{ "type": "genome", "identifier": "GCF_003182275.1", "organism": "Hoeflea marina", "title": "Hoeflea marina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003182275.1", "bioproject": "PRJNA224116", "biosample": "SAMN09074944", "wgs_master": "QGTR00000000.1", "refseq_category": "reference genome", "taxid": "274592", "species_taxid": "274592", "organism_name": "Hoeflea marina", "infraspecific_name": "strain=DSM 16791", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/31", "asm_name": "ASM318227v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003182275.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/182/275/GCF_003182275.1_ASM318227v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5261965", "genome_size_ungapped": "5261288", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "21", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003182275.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "4855", "protein_coding_gene_count": "4767", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-31", "dateModified": "2018-05-31", "datePublished": "2018-05-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Hoeflea marina" ], "sample_taxid": [ "274592" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.446 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)": "5261965", "Number of Sequences": "21", "Longest Sequences (bp)": "1454605", "N50 (bp)": "911015", "Gap Ratio (%)": "0.012866", "GCcontent (%)": "65.0", "Number of CDSs": "4853", "Average Protein Length": "318.0", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "9" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Hoeflea marina", "strain": "strain=DSM 16791", "accession": "GCA_003182275.1", "taxid": 274592, "species_taxid": 274592, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1742, "total_fragments": 1743, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Hoeflea olei", "strain": "strain=JC234", "accession": "GCA_001703635.1", "taxid": 1480615, "species_taxid": 1480615, "relation_to_type": "type", "validated": true, "ani": 80.9759, "matched_fragments": 860, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hoeflea alexandrii", "strain": "strain=DSM 16655", "accession": "GCA_024105735.1", "taxid": 288436, "species_taxid": 288436, "relation_to_type": "type", "validated": true, "ani": 79.9185, "matched_fragments": 747, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hoeflea halophila", "strain": "strain=KCTC 23107", "accession": "GCA_900220985.1", "taxid": 714899, "species_taxid": 714899, "relation_to_type": "type", "validated": true, "ani": 79.722, "matched_fragments": 662, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 79.4294, "matched_fragments": 626, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium azooxidifex", "strain": "strain=DSM 100211", "accession": "GCA_014196765.1", "taxid": 1636188, "species_taxid": 1636188, "relation_to_type": "type", "validated": true, "ani": 79.081, "matched_fragments": 565, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hoeflea phototrophica", "strain": "strain=DFL-43", "accession": "GCA_000154705.2", "taxid": 244596, "species_taxid": 244596, "relation_to_type": "type", "validated": true, "ani": 79.0537, "matched_fragments": 596, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella zoogloeoides", "strain": "strain=ATCC 19623", "accession": "GCA_020883495.1", "taxid": 352475, "species_taxid": 352475, "relation_to_type": "type", "validated": true, "ani": 79.0027, "matched_fragments": 561, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella yambaruensis", "strain": "strain=DSM 18801", "accession": "GCA_022899355.1", "taxid": 415996, "species_taxid": 415996, "relation_to_type": "type", "validated": true, "ani": 78.9795, "matched_fragments": 653, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter selenitireducens", "strain": "strain=ATCC BAA-1503", "accession": "GCA_000518785.1", "taxid": 448181, "species_taxid": 448181, "relation_to_type": "type", "validated": true, "ani": 78.8827, "matched_fragments": 578, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella oryzae", "strain": "strain=Z-25", "accession": "GCA_023038235.1", "taxid": 2871820, "species_taxid": 2871820, "relation_to_type": "type", "validated": true, "ani": 78.6732, "matched_fragments": 525, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium vignae", "strain": "strain=CCBAU 05176", "accession": "GCA_000732195.1", "taxid": 690585, "species_taxid": 690585, "relation_to_type": "type", "validated": true, "ani": 78.4679, "matched_fragments": 492, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium redzepovicii", "strain": "strain=18T", "accession": "GCA_019793435.1", "taxid": 2867518, "species_taxid": 2867518, "relation_to_type": "type", "validated": true, "ani": 78.2269, "matched_fragments": 514, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium daejeonense", "strain": "strain=CCBAU10050", "accession": "GCA_011045155.1", "taxid": 240521, "species_taxid": 240521, "relation_to_type": "type", "validated": true, "ani": 77.8295, "matched_fragments": 415, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium daejeonense", "strain": "strain=L61", "accession": "GCA_014280875.1", "taxid": 240521, "species_taxid": 240521, "relation_to_type": "type", "validated": true, "ani": 77.7621, "matched_fragments": 427, "total_fragments": 1743, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003182275.1", "gtdb_species": "s__Hoeflea marina", "ani": 100.0, "matched_fragments": 1742, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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_000759435.1", "gtdb_species": "s__Hoeflea sp000759435", "ani": 81.8847, "matched_fragments": 910, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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": "GCA_014359905.1", "gtdb_species": "s__Hoeflea sp014359905", "ani": 81.0528, "matched_fragments": 803, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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_001703635.1", "gtdb_species": "s__Hoeflea olei", "ani": 81.0048, "matched_fragments": 853, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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": "GCA_019084245.1", "gtdb_species": "s__Hoeflea sp019084245", "ani": 80.7501, "matched_fragments": 824, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_000961635.1", "gtdb_species": "s__Hoeflea sp000961635", "ani": 80.4482, "matched_fragments": 552, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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": "GCA_018829385.1", "gtdb_species": "s__Hoeflea sp018829385", "ani": 80.3356, "matched_fragments": 491, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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": "GCA_002733955.1", "gtdb_species": "s__Hoeflea sp002733955", "ani": 80.081, "matched_fragments": 745, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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_902498795.1", "gtdb_species": "s__Hoeflea sp902498795", "ani": 79.8145, "matched_fragments": 738, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900220985.1", "gtdb_species": "s__Hoeflea halophila", "ani": 79.7139, "matched_fragments": 663, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea", "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_900492205.1", "gtdb_species": "s__Allorhizobium naphthalenivorans_A", "ani": 78.9758, "matched_fragments": 567, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.27", "min_intra_species_ani": "95.27", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002796995.1", "gtdb_species": "s__Allorhizobium sp002796995", "ani": 78.923, "matched_fragments": 592, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.22", "min_intra_species_ani": "96.20", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000518785.1", "gtdb_species": "s__Allorhizobium selenitireducens", "ani": 78.8713, "matched_fragments": 580, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_014280875.1", "gtdb_species": "s__Allorhizobium daejeonense", "ani": 77.7924, "matched_fragments": 423, "total_fragments": 1743, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.097, "cell_length": 0.397, "doubling_h": null, "growth_tmp": 27.0, "optimum_tmp": 36.5, "optimum_ph": 7.0, "genome_size": 4458205.5, "gc_content": 65.552, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Hoeflea", "marina" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }