{ "type": "genome", "identifier": "GCF_013170785.1", "organism": "Mesorhizobium jarvisii", "title": "Mesorhizobium jarvisii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Otago", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013170785.1", "bioproject": "PRJNA224116", "biosample": "SAMN10272903", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1777867", "species_taxid": "1777867", "organism_name": "Mesorhizobium jarvisii", "infraspecific_name": "strain=ATCC 33669", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/26", "asm_name": "ASM1317078v1", "asm_submitter": "University of Otago", "gbrs_paired_asm": "GCA_013170785.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/170/785/GCF_013170785.1_ASM1317078v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7201057", "genome_size_ungapped": "7201057", "gc_percent": "63.000000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013170785.1-RS_2024_10_26", "annotation_date": "2024-10-26", "total_gene_count": "7138", "protein_coding_gene_count": "6913", "non_coding_gene_count": "62", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-26", "dateModified": "2020-05-26", "datePublished": "2020-05-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Mesorhizobium jarvisii" ], "sample_taxid": [ "1777867" ], "sample_host_organism": [ "Lotus corniculatus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "New Zealand: Palmerston North" ], "sample_host_location_id": [], "data_size": "1.989 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)": "7201057", "Number of Sequences": "3", "Longest Sequences (bp)": "6934624", "N50 (bp)": "6934624", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.9", "Number of CDSs": "7069", "Average Protein Length": "294.5", "Coding Ratio (%)": "86.7", "Number of rRNAs": "6", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mesorhizobium jarvisii", "strain": "strain=ATCC 33669", "accession": "GCA_013170785.1", "taxid": 1777867, "species_taxid": 1777867, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2397, "total_fragments": 2398, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mesorhizobium jarvisii", "strain": "strain=LMG 28313", "accession": "GCA_003601985.1", "taxid": 1777867, "species_taxid": 1777867, "relation_to_type": "type", "validated": true, "ani": 99.9611, "matched_fragments": 2191, "total_fragments": 2398, "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": 94.1858, "matched_fragments": 1959, "total_fragments": 2398, "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": 93.4963, "matched_fragments": 1729, "total_fragments": 2398, "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": 91.3632, "matched_fragments": 1868, "total_fragments": 2398, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium erdmanii", "strain": "strain=USDA 3471", "accession": "GCA_000472705.1", "taxid": 1777866, "species_taxid": 1777866, "relation_to_type": "type", "validated": true, "ani": 90.1348, "matched_fragments": 1790, "total_fragments": 2398, "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": 87.6166, "matched_fragments": 1609, "total_fragments": 2398, "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": 84.7235, "matched_fragments": 1395, "total_fragments": 2398, "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": 79.1378, "matched_fragments": 735, "total_fragments": 2398, "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": 79.1084, "matched_fragments": 740, "total_fragments": 2398, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor arenosus", "strain": "strain=CAU 1489", "accession": "GCA_009742725.1", "taxid": 2682096, "species_taxid": 2682096, "relation_to_type": "type", "validated": true, "ani": 78.9631, "matched_fragments": 652, "total_fragments": 2398, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003601985.1", "gtdb_species": "s__Mesorhizobium jarvisii", "ani": 99.9611, "matched_fragments": 2192, "total_fragments": 2398, "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": "conclusive" }, { "accession": "GCF_000009625.1", "gtdb_species": "s__Mesorhizobium japonicum", "ani": 94.1848, "matched_fragments": 1960, "total_fragments": 2398, "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_016467435.1", "gtdb_species": "s__Mesorhizobium sp016467435", "ani": 93.9945, "matched_fragments": 1807, "total_fragments": 2398, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "98.58", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002295115.1", "gtdb_species": "s__Mesorhizobium sp002295115", "ani": 93.9745, "matched_fragments": 1900, "total_fragments": 2398, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "96.42", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.85", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_002879535.1", "gtdb_species": "s__Mesorhizobium intechi", "ani": 93.4963, "matched_fragments": 1728, "total_fragments": 2398, "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": 92.7921, "matched_fragments": 1987, "total_fragments": 2398, "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_003353565.1", "gtdb_species": "s__Mesorhizobium sp003353565", "ani": 91.3593, "matched_fragments": 1778, "total_fragments": 2398, "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": 91.3527, "matched_fragments": 1868, "total_fragments": 2398, "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_013170825.1", "gtdb_species": "s__Mesorhizobium sp013170825", "ani": 90.5364, "matched_fragments": 1787, "total_fragments": 2398, "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": "-" } ] }, "_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", "jarvisii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }