{ "type": "genome", "identifier": "GCF_003966265.1", "organism": "Shewanella atlantica", "title": "Shewanella atlantica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography, State of Oceanic Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003966265.1", "bioproject": "PRJNA224116", "biosample": "SAMN10599942", "wgs_master": "RXNV00000000.1", "refseq_category": "reference genome", "taxid": "271099", "species_taxid": "271099", "organism_name": "Shewanella atlantica", "infraspecific_name": "strain=HAW-EB5", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/23", "asm_name": "ASM396626v1", "asm_submitter": "Third Institute of Oceanography, State of Oceanic Administration", "gbrs_paired_asm": "GCA_003966265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/966/265/GCF_003966265.1_ASM396626v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5392127", "genome_size_ungapped": "5391930", "gc_percent": "46.000000", "replicon_count": "0", "scaffold_count": "47", "contig_count": "47", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003966265.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "4645", "protein_coding_gene_count": "4459", "non_coding_gene_count": "124", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-23", "dateModified": "2018-12-23", "datePublished": "2018-12-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella atlantica" ], "sample_taxid": [ "271099" ], "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": "1.543 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)": "5392127", "Number of Sequences": "47", "Longest Sequences (bp)": "1217457", "N50 (bp)": "318714", "Gap Ratio (%)": "0.003653", "GCcontent (%)": "45.8", "Number of CDSs": "4560", "Average Protein Length": "326.9", "Coding Ratio (%)": "82.9", "Number of rRNAs": "2", "Number of tRNAs": "105", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella atlantica", "strain": "strain=HAW-EB5", "accession": "GCA_003966265.1", "taxid": 271099, "species_taxid": 271099, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1773, "total_fragments": 1773, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella sediminis", "strain": "strain=HAW-EB3", "accession": "GCA_000018025.1", "taxid": 271097, "species_taxid": 271097, "relation_to_type": "type", "validated": true, "ani": 89.8751, "matched_fragments": 1540, "total_fragments": 1773, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella canadensis", "strain": "strain=HAW-EB2", "accession": "GCA_003966225.1", "taxid": 271096, "species_taxid": 271096, "relation_to_type": "type", "validated": true, "ani": 89.2532, "matched_fragments": 1541, "total_fragments": 1773, "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": 79.6705, "matched_fragments": 602, "total_fragments": 1773, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella nanhaiensis", "strain": "strain=NR704-98", "accession": "GCA_019457885.1", "taxid": 2864872, "species_taxid": 2864872, "relation_to_type": "type", "validated": true, "ani": 79.6012, "matched_fragments": 594, "total_fragments": 1773, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella hanedai", "strain": "strain=JCM 20706", "accession": "GCA_007197645.1", "taxid": 25, "species_taxid": 25, "relation_to_type": "type", "validated": true, "ani": 79.5598, "matched_fragments": 557, "total_fragments": 1773, "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": 79.5401, "matched_fragments": 593, "total_fragments": 1773, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella hanedai", "strain": "strain=JCM 20706", "accession": "GCA_014647575.1", "taxid": 25, "species_taxid": 25, "relation_to_type": "type", "validated": true, "ani": 79.4683, "matched_fragments": 546, "total_fragments": 1773, "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": 79.4032, "matched_fragments": 360, "total_fragments": 1773, "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": 79.0856, "matched_fragments": 312, "total_fragments": 1773, "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": 79.0413, "matched_fragments": 394, "total_fragments": 1773, "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": 78.8284, "matched_fragments": 330, "total_fragments": 1773, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella saliphila", "strain": "strain=KCTC 62131", "accession": "GCA_023283695.1", "taxid": 2282698, "species_taxid": 2282698, "relation_to_type": "type", "validated": true, "ani": 78.2098, "matched_fragments": 164, "total_fragments": 1773, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, 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79.3699, "matched_fragments": 547, "total_fragments": 1773, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.26, "cell_length": 0.544, "doubling_h": 0.077, "growth_tmp": 10.0, "optimum_tmp": 10.0, "optimum_ph": 7.147, "genome_size": 4868941.65, "gc_content": 46.142, "coding_genes": 4161.776, "rRNA16S_genes": 9.437, "tRNA_genes": 107.731, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 0.565, "anaerobic_respiration": 0.021, "aerobic_respiration": 0.413, "mesophilic_range_tmp": 0.812, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.187, "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", "atlantica" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }