": 86.4208, "matched_fragments": 1035, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella eurypsychrophilus", "strain": "strain=YLB-08", "accession": "GCA_007004545.3", "taxid": 2593656, "species_taxid": 2593656, "relation_to_type": "type", "validated": true, "ani": 82.6407, "matched_fragments": 815, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella insulae", "strain": "strain=JBTF-M18", "accession": "GCA_009831655.1", "taxid": 2681496, "species_taxid": 2681496, "relation_to_type": "type", "validated": true, "ani": 78.0878, "matched_fragments": 274, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella seohaensis", "strain": "strain=CCUG 60900", "accession": "GCA_023283775.1", "taxid": 755175, "species_taxid": 755175, "relation_to_type": "type", "validated": true, "ani": 77.3681, "matched_fragments": 166, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=KCTC 22540", "accession": "GCA_014651975.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 77.2431, "matched_fragments": 145, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella corallii", "strain": "strain=DSM 21332", "accession": "GCA_023349125.1", "taxid": 560080, "species_taxid": 560080, "relation_to_type": "type", "validated": true, "ani": 77.1519, "matched_fragments": 120, "total_fragments": 1321, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_015069875.1", "gtdb_species": "s__Shewanella benthica", "ani": 100.0, "matched_fragments": 1321, "total_fragments": 1321, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.81", "min_intra_species_ani": "96.81", "mean_intra_species_af": "0.66", "min_intra_species_af": "0.66", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000172075.1", "gtdb_species": "s__Shewanella benthica_A", "ani": 93.687, "matched_fragments": 900, "total_fragments": 1321, "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_007197555.1", "gtdb_species": "s__Shewanella sp007197555", "ani": 92.06, "matched_fragments": 1079, "total_fragments": 1321, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013214165.1", "gtdb_species": "s__Shewanella sp013214165", "ani": 90.8421, "matched_fragments": 862, "total_fragments": 1321, "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_000091325.1", "gtdb_species": "s__Shewanella violacea", "ani": 86.7037, "matched_fragments": 921, "total_fragments": 1321, "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": 86.405, "matched_fragments": 1037, "total_fragments": 1321, "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_007004545.2", "gtdb_species": "s__Shewanella sp007004545", "ani": 82.6004, "matched_fragments": 808, "total_fragments": 1321, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.176, "doubling_h": 0.077, "growth_tmp": 5.0, "optimum_tmp": 4.0, "optimum_ph": 7.147, "genome_size": 4352549.5, "gc_content": 45.95, "coding_genes": 3461.0, "rRNA16S_genes": 9.437, "tRNA_genes": 98.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Shewanella", "benthica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }