{ "type": "genome", "identifier": "GCF_000473085.1", "organism": "Azorhizobium doebereinerae UFLA1-100", "title": "Azorhizobium doebereinerae UFLA1-100", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000473085.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440776", "wgs_master": "AXBA00000000.1", "refseq_category": "reference genome", "taxid": "1038858", "species_taxid": "281091", "organism_name": "Azorhizobium doebereinerae UFLA1-100", "infraspecific_name": "strain=UFLA1-100", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/30", "asm_name": "ASM47308v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000473085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/473/085/GCF_000473085.1_ASM47308v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5817514", "genome_size_ungapped": "5815903", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "104", "contig_count": "107", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000473085.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "5422", "protein_coding_gene_count": "5246", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-30", "dateModified": "2013-09-30", "datePublished": "2013-09-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Azorhizobium doebereinerae UFLA1-100" ], "sample_taxid": [ "1038858" ], "sample_host_organism": [ "Sesbania virgata" ], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "1.580 MB", "sample_ph_range": { "min": 58.0, "max": 58.0 }, "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)": "5817514", "Number of Sequences": "104", "Longest Sequences (bp)": "581759", "N50 (bp)": "174279", "Gap Ratio (%)": "0.029600", "GCcontent (%)": "68.9", "Number of CDSs": "5349", "Average Protein Length": "319.3", "Coding Ratio (%)": "88.1", "Number of rRNAs": "8", "Number of tRNAs": "58", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Azorhizobium doebereinerae", "strain": "strain=UFLA1-100", "accession": "GCA_000473085.1", "taxid": 281091, "species_taxid": 281091, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1889, "total_fragments": 1898, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Azorhizobium oxalatiphilum", "strain": "strain=CCM 7897", "accession": "GCA_014635325.1", "taxid": 980631, "species_taxid": 980631, "relation_to_type": "type", "validated": true, "ani": 84.8079, "matched_fragments": 1321, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azorhizobium caulinodans", "strain": "strain=ORS 571", "accession": "GCA_000010525.1", "taxid": 7, "species_taxid": 7, "relation_to_type": "type", "validated": true, "ani": 84.7288, "matched_fragments": 1290, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter oligotrophicus", "strain": "strain=29k", "accession": "GCA_008364685.1", "taxid": 2607286, "species_taxid": 2607286, "relation_to_type": "type", "validated": true, "ani": 81.7211, "matched_fragments": 931, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter aminoxidans", "strain": "strain=ATCC BAA-299", "accession": "GCA_023571765.1", "taxid": 186280, "species_taxid": 186280, "relation_to_type": "type", "validated": true, "ani": 81.5993, "matched_fragments": 926, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter autotrophicus", "strain": "strain=DSM 432", "accession": "GCA_005871085.1", "taxid": 280, "species_taxid": 280, "relation_to_type": "type", "validated": true, "ani": 81.5464, "matched_fragments": 869, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter dioxanivorans", "strain": "strain=YN2", "accession": "GCA_016807805.1", "taxid": 2528964, "species_taxid": 2528964, "relation_to_type": "type", "validated": true, "ani": 81.5103, "matched_fragments": 932, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=ATCC 700314", "accession": "GCA_003667445.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 81.4885, "matched_fragments": 842, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=DSM 11105", "accession": "GCA_014206845.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 81.4202, "matched_fragments": 857, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter agilis", "strain": "strain=LMG 16336", "accession": "GCA_021730435.1", "taxid": 47492, "species_taxid": 47492, "relation_to_type": "type", "validated": true, "ani": 80.4588, "matched_fragments": 748, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Starkeya novella", "strain": "strain=DSM 506", "accession": "GCA_000092925.1", "taxid": 921, "species_taxid": 921, "relation_to_type": "type", "validated": true, "ani": 79.4634, "matched_fragments": 664, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phreatobacter cathodiphilus", "strain": "strain=S-12", "accession": "GCA_003008515.1", "taxid": 1868589, "species_taxid": 1868589, "relation_to_type": "type", "validated": true, "ani": 77.8012, "matched_fragments": 523, "total_fragments": 1898, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000473085.1", "gtdb_species": "s__Azorhizobium doebereinerae", "ani": 100.0, "matched_fragments": 1888, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium", "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_014635325.1", "gtdb_species": "s__Azorhizobium oxalatiphilum", "ani": 84.828, "matched_fragments": 1318, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium", "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_000010525.1", "gtdb_species": "s__Azorhizobium caulinodans", "ani": 84.7838, "matched_fragments": 1281, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.54", "min_intra_species_ani": "97.54", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013911975.1", "gtdb_species": "s__Aquabacter sp013911975", "ani": 81.8826, "matched_fragments": 844, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter", "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_008364685.1", "gtdb_species": "s__Xanthobacter sp008364685", "ani": 81.716, "matched_fragments": 932, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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_000702385.1", "gtdb_species": "s__Xanthobacter sp000702385", "ani": 81.5923, "matched_fragments": 929, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.09", "min_intra_species_ani": "96.09", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005871085.1", "gtdb_species": "s__Xanthobacter autotrophicus_A", "ani": 81.5161, "matched_fragments": 872, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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_000017645.1", "gtdb_species": "s__Xanthobacter autotrophicus", "ani": 81.5097, "matched_fragments": 911, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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_003993795.1", "gtdb_species": "s__Aquabacter cavernae", "ani": 81.4985, "matched_fragments": 847, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter", "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_003667445.1", "gtdb_species": "s__Xanthobacter tagetidis", "ani": 81.4372, "matched_fragments": 848, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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_002257205.1", "gtdb_species": "s__NCEH01 sp002257205", "ani": 81.4083, "matched_fragments": 595, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__NCEH01", "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_017742835.1", "gtdb_species": "s__Aquabacter sp017742835", "ani": 81.3764, "matched_fragments": 903, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter", "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_002279855.1", "gtdb_species": "s__Aquabacter sp002279855", "ani": 81.3015, "matched_fragments": 620, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.72", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004346185.1", "gtdb_species": "s__Aquabacter spiritensis", "ani": 80.0447, "matched_fragments": 760, "total_fragments": 1898, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter", "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": 0.0, "cell_length": 0.439, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.0, "optimum_ph": null, "genome_size": 5817514.0, "gc_content": 67.3, "coding_genes": 4713.667, "rRNA16S_genes": 3.0, "tRNA_genes": 53.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 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": [ "Azorhizobium", "doebereinerae", "UFLA1-100" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }