{ "type": "genome", "identifier": "GCF_003254005.1", "organism": "Roseinatronobacter thiooxidans", "title": "Roseinatronobacter thiooxidans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003254005.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660267", "wgs_master": "QKZQ00000000.1", "refseq_category": "na", "taxid": "121821", "species_taxid": "121821", "organism_name": "Roseinatronobacter thiooxidans", "infraspecific_name": "strain=DSM 13087", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/19", "asm_name": "ASM325400v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003254005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/005/GCF_003254005.1_ASM325400v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3685266", "genome_size_ungapped": "3680859", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003254005.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "3590", "protein_coding_gene_count": "3479", "non_coding_gene_count": "46", "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": [ "Roseinatronobacter thiooxidans" ], "sample_taxid": [ "121821" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia" ], "sample_host_location_id": [], "data_size": "1.029 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)": "3685266", "Number of Sequences": "58", "Longest Sequences (bp)": "402835", "N50 (bp)": "172768", "Gap Ratio (%)": "0.119584", "GCcontent (%)": "60.1", "Number of CDSs": "3517", "Average Protein Length": "308.6", "Coding Ratio (%)": "88.4", "Number of rRNAs": "3", "Number of tRNAs": "40", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseinatronobacter thiooxidans", "strain": "strain=DSM 13087", "accession": "GCA_003254005.1", "taxid": 121821, "species_taxid": 121821, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1192, "total_fragments": 1196, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseinatronobacter thiooxidans", "strain": "strain=ALG1", "accession": "GCA_001870675.1", "taxid": 121821, "species_taxid": 121821, "relation_to_type": "type", "validated": true, "ani": 99.9633, "matched_fragments": 1122, "total_fragments": 1196, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseinatronobacter monicus", "strain": "strain=DSM 18423", "accession": "GCA_006716865.1", "taxid": 393481, "species_taxid": 393481, "relation_to_type": "type", "validated": true, "ani": 83.4823, "matched_fragments": 805, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobaca barguzinensis", "strain": "strain=DSM 19920", "accession": "GCA_004365885.1", "taxid": 441209, "species_taxid": 441209, "relation_to_type": "suspected-type", "validated": true, "ani": 82.4946, "matched_fragments": 789, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobaca bogoriensis", "strain": "strain=DSM 18756", "accession": "GCA_004366635.1", "taxid": 119542, "species_taxid": 119542, "relation_to_type": "suspected-type", "validated": true, "ani": 82.4818, "matched_fragments": 790, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobaca barguzinensis", "strain": "strain=alga05", "accession": "GCA_001870665.2", "taxid": 441209, "species_taxid": 441209, "relation_to_type": "suspected-type", "validated": true, "ani": 82.4609, "matched_fragments": 794, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhabdonatronobacter sediminivivens", "strain": "strain=IM2376", "accession": "GCA_013415485.1", "taxid": 2743469, "species_taxid": 2743469, "relation_to_type": "type", "validated": true, "ani": 78.2322, "matched_fragments": 404, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum steppense", "strain": "strain=DSM 21153", "accession": "GCA_004339675.1", "taxid": 540251, "species_taxid": 540251, "relation_to_type": "type", "validated": true, "ani": 77.2872, "matched_fragments": 241, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola sediminis", "strain": "strain=DRYC-M-16", "accession": "GCA_004745575.1", "taxid": 2486418, "species_taxid": 2486418, "relation_to_type": "type", "validated": true, "ani": 77.2783, "matched_fragments": 243, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola alkalilacus", "strain": "strain=DJC", "accession": "GCA_003443995.1", "taxid": 2305252, "species_taxid": 2305252, "relation_to_type": "type", "validated": true, "ani": 77.231, "matched_fragments": 280, "total_fragments": 1196, "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": 77.0684, "matched_fragments": 240, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger marinus", "strain": "strain=DSM 26424", "accession": "GCA_900100085.1", "taxid": 555512, "species_taxid": 555512, "relation_to_type": "type", "validated": true, "ani": 76.9943, "matched_fragments": 306, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 76.963, "matched_fragments": 278, "total_fragments": 1196, "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": 76.9462, "matched_fragments": 280, "total_fragments": 1196, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001870675.1", "gtdb_species": "s__Roseinatronobacter thiooxidans", "ani": 99.9633, "matched_fragments": 1122, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.65", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_006716865.1", "gtdb_species": "s__Roseinatronobacter monicus", "ani": 83.4822, "matched_fragments": 805, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.80", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.77", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_004366635.1", "gtdb_species": "s__Roseinatronobacter bogoriensis", "ani": 82.4781, "matched_fragments": 790, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_007126715.1", "gtdb_species": "s__Roseinatronobacter sp007126715", "ani": 82.4261, "matched_fragments": 658, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001884735.1", "gtdb_species": "s__Roseinatronobacter thiooxidans_A", "ani": 80.1961, "matched_fragments": 633, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "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_007118295.1", "gtdb_species": "s__Roseinatronobacter sp007118295", "ani": 80.0644, "matched_fragments": 525, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017510335.1", "gtdb_species": "s__Roseinatronobacter sp017510335", "ani": 80.0483, "matched_fragments": 551, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "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_007131465.1", "gtdb_species": "s__Roseinatronobacter sp007131465", "ani": 79.9779, "matched_fragments": 384, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "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_003561595.1", "gtdb_species": "s__Roseinatronobacter sp003561595", "ani": 79.7575, "matched_fragments": 468, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.90", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_003565055.1", "gtdb_species": "s__Roseinatronobacter sp003565055", "ani": 79.2993, "matched_fragments": 415, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "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_016937725.1", "gtdb_species": "s__Roseinatronobacter sp016937725", "ani": 78.7583, "matched_fragments": 376, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "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_009908405.1", "gtdb_species": "s__Roseinatronobacter sp009908405", "ani": 78.7545, "matched_fragments": 375, "total_fragments": 1196, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 3685266.0, "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": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Roseinatronobacter", "thiooxidans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }