{ "type": "genome", "identifier": "GCA_025463515.1", "organism": "Rhodoglobus sp.", "title": "Rhodoglobus sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Colorado State University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_025463515.1", "bioproject": "PRJNA682830", "biosample": "SAMN17837158", "wgs_master": "JAODAQ000000000.1", "refseq_category": "na", "taxid": "1950123", "species_taxid": "1950123", "organism_name": "Rhodoglobus sp.", "infraspecific_name": "", "isolate": "RYN_70", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/09/28", "asm_name": "ASM2546351v1", "submitter": "Colorado State University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/463/515/GCA_025463515.1_ASM2546351v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-09-28", "dateModified": "2022-09-28", "datePublished": "2022-09-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodoglobus sp." ], "sample_taxid": [ "1950123" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Wyoming" ], "sample_host_location_id": [], "data_size": "0.899 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 86.34, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3319813", "Number of Sequences": "78", "Longest Sequences (bp)": "187347", "N50 (bp)": "78087", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.4", "Number of CDSs": "3262", "Average Protein Length": "311.0", "Coding Ratio (%)": "91.7", "Number of rRNAs": "1", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Conyzicola lurida", "strain": "strain=DSM 105784", "accession": "GCA_014204935.1", "taxid": 1172621, "species_taxid": 1172621, "relation_to_type": "type", "validated": true, "ani": 80.0898, "matched_fragments": 510, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conyzicola nivalis", "strain": "strain=CGMCC 1.12813", "accession": "GCA_014639655.1", "taxid": 1477021, "species_taxid": 1477021, "relation_to_type": "type", "validated": true, "ani": 79.8663, "matched_fragments": 473, "total_fragments": 1066, "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": 79.51, "matched_fragments": 415, "total_fragments": 1066, "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": 79.4672, "matched_fragments": 420, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter californiensis", "strain": "strain=CFBP 8216", "accession": "GCA_003576155.1", "taxid": 1401995, "species_taxid": 1401995, "relation_to_type": "type", "validated": true, "ani": 79.2735, "matched_fragments": 313, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinibacterium xinjiangense", "strain": "strain=CGMCC 1.5381", "accession": "GCA_014645015.1", "taxid": 386302, "species_taxid": 386302, "relation_to_type": "type", "validated": true, "ani": 79.2135, "matched_fragments": 386, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leifsonia aquatica", "strain": "strain=ATCC 14665", "accession": "GCA_000469485.1", "taxid": 144185, "species_taxid": 144185, "relation_to_type": "type", "validated": true, "ani": 79.1937, "matched_fragments": 321, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinibacterium xinjiangense", "strain": "strain=CGMCC 1.05381", "accession": "GCA_900230175.1", "taxid": 386302, "species_taxid": 386302, "relation_to_type": "type", "validated": true, "ani": 79.1126, "matched_fragments": 396, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacisediminihabitans profunda", "strain": "strain=CHu50b-6-2", "accession": "GCA_008040105.1", "taxid": 2594790, "species_taxid": 2594790, "relation_to_type": "type", "validated": true, "ani": 79.0173, "matched_fragments": 454, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_002240635.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.9886, "matched_fragments": 397, "total_fragments": 1066, "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": 78.9561, "matched_fragments": 464, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter californiensis", "strain": "strain=CFBP 8216", "accession": "GCA_021952865.1", "taxid": 1401995, "species_taxid": 1401995, "relation_to_type": "type", "validated": true, "ani": 78.9056, "matched_fragments": 394, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter phaseoli", "strain": "strain=LPPA 982", "accession": "GCA_021922925.1", "taxid": 1734031, "species_taxid": 1734031, "relation_to_type": "type", "validated": true, "ani": 78.9014, "matched_fragments": 401, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. michiganensis", "strain": "strain=LMG 7333", "accession": "GCA_002240575.1", "taxid": 33013, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.8652, "matched_fragments": 385, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_021922985.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.8644, "matched_fragments": 398, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter zhangzhiyongii", "strain": "strain=DM1", "accession": "GCA_014775655.1", "taxid": 2768071, "species_taxid": 2768071, "relation_to_type": "type", "validated": true, "ani": 78.8572, "matched_fragments": 396, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis", "strain": "strain=LMG7333", "accession": "GCA_021216655.1", "taxid": 28447, "species_taxid": 28447, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8295, "matched_fragments": 390, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis", "strain": "strain=VKM Ac-1403", "accession": "GCA_900168345.1", "taxid": 28447, "species_taxid": 28447, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8268, "matched_fragments": 389, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=ATCC 10253", "accession": "GCA_003076355.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.8153, "matched_fragments": 390, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacisediminihabitans changchengi", "strain": "strain=G11-30", "accession": "GCA_016634425.1", "taxid": 2787634, "species_taxid": 2787634, "relation_to_type": "type", "validated": true, "ani": 78.8026, "matched_fragments": 353, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leifsonia shinshuensis", "strain": "strain=DSM 15165", "accession": "GCA_013410375.1", "taxid": 150026, "species_taxid": 150026, "relation_to_type": "type", "validated": true, "ani": 78.6726, "matched_fragments": 441, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbiconiux moechotypicola", "strain": "strain=KCTC 19653", "accession": "GCA_024979255.1", "taxid": 637393, "species_taxid": 637393, "relation_to_type": "type", "validated": true, "ani": 78.5611, "matched_fragments": 409, "total_fragments": 1066, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 86.34, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903920435.1", "gtdb_species": "s__Rhodoglobus sp903920435", "ani": 85.513, "matched_fragments": 683, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "97.73", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_001725325.1", "gtdb_species": "s__Rhodoglobus sp001725325", "ani": 85.3673, "matched_fragments": 729, "total_fragments": 1066, "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": "GCA_013297645.1", "gtdb_species": "s__JAAFHU01 sp013297645", "ani": 80.0558, "matched_fragments": 385, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAAFHU01", "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_004310685.1", "gtdb_species": "s__Conyzicola arctica", "ani": 79.9595, "matched_fragments": 473, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola", "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_015752305.1", "gtdb_species": "s__Rhodoglobus sp015752305", "ani": 79.8743, "matched_fragments": 463, "total_fragments": 1066, "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_013410945.1", "gtdb_species": "s__Rhodoglobus sp013410945", "ani": 79.8478, "matched_fragments": 468, "total_fragments": 1066, "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_014595885.1", "gtdb_species": "s__Yonghaparkia alkaliphila_A", "ani": 79.584, "matched_fragments": 399, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia", "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": 2, "status": "-" }, { "accession": "GCA_004297555.1", "gtdb_species": "s__Rhodoglobus sp004297555", "ani": 79.5629, "matched_fragments": 243, "total_fragments": 1066, "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_014483895.1", "gtdb_species": "s__Protaetiibacter sp014483895", "ani": 79.4492, "matched_fragments": 460, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter", "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_001898835.1", "gtdb_species": "s__Protaetiibacter sp001898835", "ani": 79.1115, "matched_fragments": 453, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter", "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": 2, "status": "-" }, { "accession": "GCF_008040105.1", "gtdb_species": "s__Lacisediminihabitans profunda", "ani": 79.0236, "matched_fragments": 452, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans", "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_001618005.1", "gtdb_species": "s__Clavibacter tessellarius_A", "ani": 78.9114, "matched_fragments": 384, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "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_002931175.1", "gtdb_species": "s__Clavibacter californiensis", "ani": 78.8478, "matched_fragments": 387, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "98.71", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900168345.1", "gtdb_species": "s__Clavibacter michiganensis", "ani": 78.8383, "matched_fragments": 388, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "95.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.88", "num_clustered_genomes": 49, "status": "-" }, { "accession": "GCF_014217685.1", "gtdb_species": "s__Lacisediminihabitans sp014217685", "ani": 78.3871, "matched_fragments": 382, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans", "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_014645235.1", "gtdb_species": "s__Agrococcus terreus", "ani": 78.2416, "matched_fragments": 349, "total_fragments": 1066, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "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": -0.577, "cell_length": 0.0, "doubling_h": 0.973, "growth_tmp": 19.225, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Actinomycetota", "c__Actinomycetes", "o__Actinomycetales", "f__Microbacteriaceae", "g__Rhodoglobus", "s__Rhodoglobus sp025463515" ], "_genome_taxon": [ "Rhodoglobus", "sp.", "d__Bacteria", "p__Actinomycetota", "c__Actinomycetes", "o__Actinomycetales", "f__Microbacteriaceae", "g__Rhodoglobus", "s__Rhodoglobus sp025463515", "Bacteria", "Actinomycetota", "Actinomycetes", "Actinomycetales", "Microbacteriaceae", "Rhodoglobus", "Rhodoglobus", "sp025463515" ], "_meo": [ { "id": "MEO_0000007", "label": "soil" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }