{ "type": "genome", "identifier": "GCF_900217815.1", "organism": "Rhodobacter maris", "title": "Rhodobacter maris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900217815.1", "bioproject": "PRJNA224116", "biosample": "SAMN05877831", "wgs_master": "OBMT00000000.1", "refseq_category": "reference genome", "taxid": "446682", "species_taxid": "446682", "organism_name": "Rhodobacter maris", "infraspecific_name": "strain=JA276", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/09/28", "asm_name": "IMG-taxon 2739368070 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900217815.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/217/815/GCF_900217815.1_IMG-taxon_2739368070_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": "3833743", "genome_size_ungapped": "3833450", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "57", "contig_count": "57", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900217815.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "3736", "protein_coding_gene_count": "3634", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-09-28", "dateModified": "2017-09-28", "datePublished": "2017-09-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodobacter maris" ], "sample_taxid": [ "446682" ], "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": "1.055 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)": "3833743", "Number of Sequences": "57", "Longest Sequences (bp)": "888897", "N50 (bp)": "218673", "Gap Ratio (%)": "0.007643", "GCcontent (%)": "65.1", "Number of CDSs": "3662", "Average Protein Length": "311.5", "Coding Ratio (%)": "89.3", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodobacter capsulatus", "strain": "strain=DSM 1710", "accession": "GCA_003254295.1", "taxid": 1061, "species_taxid": 1061, "relation_to_type": "type", "validated": true, "ani": 82.7078, "matched_fragments": 808, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter viridis", "strain": "strain=JA737", "accession": "GCA_003217355.1", "taxid": 1054202, "species_taxid": 1054202, "relation_to_type": "type", "validated": true, "ani": 82.368, "matched_fragments": 781, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter aestuarii", "strain": "strain=JA296", "accession": "GCA_003053525.1", "taxid": 453582, "species_taxid": 453582, "relation_to_type": "type", "validated": true, "ani": 81.6445, "matched_fragments": 777, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter aestuarii", "strain": "strain=DSM 19945", "accession": "GCA_900156655.1", "taxid": 453582, "species_taxid": 453582, "relation_to_type": "type", "validated": true, "ani": 81.6023, "matched_fragments": 779, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter huangdaonensis", "strain": "strain=CGMCC 1.12963", "accession": "GCA_004022465.1", "taxid": 2501515, "species_taxid": 2501515, "relation_to_type": "type", "validated": true, "ani": 81.2145, "matched_fragments": 639, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter ferrireducens", "strain": "strain=CCTCC AB2012026", "accession": "GCA_004022265.1", "taxid": 1215032, "species_taxid": 1215032, "relation_to_type": "type", "validated": true, "ani": 81.1418, "matched_fragments": 636, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter hankyongi", "strain": "strain=BO-81", "accession": "GCA_003664585.1", "taxid": 2294033, "species_taxid": 2294033, "relation_to_type": "type", "validated": true, "ani": 81.0679, "matched_fragments": 655, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava atlantica", "strain": "strain=13D2W-2", "accession": "GCA_000737065.1", "taxid": 1317124, "species_taxid": 1317124, "relation_to_type": "type", "validated": true, "ani": 79.6072, "matched_fragments": 528, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava nitratireducens", "strain": "strain=25B10_4", "accession": "GCA_001940525.2", "taxid": 1915078, "species_taxid": 1915078, "relation_to_type": "type", "validated": true, "ani": 78.8243, "matched_fragments": 490, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 78.1009, "matched_fragments": 366, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 78.0829, "matched_fragments": 407, "total_fragments": 1245, "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": 77.7374, "matched_fragments": 315, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter ruber", "strain": "strain=CCP-1", "accession": "GCA_009908315.1", "taxid": 1985673, "species_taxid": 1985673, "relation_to_type": "type", "validated": true, "ani": 77.6895, "matched_fragments": 376, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus nototheniae", "strain": "strain=I-41R45", "accession": "GCA_004335005.1", "taxid": 2489002, "species_taxid": 2489002, "relation_to_type": "type", "validated": true, "ani": 77.3911, "matched_fragments": 316, "total_fragments": 1245, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900217815.1", "gtdb_species": "s__Rhodobacter maris", "ani": 100.0, "matched_fragments": 1241, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "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_003254295.1", "gtdb_species": "s__Rhodobacter capsulatus", "ani": 82.7349, "matched_fragments": 805, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.61", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_005144475.1", "gtdb_species": "s__Rhodobacter capsulatus_C", "ani": 82.5978, "matched_fragments": 821, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "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_000021865.1", "gtdb_species": "s__Rhodobacter capsulatus_B", "ani": 82.5813, "matched_fragments": 833, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003217355.1", "gtdb_species": "s__Rhodobacter viridis", "ani": 82.3718, "matched_fragments": 781, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "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_900156655.1", "gtdb_species": "s__Rhodobacter aestuarii", "ani": 81.5893, "matched_fragments": 781, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.72", "min_intra_species_ani": "97.43", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001856665.1", "gtdb_species": "s__LPB0142 sp001856665", "ani": 81.5851, "matched_fragments": 674, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003664585.1", "gtdb_species": "s__Paenirhodobacter hankyongi", "ani": 81.0545, "matched_fragments": 656, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter", "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_003249215.1", "gtdb_species": "s__SZUA-611 sp003249215", "ani": 80.6145, "matched_fragments": 539, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611", "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_002452815.1", "gtdb_species": "s__UBA6796 sp002452815", "ani": 80.2015, "matched_fragments": 567, "total_fragments": 1245, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.0, "doubling_h": 0.531, "growth_tmp": 28.333, "optimum_tmp": 30.0, "optimum_ph": 6.75, "genome_size": 3833743.0, "gc_content": 66.914, "coding_genes": 3782.589, "rRNA16S_genes": 3.9, "tRNA_genes": 50.925, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhodobacter", "maris" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }