{ "type": "genome", "identifier": "GCF_014197755.1", "organism": "Rhodocyclus tenuis", "title": "Rhodocyclus tenuis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014197755.1", "bioproject": "PRJNA224116", "biosample": "SAMN13165094", "wgs_master": "JACIGE000000000.1", "refseq_category": "na", "taxid": "1066", "species_taxid": "1066", "organism_name": "Rhodocyclus tenuis", "infraspecific_name": "strain=2761", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1419775v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014197755.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/197/755/GCF_014197755.1_ASM1419775v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3852278", "genome_size_ungapped": "3852180", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-18", "total_gene_count": "3555", "protein_coding_gene_count": "3477", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodocyclus tenuis" ], "sample_taxid": [ "1066" ], "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": "1.057 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)": "3852278", "Number of Sequences": "25", "Longest Sequences (bp)": "576846", "N50 (bp)": "279408", "Gap Ratio (%)": "0.002544", "GCcontent (%)": "64.7", "Number of CDSs": "3491", "Average Protein Length": "331.8", "Coding Ratio (%)": "90.2", "Number of rRNAs": "2", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodocyclus tenuis", "strain": "strain=2761", "accession": "GCA_014197755.1", "taxid": 1066, "species_taxid": 1066, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1270, "total_fragments": 1271, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodocyclus tenuis", "strain": "strain=2761", "accession": "GCA_009469755.1", "taxid": 1066, "species_taxid": 1066, "relation_to_type": "type", "validated": true, "ani": 99.9957, "matched_fragments": 1269, "total_fragments": 1271, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodocyclus gracilis", "strain": "strain=DSM 110", "accession": "GCA_009617575.1", "taxid": 2929842, "species_taxid": 2929842, "relation_to_type": "type", "validated": true, "ani": 83.3092, "matched_fragments": 663, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodocyclus purpureus", "strain": "strain=DSM 168", "accession": "GCA_016653115.1", "taxid": 1067, "species_taxid": 1067, "relation_to_type": "type", "validated": true, "ani": 83.2491, "matched_fragments": 627, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propionivibrio dicarboxylicus", "strain": "strain=DSM 5885", "accession": "GCA_900099695.1", "taxid": 83767, "species_taxid": 83767, "relation_to_type": "type", "validated": true, "ani": 78.9249, "matched_fragments": 367, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propionivibrio limicola", "strain": "strain=GolChi1", "accession": "GCA_009469695.1", "taxid": 167645, "species_taxid": 167645, "relation_to_type": "type", "validated": true, "ani": 78.8733, "matched_fragments": 334, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospira oryzae", "strain": "strain=DSM 21223", "accession": "GCA_004217225.1", "taxid": 146939, "species_taxid": 146939, "relation_to_type": "type", "validated": true, "ani": 78.3873, "matched_fragments": 379, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crenobacter luteus", "strain": "strain=DSM 27258", "accession": "GCA_004345725.1", "taxid": 1452487, "species_taxid": 1452487, "relation_to_type": "type", "validated": true, "ani": 77.5463, "matched_fragments": 304, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia ubonensis", "strain": "", "accession": "GCA_902499185.1", "taxid": 101571, "species_taxid": 101571, "relation_to_type": "type", "validated": true, "ani": 76.8837, "matched_fragments": 319, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia ubonensis", "strain": "strain=LMG 20358", "accession": "GCA_902833085.1", "taxid": 101571, "species_taxid": 101571, "relation_to_type": "type", "validated": true, "ani": 76.8787, "matched_fragments": 333, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia pallida", "strain": "strain=7MH5", "accession": "GCA_004524855.1", "taxid": 2547399, "species_taxid": 2547399, "relation_to_type": "type", "validated": true, "ani": 76.7518, "matched_fragments": 273, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia anthina", "strain": "strain=DSM 16086", "accession": "GCA_016836725.1", "taxid": 179879, "species_taxid": 179879, "relation_to_type": "suspected-type", "validated": true, "ani": 76.6933, "matched_fragments": 302, "total_fragments": 1271, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014197755.1", "gtdb_species": "s__Rhodocyclus tenuis", "ani": 100.0, "matched_fragments": 1270, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.58", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_011881425.1", "gtdb_species": "s__Rhodocyclus tenuis_A", "ani": 83.2902, "matched_fragments": 663, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016653115.1", "gtdb_species": "s__Rhodocyclus purpureus", "ani": 83.1999, "matched_fragments": 630, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus", "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_001897745.1", "gtdb_species": "s__66-26 sp001897745", "ani": 81.6461, "matched_fragments": 623, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "95.98", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016858125.1", "gtdb_species": "s__Azospira_A restricta", "ani": 80.7642, "matched_fragments": 573, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A", "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_016183655.1", "gtdb_species": "s__Azospira_A sp016183655", "ani": 80.2187, "matched_fragments": 543, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A", "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_018262095.1", "gtdb_species": "s__Propionivibrio sp018262095", "ani": 79.4395, "matched_fragments": 475, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio", "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_017995515.1", "gtdb_species": "s__Propionivibrio sp017995515", "ani": 79.2764, "matched_fragments": 397, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio", "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_002345025.1", "gtdb_species": "s__Accumulibacter phosphatis_B", "ani": 78.5448, "matched_fragments": 401, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000428465.1", "gtdb_species": "s__Chitinimonas koreensis", "ani": 77.2588, "matched_fragments": 373, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas", "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_008929045.1", "gtdb_species": "s__Noviherbaspirillum aerium", "ani": 76.9757, "matched_fragments": 206, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_903831455.1", "gtdb_species": "s__CAIKXV01 sp903831455", "ani": 76.4129, "matched_fragments": 164, "total_fragments": 1271, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__CAIKXV01;g__CAIKXV01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.62", "min_intra_species_ani": "99.56", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Rhodocyclus", "tenuis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }