{ "type": "genome", "identifier": "GCF_006788895.1", "organism": "Rhodoglobus vestalii", "title": "Rhodoglobus vestalii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006788895.1", "bioproject": "PRJNA224116", "biosample": "SAMN11512386", "wgs_master": "VFRA00000000.1", "refseq_category": "reference genome", "taxid": "193384", "species_taxid": "193384", "organism_name": "Rhodoglobus vestalii", "infraspecific_name": "strain=DSM 21947", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/09", "asm_name": "ASM678889v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_006788895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/788/895/GCF_006788895.1_ASM678889v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2835882", "genome_size_ungapped": "2835882", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006788895.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "2789", "protein_coding_gene_count": "2684", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-09", "dateModified": "2019-07-09", "datePublished": "2019-07-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodoglobus vestalii" ], "sample_taxid": [ "193384" ], "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": "0.800 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)": "2835882", "Number of Sequences": "1", "Longest Sequences (bp)": "2835882", "N50 (bp)": "2835882", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.8", "Number of CDSs": "2840", "Average Protein Length": "299.9", "Coding Ratio (%)": "90.1", "Number of rRNAs": "6", "Number of tRNAs": "44", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Salinibacterium amurskyense", "strain": "strain=JCM 12362", "accession": "GCA_003668745.1", "taxid": 205941, "species_taxid": 205941, "relation_to_type": "type", "validated": true, "ani": 80.6788, "matched_fragments": 476, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinibacterium amurskyense", "strain": "strain=KCTC 9931", "accession": "GCA_014652955.1", "taxid": 205941, "species_taxid": 205941, "relation_to_type": "type", "validated": true, "ani": 80.6764, "matched_fragments": 483, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinibacterium amurskyense", "strain": "strain=DSM 16400", "accession": "GCA_002797685.1", "taxid": 205941, "species_taxid": 205941, "relation_to_type": "type", "validated": true, "ani": 80.6613, "matched_fragments": 471, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conyzicola lurida", "strain": "strain=DSM 105784", "accession": "GCA_014204935.1", "taxid": 1172621, "species_taxid": 1172621, "relation_to_type": "type", "validated": true, "ani": 77.9301, "matched_fragments": 158, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agreia pratensis", "strain": "strain=VKM Ac-2510", "accession": "GCA_900177685.1", "taxid": 150121, "species_taxid": 150121, "relation_to_type": "type", "validated": true, "ani": 77.3736, "matched_fragments": 100, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Galbitalea soli", "strain": "strain=NBRC 108727", "accession": "GCA_010686725.1", "taxid": 1268042, "species_taxid": 1268042, "relation_to_type": "type", "validated": true, "ani": 77.2918, "matched_fragments": 131, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marisediminicola senii", "strain": "strain=SM7_A14", "accession": "GCA_011057645.1", "taxid": 2711233, "species_taxid": 2711233, "relation_to_type": "type", "validated": true, "ani": 77.239, "matched_fragments": 129, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Galbitalea soli", "strain": "strain=DSM 105515", "accession": "GCA_013410525.1", "taxid": 1268042, "species_taxid": 1268042, "relation_to_type": "type", "validated": true, "ani": 77.1655, "matched_fragments": 130, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Glaciihabitans tibetensis", "strain": "strain=CGMCC 1.12484", "accession": "GCA_003003265.1", "taxid": 1266600, "species_taxid": 1266600, "relation_to_type": "type", "validated": true, "ani": 76.9782, "matched_fragments": 120, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrimesophilobacter mesophilus", "strain": "strain=DSM 19267", "accession": "GCA_014200375.1", "taxid": 433647, "species_taxid": 433647, "relation_to_type": "type", "validated": true, "ani": 76.9694, "matched_fragments": 86, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigoribacterium faeni", "strain": "strain=NBRC 103066", "accession": "GCA_007988805.1", "taxid": 145483, "species_taxid": 145483, "relation_to_type": "type", "validated": true, "ani": 76.9131, "matched_fragments": 91, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium atlanticum", "strain": "strain=WY121", "accession": "GCA_015277815.1", "taxid": 2782168, "species_taxid": 2782168, "relation_to_type": "type", "validated": true, "ani": 76.8694, "matched_fragments": 70, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces subbeticus", "strain": "strain=DSM 16689", "accession": "GCA_000421565.1", "taxid": 293890, "species_taxid": 293890, "relation_to_type": "type", "validated": true, "ani": 76.8455, "matched_fragments": 109, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces cerinus subsp. cerinus", "strain": "strain=DSM 8595", "accession": "GCA_900142065.1", "taxid": 232089, "species_taxid": 33878, "relation_to_type": "type", "validated": true, "ani": 76.6992, "matched_fragments": 103, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycetocola saprophilus", "strain": "strain=NRRL B-24119", "accession": "GCA_000718085.1", "taxid": 76636, "species_taxid": 76636, "relation_to_type": "type", "validated": true, "ani": 76.6944, "matched_fragments": 64, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces mariniharenae", "strain": "strain=NEAU-184", "accession": "GCA_008122505.1", "taxid": 2604423, "species_taxid": 2604423, "relation_to_type": "type", "validated": true, "ani": 76.5827, "matched_fragments": 96, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sulfonylureivorans", "strain": "strain=LAM7116", "accession": "GCA_003999995.1", "taxid": 2486854, "species_taxid": 2486854, "relation_to_type": "type", "validated": true, "ani": 76.4128, "matched_fragments": 78, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006788895.1", "gtdb_species": "s__Rhodoglobus vestalii", "ani": 100.0, "matched_fragments": 945, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.85", "min_intra_species_ani": "96.85", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000247645.1", "gtdb_species": "s__Rhodoglobus sp000247645", "ani": 80.9044, "matched_fragments": 496, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "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_015864955.1", "gtdb_species": "s__Rhodoglobus sp015864955", "ani": 80.8491, "matched_fragments": 451, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "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_000153145.1", "gtdb_species": "s__Rhodoglobus sp000153145", "ani": 80.8381, "matched_fragments": 482, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "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_015864575.1", "gtdb_species": "s__Rhodoglobus sp015864575", "ani": 80.8226, "matched_fragments": 493, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "96.11", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_015864665.1", "gtdb_species": "s__Rhodoglobus sp015864665", "ani": 80.6707, "matched_fragments": 472, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002797685.1", "gtdb_species": "s__Rhodoglobus amurskyensis", "ani": 80.6485, "matched_fragments": 472, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "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": "-" }, { "accession": "GCF_015864945.1", "gtdb_species": "s__Rhodoglobus sp015864945", "ani": 80.6032, "matched_fragments": 482, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "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_004118935.1", "gtdb_species": "s__Rhodoglobus sp004118935", "ani": 80.5622, "matched_fragments": 457, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.46", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.824, "cell_length": 0.0, "doubling_h": 0.973, "growth_tmp": 17.95, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "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": [ "Rhodoglobus", "vestalii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }