{ "type": "genome", "identifier": "GCF_014640615.1", "organism": "Brucella endophytica", "title": "Brucella endophytica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014640615.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245013", "wgs_master": "BMHH00000000.1", "refseq_category": "reference genome", "taxid": "1963359", "species_taxid": "1963359", "organism_name": "Brucella endophytica", "infraspecific_name": "strain=CGMCC 1.15082", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1464061v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014640615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/640/615/GCF_014640615.1_ASM1464061v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4932019", "genome_size_ungapped": "4931833", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "83", "contig_count": "83", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014640615.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "4774", "protein_coding_gene_count": "4583", "non_coding_gene_count": "53", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Brucella endophytica" ], "sample_taxid": [ "1963359" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.382 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)": "4932019", "Number of Sequences": "83", "Longest Sequences (bp)": "491865", "N50 (bp)": "219690", "Gap Ratio (%)": "0.003771", "GCcontent (%)": "60.7", "Number of CDSs": "4714", "Average Protein Length": "298.9", "Coding Ratio (%)": "85.7", "Number of rRNAs": "2", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phyllobacterium leguminum", "strain": "strain=ORS 1419", "accession": "GCA_003217235.1", "taxid": 314237, "species_taxid": 314237, "relation_to_type": "type", "validated": true, "ani": 83.5719, "matched_fragments": 908, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium phragmitis", "strain": "strain=1N-3", "accession": "GCA_002980495.1", "taxid": 2670329, "species_taxid": 2670329, "relation_to_type": "type", "validated": true, "ani": 81.7882, "matched_fragments": 851, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium salinisoli", "strain": "strain=LLAN61", "accession": "GCA_003335045.1", "taxid": 1899321, "species_taxid": 1899321, "relation_to_type": "type", "validated": true, "ani": 81.5955, "matched_fragments": 827, "total_fragments": 1606, "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": 79.0254, "matched_fragments": 505, "total_fragments": 1606, "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": 78.6736, "matched_fragments": 502, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium myrsinacearum", "strain": "strain=DSM 5892", "accession": "GCA_002980555.1", "taxid": 28101, "species_taxid": 28101, "relation_to_type": "type", "validated": true, "ani": 78.5333, "matched_fragments": 448, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium sanjuanii", "strain": "strain=BSA136", "accession": "GCA_002529485.1", "taxid": 2037900, "species_taxid": 2037900, "relation_to_type": "type", "validated": true, "ani": 78.5109, "matched_fragments": 416, "total_fragments": 1606, "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": 78.4945, "matched_fragments": 465, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium myrsinacearum", "strain": "strain=IAM 13584", "accession": "GCA_003182235.1", "taxid": 28101, "species_taxid": 28101, "relation_to_type": "type", "validated": true, "ani": 78.4903, "matched_fragments": 461, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brucella haematophila", "strain": "strain=CCUG 38531", "accession": "GCA_005938105.1", "taxid": 419474, "species_taxid": 419474, "relation_to_type": "type", "validated": true, "ani": 78.4223, "matched_fragments": 452, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aminobacter niigataensis", "strain": "strain=DSM 7050", "accession": "GCA_014200015.1", "taxid": 83265, "species_taxid": 83265, "relation_to_type": "type", "validated": true, "ani": 78.3951, "matched_fragments": 428, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium calauticae", "strain": "strain=R2-JL", "accession": "GCA_019991125.1", "taxid": 2817027, "species_taxid": 2817027, "relation_to_type": "type", "validated": true, "ani": 78.3641, "matched_fragments": 473, "total_fragments": 1606, "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": 78.284, "matched_fragments": 456, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium temperatum", "strain": "strain=SDW018", "accession": "GCA_002284575.1", "taxid": 241416, "species_taxid": 241416, "relation_to_type": "type", "validated": true, "ani": 78.2715, "matched_fragments": 448, "total_fragments": 1606, "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": 78.0453, "matched_fragments": 366, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phyllobacterium brassicacearum", "strain": "strain=STM 196", "accession": "GCA_003010955.1", "taxid": 314235, "species_taxid": 314235, "relation_to_type": "type", "validated": true, "ani": 77.5984, "matched_fragments": 329, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudaminobacter soli", "strain": "strain=19-2017", "accession": "GCA_018310375.1", "taxid": 2831468, "species_taxid": 2831468, "relation_to_type": "type", "validated": true, "ani": 77.5801, "matched_fragments": 358, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudaminobacter soli", "strain": "strain=HC19", "accession": "GCA_014595955.1", "taxid": 2831468, "species_taxid": 2831468, "relation_to_type": "type", "validated": true, "ani": 77.5773, "matched_fragments": 359, "total_fragments": 1606, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014640615.1", "gtdb_species": "s__Paramesorhizobium endophyticum", "ani": 100.0, "matched_fragments": 1603, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium", "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": "conclusive" }, { "accession": "GCF_014191375.1", "gtdb_species": "s__Paramesorhizobium sp014191375", "ani": 83.7105, "matched_fragments": 931, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium", "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_003217235.1", "gtdb_species": "s__Paramesorhizobium leguminum", "ani": 83.5829, "matched_fragments": 907, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium", "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_001558695.1", "gtdb_species": "s__Paramesorhizobium deserti", "ani": 82.4626, "matched_fragments": 898, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium", "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_002980495.1", "gtdb_species": "s__Paramesorhizobium phragmitis", "ani": 81.7844, "matched_fragments": 852, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium", "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_003335045.1", "gtdb_species": "s__Paramesorhizobium salinisoli", "ani": 81.579, "matched_fragments": 830, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium", "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_001898995.1", "gtdb_species": "s__63-22 sp001898995", "ani": 79.8909, "matched_fragments": 560, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014192095.1", "gtdb_species": "s__Phyllobacterium trifolii", "ani": 77.4087, "matched_fragments": 297, "total_fragments": 1606, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "99.28", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.247, "cell_length": -0.081, "doubling_h": 0.301, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.015, "genome_size": 3303524.072, "gc_content": 57.224, "coding_genes": 3076.459, "rRNA16S_genes": 3.0, "tRNA_genes": 54.285, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.111, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.888, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.714, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.285, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Brucella", "endophytica" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }