{ "type": "genome", "identifier": "GCF_000018025.1", "organism": "Shewanella sediminis HAW-EB3", "title": "Shewanella sediminis HAW-EB3", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US DOE Joint Genome Institute (JGI-PGF)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000018025.1", "bioproject": "PRJNA224116", "biosample": "SAMN02598412", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "425104", "species_taxid": "271097", "organism_name": "Shewanella sediminis HAW-EB3", "infraspecific_name": "strain=HAW-EB3", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2007/09/18", "asm_name": "ASM1802v1", "asm_submitter": "US DOE Joint Genome Institute (JGI-PGF)", "gbrs_paired_asm": "GCA_000018025.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/025/GCF_000018025.1_ASM1802v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5517674", "genome_size_ungapped": "5517674", "gc_percent": "46.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2023-10-31", "total_gene_count": "4745", "protein_coding_gene_count": "4554", "non_coding_gene_count": "168", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2007-09-18", "dateModified": "2007-09-18", "datePublished": "2007-09-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella sediminis HAW-EB3" ], "sample_taxid": [ "425104" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.568 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)": "5517674", "Number of Sequences": "1", "Longest Sequences (bp)": "5517674", "N50 (bp)": "5517674", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "46.1", "Number of CDSs": "4595", "Average Protein Length": "332.5", "Coding Ratio (%)": "83.1", "Number of rRNAs": "37", "Number of tRNAs": "128", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella sediminis", "strain": "strain=HAW-EB3", "accession": "GCA_000018025.1", "taxid": 271097, "species_taxid": 271097, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1838, "total_fragments": 1839, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella canadensis", "strain": "strain=HAW-EB2", "accession": "GCA_003966225.1", "taxid": 271096, "species_taxid": 271096, "relation_to_type": "type", "validated": true, "ani": 93.1982, "matched_fragments": 1589, "total_fragments": 1839, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella atlantica", "strain": "strain=HAW-EB5", "accession": "GCA_003966265.1", "taxid": 271099, "species_taxid": 271099, "relation_to_type": "type", "validated": true, "ani": 89.8268, "matched_fragments": 1541, "total_fragments": 1839, "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": 80.7719, "matched_fragments": 667, "total_fragments": 1839, "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": 79.9811, "matched_fragments": 621, "total_fragments": 1839, "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": 79.783, "matched_fragments": 562, "total_fragments": 1839, "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": 79.7416, "matched_fragments": 610, "total_fragments": 1839, "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": 79.6018, "matched_fragments": 561, "total_fragments": 1839, "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": 78.7379, "matched_fragments": 348, "total_fragments": 1839, "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": 78.1184, "matched_fragments": 227, "total_fragments": 1839, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella profunda", "strain": "strain=DSM 15900", "accession": "GCA_023283765.1", "taxid": 254793, "species_taxid": 254793, "relation_to_type": "type", "validated": true, "ani": 77.7864, "matched_fragments": 238, "total_fragments": 1839, "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": 77.5972, "matched_fragments": 187, "total_fragments": 1839, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000018025.1", "gtdb_species": "s__Shewanella sediminis", "ani": 100.0, "matched_fragments": 1838, "total_fragments": 1839, "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_003966225.1", "gtdb_species": "s__Shewanella canadensis", "ani": 93.1951, "matched_fragments": 1589, "total_fragments": 1839, "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_003966265.1", "gtdb_species": "s__Shewanella atlantica", "ani": 89.8219, "matched_fragments": 1542, "total_fragments": 1839, "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": 80.5935, "matched_fragments": 655, "total_fragments": 1839, "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_000019525.1", "gtdb_species": "s__Shewanella woodyi", "ani": 80.0133, "matched_fragments": 620, "total_fragments": 1839, "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_002005305.1", "gtdb_species": "s__Shewanella psychrophila", "ani": 79.997, "matched_fragments": 626, "total_fragments": 1839, "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_015069875.1", "gtdb_species": "s__Shewanella benthica", "ani": 79.9233, "matched_fragments": 479, "total_fragments": 1839, "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": "-" }, { "accession": "GCF_000091325.1", "gtdb_species": "s__Shewanella violacea", "ani": 79.883, "matched_fragments": 577, "total_fragments": 1839, "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_001957125.1", "gtdb_species": "s__Shewanella sp001957125", "ani": 79.8422, "matched_fragments": 589, "total_fragments": 1839, "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_007197645.1", "gtdb_species": "s__Shewanella hanedai", "ani": 79.8151, "matched_fragments": 558, "total_fragments": 1839, "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_000018285.1", "gtdb_species": "s__Shewanella pealeana", "ani": 79.3704, "matched_fragments": 415, "total_fragments": 1839, "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": -0.155, "cell_length": 0.23, "doubling_h": 0.077, "growth_tmp": 17.0, "optimum_tmp": 10.0, "optimum_ph": 7.147, "genome_size": 5517673.2, "gc_content": 46.1, "coding_genes": 4524.667, "rRNA16S_genes": 12.0, "tRNA_genes": 126.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 1.0, "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", "sediminis", "HAW-EB3" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }