{ "type": "genome", "identifier": "GCF_000472705.1", "organism": "Mesorhizobium erdmanii USDA 3471", "title": "Mesorhizobium erdmanii USDA 3471", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000472705.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441124", "wgs_master": "AXAE00000000.1", "refseq_category": "na", "taxid": "1040983", "species_taxid": "1777866", "organism_name": "Mesorhizobium erdmanii USDA 3471", "infraspecific_name": "strain=USDA 3471", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/30", "asm_name": "ASM47270v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000472705.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/472/705/GCF_000472705.1_ASM47270v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7023073", "genome_size_ungapped": "7018265", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "50", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-03", "total_gene_count": "6791", "protein_coding_gene_count": "6569", "non_coding_gene_count": "62", "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": [ "Mesorhizobium erdmanii USDA 3471" ], "sample_taxid": [ "1040983" ], "sample_host_organism": [ "Lotus corniculatus" ], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "New Zealand" ], "sample_host_location_id": [], "data_size": "1.953 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)": "7023073", "Number of Sequences": "50", "Longest Sequences (bp)": "646817", "N50 (bp)": "316419", "Gap Ratio (%)": "0.069087", "GCcontent (%)": "62.7", "Number of CDSs": "6753", "Average Protein Length": "300.7", "Coding Ratio (%)": "86.7", "Number of rRNAs": "6", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mesorhizobium erdmanii", "strain": "strain=USDA 3471", "accession": "GCA_000472705.1", "taxid": 1777866, "species_taxid": 1777866, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2311, "total_fragments": 2320, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mesorhizobium japonicum", "strain": "strain=MAFF 303099", "accession": "GCA_000009625.1", "taxid": 2066070, "species_taxid": 2066070, "relation_to_type": "type", "validated": true, "ani": 90.2987, "matched_fragments": 1803, "total_fragments": 2320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium jarvisii", "strain": "strain=ATCC 33669", "accession": "GCA_013170785.1", "taxid": 1777867, "species_taxid": 1777867, "relation_to_type": "type", "validated": true, "ani": 90.2239, "matched_fragments": 1796, "total_fragments": 2320, "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": 90.115, "matched_fragments": 1816, "total_fragments": 2320, "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": 90.0923, "matched_fragments": 1689, "total_fragments": 2320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium intechi", "strain": "strain=BD68", "accession": "GCA_002879535.2", "taxid": 537601, "species_taxid": 537601, "relation_to_type": "type", "validated": true, "ani": 89.9158, "matched_fragments": 1619, "total_fragments": 2320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium opportunistum", "strain": "strain=WSM2075", "accession": "GCA_000176035.2", "taxid": 593909, "species_taxid": 593909, "relation_to_type": "type", "validated": true, "ani": 88.4951, "matched_fragments": 1681, "total_fragments": 2320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium loti", "strain": "strain=DSM 2626", "accession": "GCA_003148495.1", "taxid": 381, "species_taxid": 381, "relation_to_type": "suspected-type", "validated": true, "ani": 87.9799, "matched_fragments": 1713, "total_fragments": 2320, "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": 87.4177, "matched_fragments": 1607, "total_fragments": 2320, "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": 84.4162, "matched_fragments": 1383, "total_fragments": 2320, "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": 79.0161, "matched_fragments": 699, "total_fragments": 2320, "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": 79.0147, "matched_fragments": 699, "total_fragments": 2320, "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": 78.82, "matched_fragments": 675, "total_fragments": 2320, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000472705.1", "gtdb_species": "s__Mesorhizobium erdmanii", "ani": 100.0, "matched_fragments": 2312, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.40", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_002356515.1", "gtdb_species": "s__Mesorhizobium loti_C", "ani": 90.5894, "matched_fragments": 1881, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003353565.1", "gtdb_species": "s__Mesorhizobium sp003353565", "ani": 90.4001, "matched_fragments": 1699, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_000688075.1", "gtdb_species": "s__Mesorhizobium sp000688075", "ani": 90.3907, "matched_fragments": 1731, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_016756495.1", "gtdb_species": "s__Mesorhizobium sp016756495", "ani": 90.3684, "matched_fragments": 1835, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_013170805.1", "gtdb_species": "s__Mesorhizobium sp013170805", "ani": 90.3308, "matched_fragments": 1840, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_000009625.1", "gtdb_species": "s__Mesorhizobium japonicum", "ani": 90.3097, "matched_fragments": 1801, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "97.93", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_014189455.1", "gtdb_species": "s__Mesorhizobium huakuii_A", "ani": 90.2033, "matched_fragments": 1801, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_900199455.1", "gtdb_species": "s__Mesorhizobium carmichaelinearum", "ani": 90.1144, "matched_fragments": 1816, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_003601985.1", "gtdb_species": "s__Mesorhizobium jarvisii", "ani": 90.0936, "matched_fragments": 1687, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_013170825.1", "gtdb_species": "s__Mesorhizobium sp013170825", "ani": 90.0835, "matched_fragments": 1744, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.36", "min_intra_species_ani": "95.35", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.81", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013170845.1", "gtdb_species": "s__Mesorhizobium loti_B", "ani": 89.704, "matched_fragments": 1811, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_000472785.1", "gtdb_species": "s__Mesorhizobium loti_E", "ani": 89.6981, "matched_fragments": 1792, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_018588885.1", "gtdb_species": "s__Mesorhizobium sp018588885", "ani": 88.8613, "matched_fragments": 1634, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "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_000176035.2", "gtdb_species": "s__Mesorhizobium opportunistum", "ani": 88.4941, "matched_fragments": 1683, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.26", "min_intra_species_ani": "95.55", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.80", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_006658505.1", "gtdb_species": "s__Mesorhizobium sp006658505", "ani": 87.9842, "matched_fragments": 1517, "total_fragments": 2320, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.84", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.81", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.394, "cell_length": 0.163, "doubling_h": 0.38, "growth_tmp": 28.738, "optimum_tmp": 28.233, "optimum_ph": 7.1, "genome_size": 6924855.425, "gc_content": 61.795, "coding_genes": 6455.004, "rRNA16S_genes": 2.0, "tRNA_genes": 52.916, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.923, "range_salinity": null, "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": [ "Mesorhizobium", "erdmanii", "USDA", "3471" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }