{ "type": "genome", "identifier": "GCF_003664555.1", "organism": "Ochrobactrum soli", "title": "Ochrobactrum soli", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hankyong National University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003664555.1", "bioproject": "PRJNA224116", "biosample": "SAMN10187550", "wgs_master": "RCHH00000000.1", "refseq_category": "reference genome", "taxid": "2448455", "species_taxid": "2448455", "organism_name": "Ochrobactrum soli", "infraspecific_name": "strain=BO-7", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/16", "asm_name": "ASM366455v1", "asm_submitter": "Hankyong National University", "gbrs_paired_asm": "GCA_003664555.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/664/555/GCF_003664555.1_ASM366455v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5024120", "genome_size_ungapped": "5024120", "gc_percent": "57.000000", "replicon_count": "0", "scaffold_count": "48", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003664555.1-RS_2024_08_25", "annotation_date": "2024-08-25", "total_gene_count": "4740", "protein_coding_gene_count": "4613", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-16", "dateModified": "2018-10-16", "datePublished": "2018-10-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Ochrobactrum soli" ], "sample_taxid": [ "2448455" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Seosan-si" ], "sample_host_location_id": [], "data_size": "1.416 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)": "5024120", "Number of Sequences": "48", "Longest Sequences (bp)": "888782", "N50 (bp)": "359264", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.2", "Number of CDSs": "4687", "Average Protein Length": "310.2", "Coding Ratio (%)": "86.8", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brucella haematophila", "strain": "strain=CCUG 38531", "accession": "GCA_005938105.1", "taxid": 419474, "species_taxid": 419474, "relation_to_type": "type", "validated": true, "ani": 90.2659, "matched_fragments": 1331, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella tritici", "strain": "strain=LMG 18957", "accession": "GCA_008932295.1", "taxid": 94626, "species_taxid": 94626, "relation_to_type": "type", "validated": true, "ani": 83.2852, "matched_fragments": 962, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella pecoris", "strain": "strain=DSM 23868", "accession": "GCA_014197065.1", "taxid": 867683, "species_taxid": 867683, "relation_to_type": "type", "validated": true, "ani": 83.1166, "matched_fragments": 981, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella intermedia", "strain": "strain=NCTC12171", "accession": "GCA_900454225.1", "taxid": 94625, "species_taxid": 94625, "relation_to_type": "suspected-type", "validated": true, "ani": 83.0818, "matched_fragments": 989, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella pecoris", "strain": "strain=08RB2639", "accession": "GCA_006376675.1", "taxid": 867683, "species_taxid": 867683, "relation_to_type": "type", "validated": true, "ani": 82.9954, "matched_fragments": 992, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella anthropi", "strain": "strain=NCTC12168", "accession": "GCA_900454235.1", "taxid": 529, "species_taxid": 529, "relation_to_type": "type", "validated": true, "ani": 82.9884, "matched_fragments": 997, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella anthropi", "strain": "strain=ATCC 49188", "accession": "GCA_000017405.1", "taxid": 529, "species_taxid": 529, "relation_to_type": "type", "validated": true, "ani": 82.9153, "matched_fragments": 1008, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella daejeonensis", "strain": "strain=DSM 26944", "accession": "GCA_014199265.1", "taxid": 659015, "species_taxid": 659015, "relation_to_type": "type", "validated": true, "ani": 82.7279, "matched_fragments": 918, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella melitensis", "strain": "strain=16M", "accession": "GCA_000160295.1", "taxid": 29459, "species_taxid": 29459, "relation_to_type": "suspected-type", "validated": true, "ani": 82.1517, "matched_fragments": 758, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella pseudogrignonensis", "strain": "strain=CCUG 30717", "accession": "GCA_002252525.1", "taxid": 419475, "species_taxid": 419475, "relation_to_type": "type", "validated": true, "ani": 80.8398, "matched_fragments": 806, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella pituitosa", "strain": "strain=CCUG 50899", "accession": "GCA_003049685.2", "taxid": 571256, "species_taxid": 571256, "relation_to_type": "type", "validated": true, "ani": 80.7229, "matched_fragments": 856, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella pituitosa", "strain": "strain=CCUG 50899", "accession": "GCA_008801705.1", "taxid": 571256, "species_taxid": 571256, "relation_to_type": "type", "validated": true, "ani": 80.7201, "matched_fragments": 839, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium anhuiense", "strain": "strain=CCBAU 23252", "accession": "GCA_003985145.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 77.7247, "matched_fragments": 319, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudochrobactrum algeriensis", "strain": "", "accession": "GCA_018436245.1", "taxid": 2834768, "species_taxid": 2834768, "relation_to_type": "type", "validated": true, "ani": 77.6831, "matched_fragments": 315, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium anhuiense", "strain": "strain=CGMCC 1.12621", "accession": "GCA_014638185.1", "taxid": 1184720, "species_taxid": 1184720, "relation_to_type": "type", "validated": true, "ani": 77.6765, "matched_fragments": 316, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudochrobactrum algeriensis", "strain": "", "accession": "GCA_907164595.1", "taxid": 2834768, "species_taxid": 2834768, "relation_to_type": "type", "validated": true, "ani": 77.6726, "matched_fragments": 316, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium carmichaelinearum", "strain": "strain=ICMP 18942", "accession": "GCA_900199455.1", "taxid": 1208188, "species_taxid": 1208188, "relation_to_type": "type", "validated": true, "ani": 77.5623, "matched_fragments": 369, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium jarvisii", "strain": "strain=LMG 28313", "accession": "GCA_003601985.1", "taxid": 1777867, "species_taxid": 1777867, "relation_to_type": "type", "validated": true, "ani": 77.4283, "matched_fragments": 358, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium comanense", "strain": "strain=3P27G6", "accession": "GCA_005503535.1", "taxid": 2502215, "species_taxid": 2502215, "relation_to_type": "type", "validated": true, "ani": 77.22, "matched_fragments": 357, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium onobrychidis", "strain": "strain=OM4", "accession": "GCA_024707545.1", "taxid": 2775404, "species_taxid": 2775404, "relation_to_type": "type", "validated": true, "ani": 77.2026, "matched_fragments": 308, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor alexandrii", "strain": "strain=Z3-1", "accession": "GCA_004000215.1", "taxid": 2448161, "species_taxid": 2448161, "relation_to_type": "type", "validated": true, "ani": 77.0366, "matched_fragments": 263, "total_fragments": 1655, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006376685.1", "gtdb_species": "s__Ochrobactrum_B teleogrylli", "ani": 98.1596, "matched_fragments": 1408, "total_fragments": 1655, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_016427605.1", "gtdb_species": "s__Ochrobactrum_B sp016427605", "ani": 91.3687, "matched_fragments": 1360, "total_fragments": 1655, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B", "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_005938105.1", "gtdb_species": "s__Ochrobactrum_B haematophila", "ani": 90.2439, "matched_fragments": 1333, "total_fragments": 1655, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "97.38", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900465685.1", "gtdb_species": "s__Ochrobactrum_B sp900465685", "ani": 90.2322, "matched_fragments": 1338, "total_fragments": 1655, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014138095.1", "gtdb_species": "s__Ochrobactrum_B sp014138095", "ani": 90.203, "matched_fragments": 1383, "total_fragments": 1655, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B", "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": -0.126, "cell_length": 0.239, "doubling_h": null, "growth_tmp": 29.529, "optimum_tmp": 30.583, "optimum_ph": 7.0, "genome_size": 5068981.475, "gc_content": 55.295, "coding_genes": 4718.489, "rRNA16S_genes": 4.666, "tRNA_genes": 59.222, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.727, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Ochrobactrum", "soli" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }