{ "type": "genome", "identifier": "GCF_003254295.1", "organism": "Rhodobacter capsulatus", "title": "Rhodobacter capsulatus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003254295.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660778", "wgs_master": "QKZO00000000.1", "refseq_category": "na", "taxid": "1061", "species_taxid": "1061", "organism_name": "Rhodobacter capsulatus", "infraspecific_name": "strain=DSM 1710", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/19", "asm_name": "ASM325429v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003254295.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/295/GCF_003254295.1_ASM325429v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3668822", "genome_size_ungapped": "3667154", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "24", "contig_count": "24", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003254295.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3560", "protein_coding_gene_count": "3456", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-19", "dateModified": "2018-06-19", "datePublished": "2018-06-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodobacter capsulatus" ], "sample_taxid": [ "1061" ], "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": "0.996 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)": "3668822", "Number of Sequences": "24", "Longest Sequences (bp)": "499662", "N50 (bp)": "314919", "Gap Ratio (%)": "0.045464", "GCcontent (%)": "66.5", "Number of CDSs": "3487", "Average Protein Length": "315.4", "Coding Ratio (%)": "89.9", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "3" }, "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": 100.0, "matched_fragments": 1212, "total_fragments": 1213, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodobacter viridis", "strain": "strain=JA737", "accession": "GCA_003217355.1", "taxid": 1054202, "species_taxid": 1054202, "relation_to_type": "type", "validated": true, "ani": 89.3363, "matched_fragments": 968, "total_fragments": 1213, "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": 82.0799, "matched_fragments": 683, "total_fragments": 1213, "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": 81.8974, "matched_fragments": 693, "total_fragments": 1213, "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": 81.7042, "matched_fragments": 698, "total_fragments": 1213, "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": 80.2627, "matched_fragments": 683, "total_fragments": 1213, "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": 80.2598, "matched_fragments": 676, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter albus", "strain": "strain=SP32", "accession": "GCA_009908165.1", "taxid": 1465486, "species_taxid": 1465486, "relation_to_type": "type", "validated": true, "ani": 79.2496, "matched_fragments": 557, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter albus", "strain": "strain=SP32", "accession": "GCA_009881095.1", "taxid": 1465486, "species_taxid": 1465486, "relation_to_type": "type", "validated": true, "ani": 79.2436, "matched_fragments": 559, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 79.0583, "matched_fragments": 512, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter ovatus", "strain": "strain=JA234", "accession": "GCA_900207575.1", "taxid": 439529, "species_taxid": 439529, "relation_to_type": "type", "validated": true, "ani": 79.0552, "matched_fragments": 507, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 79.0385, "matched_fragments": 471, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter mobilis", "strain": "strain=cai42", "accession": "GCA_001620265.1", "taxid": 1335048, "species_taxid": 1335048, "relation_to_type": "type", "validated": true, "ani": 78.891, "matched_fragments": 574, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter azotoformans", "strain": "strain=KA25", "accession": "GCA_003050905.1", "taxid": 43057, "species_taxid": 43057, "relation_to_type": "type", 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1212, "total_fragments": 1213, "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": "conclusive" }, { "accession": "GCF_005144475.1", "gtdb_species": "s__Rhodobacter capsulatus_C", "ani": 94.5722, "matched_fragments": 1015, "total_fragments": 1213, "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": 93.8305, "matched_fragments": 1085, 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