{ "type": "genome", "identifier": "GCF_900115865.1", "organism": "Donghicola eburneus", "title": "Donghicola eburneus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900115865.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421764", "wgs_master": "FOXY00000000.1", "refseq_category": "reference genome", "taxid": "393278", "species_taxid": "393278", "organism_name": "Donghicola eburneus", "infraspecific_name": "strain=DSM 29127", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2684622851 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900115865.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/115/865/GCF_900115865.1_IMG-taxon_2684622851_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4426466", "genome_size_ungapped": "4426466", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "59", "contig_count": "59", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900115865.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4319", "protein_coding_gene_count": "4188", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Donghicola eburneus" ], "sample_taxid": [ "393278" ], "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": "1.253 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4426466", "Number of Sequences": "59", "Longest Sequences (bp)": "559141", "N50 (bp)": "397211", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.8", "Number of CDSs": "4280", "Average Protein Length": "306.8", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Donghicola eburneus", "strain": "strain=DSM 29127", "accession": "GCA_900115865.1", "taxid": 393278, "species_taxid": 393278, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1443, "total_fragments": 1448, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Donghicola mangrovi", "strain": "strain=B5-SW-15", "accession": "GCA_013377535.1", "taxid": 2729614, "species_taxid": 2729614, "relation_to_type": "type", "validated": true, "ani": 84.5754, "matched_fragments": 928, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Donghicola tyrosinivorans", "strain": "strain=DSM 100212", "accession": "GCA_003003355.1", "taxid": 1652492, "species_taxid": 1652492, "relation_to_type": "type", "validated": true, "ani": 81.3748, "matched_fragments": 698, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassococcus halodurans", "strain": "strain=DSM 26915", "accession": "GCA_900108225.1", "taxid": 373675, "species_taxid": 373675, "relation_to_type": "type", "validated": true, "ani": 78.5957, "matched_fragments": 296, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alexandriicola marinus", "strain": "strain=LZ-14", "accession": "GCA_004000435.1", "taxid": 2081710, "species_taxid": 2081710, "relation_to_type": "type", "validated": true, "ani": 78.2452, "matched_fragments": 210, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actibacterium pelagium", "strain": "strain=JN33", "accession": "GCA_002285415.1", "taxid": 2029103, "species_taxid": 2029103, "relation_to_type": "type", "validated": true, "ani": 78.0721, "matched_fragments": 241, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actibacterium pelagium", "strain": "strain=CGMCC 1.16012", "accession": "GCA_014644355.1", "taxid": 2029103, "species_taxid": 2029103, "relation_to_type": "type", "validated": true, "ani": 78.0088, "matched_fragments": 243, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola endophyticus", "strain": "strain=CBS1P-1", "accession": "GCA_018760365.1", "taxid": 2841273, "species_taxid": 2841273, "relation_to_type": "type", "validated": true, "ani": 77.8976, "matched_fragments": 292, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassobius mangrovi", "strain": "strain=GS-10", "accession": "GCA_009857745.1", "taxid": 2692236, "species_taxid": 2692236, "relation_to_type": "type", "validated": true, "ani": 77.7416, "matched_fragments": 294, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliiroseovarius marinus", "strain": "strain=A6024", "accession": "GCA_004360145.1", "taxid": 2500159, "species_taxid": 2500159, "relation_to_type": "type", "validated": true, "ani": 77.6545, "matched_fragments": 230, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliiroseovarius pelagivivens", "strain": "strain=CECT 8811", "accession": "GCA_900302485.1", "taxid": 1639690, "species_taxid": 1639690, "relation_to_type": "type", "validated": true, "ani": 77.6127, "matched_fragments": 203, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=DSM 26824", "accession": "GCA_900129395.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 77.5864, "matched_fragments": 288, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=H3", "accession": "GCA_000712315.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 77.518, "matched_fragments": 292, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chachezhania sediminis", "strain": "strain=CAU 1508", "accession": "GCA_009765275.1", "taxid": 2599291, "species_taxid": 2599291, "relation_to_type": "type", "validated": true, "ani": 77.0806, "matched_fragments": 222, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibacterium elongatum", "strain": "strain=DFL-43", "accession": "GCA_000590925.1", "taxid": 159346, "species_taxid": 159346, "relation_to_type": "type", "validated": true, "ani": 77.0797, "matched_fragments": 206, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Primorskyibacter marinus", "strain": "strain=PX7", "accession": "GCA_003313245.1", "taxid": 1977320, "species_taxid": 1977320, "relation_to_type": "type", "validated": true, "ani": 76.9337, "matched_fragments": 218, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius halotolerans", "strain": "strain=DSM 29507", "accession": "GCA_003634925.1", "taxid": 505353, "species_taxid": 505353, "relation_to_type": "type", "validated": true, "ani": 76.9321, "matched_fragments": 203, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mangrovicoccus algicola", "strain": "strain=HB182678", "accession": "GCA_014903745.1", "taxid": 2771008, "species_taxid": 2771008, "relation_to_type": "type", "validated": true, "ani": 76.9167, "matched_fragments": 183, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola algicola", "strain": "strain=ETT8", "accession": "GCA_010915705.1", "taxid": 2709381, "species_taxid": 2709381, "relation_to_type": "type", "validated": true, "ani": 76.8544, "matched_fragments": 188, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum tesquicola", "strain": "strain=A-36s", "accession": "GCA_024128855.1", "taxid": 540254, "species_taxid": 540254, "relation_to_type": "type", "validated": true, "ani": 76.779, "matched_fragments": 208, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter donghicola", "strain": "strain=KCTC 12864", "accession": "GCA_000622405.1", "taxid": 421000, "species_taxid": 421000, "relation_to_type": "type", "validated": true, "ani": 76.6503, "matched_fragments": 143, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aestuarii", "strain": "strain=DSM 19484", "accession": "GCA_003594815.1", "taxid": 453842, "species_taxid": 453842, "relation_to_type": "type", "validated": true, "ani": 76.5112, "matched_fragments": 178, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900115865.1", "gtdb_species": "s__Donghicola eburneus", "ani": 100.0, "matched_fragments": 1443, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "99.41", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_013377535.1", "gtdb_species": "s__Donghicola mangrovi", "ani": 84.5754, "matched_fragments": 928, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003003355.1", "gtdb_species": "s__Donghicola tyrosinivorans", "ani": 81.3646, "matched_fragments": 699, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola", "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_900108225.1", "gtdb_species": "s__Thalassococcus halodurans", "ani": 78.587, "matched_fragments": 295, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "96.13", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900176475.1", "gtdb_species": "s__Tropicibacter naphthalenivorans", "ani": 78.3624, "matched_fragments": 364, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter", "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_002210095.1", "gtdb_species": "s__Marinibacterium profundimaris", "ani": 78.1835, "matched_fragments": 320, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium", "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_002285415.1", "gtdb_species": "s__Actibacterium pelagium", "ani": 78.1199, "matched_fragments": 240, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium", "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": 2, "status": "-" }, { "accession": "GCA_002701395.1", "gtdb_species": "s__Rhodobacter_B sp002701395", "ani": 77.7861, "matched_fragments": 301, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B", "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_009857745.1", "gtdb_species": "s__Thalassobius mangrovi", "ani": 77.7309, "matched_fragments": 295, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius", "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_900129345.1", "gtdb_species": "s__Ruegeria intermedia", "ani": 77.6855, "matched_fragments": 282, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria", "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_004360145.1", "gtdb_species": "s__Aliiroseovarius marinus", "ani": 77.6638, "matched_fragments": 230, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_010500215.1", "gtdb_species": "s__Aliiroseovarius sp010500215", "ani": 77.6599, "matched_fragments": 237, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_005938225.1", "gtdb_species": "s__Arenibacterium halophilum", "ani": 77.6349, "matched_fragments": 255, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.35", "min_intra_species_ani": "96.35", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000813725.1", "gtdb_species": "s__Leisingera sp000813725", "ani": 77.5888, "matched_fragments": 263, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera", "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_900129395.1", "gtdb_species": "s__Ascidiaceihabitans pseudonitzschiae", "ani": 77.5887, "matched_fragments": 288, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000620505.1", "gtdb_species": "s__Ascidiaceihabitans sp000620505", "ani": 77.5166, "matched_fragments": 285, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "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_900107235.1", "gtdb_species": "s__Citreimonas salinaria", "ani": 77.4222, "matched_fragments": 219, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas", "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_001975705.1", "gtdb_species": "s__Salipiger abyssi", "ani": 77.2391, "matched_fragments": 272, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger", "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_900176485.1", "gtdb_species": "s__Primorskyibacter flagellatus_A", "ani": 77.2121, "matched_fragments": 228, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter", "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_002747035.1", "gtdb_species": "s__GCA-2747035 sp002747035", "ani": 76.9516, "matched_fragments": 131, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-2747035", "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": 0.113, "doubling_h": null, "growth_tmp": 32.0, "optimum_tmp": 26.0, "optimum_ph": 7.5, "genome_size": 4426466.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Donghicola", "eburneus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }