{ "type": "genome", "identifier": "GCA_004019145.1", "organism": "Mesorhizobium sp.", "title": "Mesorhizobium sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Cook Lab - University of California at Davis", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004019145.1", "bioproject": "PRJNA453501", "biosample": "SAMN10686648", "wgs_master": "SAND00000000.1", "refseq_category": "na", "taxid": "1871066", "species_taxid": "1871066", "organism_name": "Mesorhizobium sp.", "infraspecific_name": "", "isolate": "N.Ca.IN.000.67.1", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/14", "asm_name": "ASM401914v1", "submitter": "Cook Lab - University of California at Davis", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/019/145/GCA_004019145.1_ASM401914v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-14", "dateModified": "2019-01-14", "datePublished": "2019-01-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Mesorhizobium sp." ], "sample_taxid": [ "1871066" ], "sample_host_organism": [ "Cicer arietinum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Telangana, Patancheru" ], "sample_host_location_id": [], "data_size": "1.725 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "6168968", "Number of Sequences": "187", "Longest Sequences (bp)": "232055", "N50 (bp)": "91310", "Gap Ratio (%)": "0.023213", "GCcontent (%)": "63.3", "Number of CDSs": "5956", "Average Protein Length": "290.9", "Coding Ratio (%)": "84.3", "Number of rRNAs": "4", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mesorhizobium silamurunense", "strain": "strain=CCBAU 01550", "accession": "GCA_014843825.1", "taxid": 499528, "species_taxid": 499528, "relation_to_type": "type", "validated": true, "ani": 89.6664, "matched_fragments": 1424, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium tamadayense", "strain": "strain=DSM 28320", "accession": "GCA_003863365.1", "taxid": 425306, "species_taxid": 425306, "relation_to_type": "type", "validated": true, "ani": 89.405, "matched_fragments": 1506, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium hawassense", "strain": "strain=AC99b", "accession": "GCA_003289945.1", "taxid": 1209954, "species_taxid": 1209954, "relation_to_type": "type", "validated": true, "ani": 86.9343, "matched_fragments": 1457, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium atlanticum", "strain": "strain=CNPSo 3140", "accession": "GCA_003289965.1", "taxid": 2233532, "species_taxid": 2233532, "relation_to_type": "type", "validated": true, "ani": 86.8112, "matched_fragments": 1421, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium waimense", "strain": "strain=ICMP19557", "accession": "GCA_003601975.1", "taxid": 1300307, "species_taxid": 1300307, "relation_to_type": "type", "validated": true, "ani": 85.0408, "matched_fragments": 1443, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium metallidurans", "strain": "strain=STM 2683", "accession": "GCA_000350085.1", "taxid": 489722, "species_taxid": 489722, "relation_to_type": "type", "validated": true, "ani": 84.565, "matched_fragments": 1206, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium neociceri", "strain": "strain=CCANP35", "accession": "GCA_013520985.1", "taxid": 1307853, "species_taxid": 1307853, "relation_to_type": "type", "validated": true, "ani": 84.3303, "matched_fragments": 1377, "total_fragments": 1981, "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": 84.3235, "matched_fragments": 1383, "total_fragments": 1981, "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": 84.0535, "matched_fragments": 1233, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium sophorae", "strain": "strain=ICMP 19535", "accession": "GCA_002270415.1", "taxid": 1300294, "species_taxid": 1300294, "relation_to_type": "type", "validated": true, "ani": 83.9219, "matched_fragments": 1333, "total_fragments": 1981, "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": 83.7372, "matched_fragments": 1284, "total_fragments": 1981, "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": 79.3645, "matched_fragments": 688, "total_fragments": 1981, "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": 79.0256, "matched_fragments": 606, "total_fragments": 1981, "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": 78.8279, "matched_fragments": 578, "total_fragments": 1981, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002294985.1", "gtdb_species": "s__Mesorhizobium sp002294985", "ani": 97.3526, "matched_fragments": 1712, "total_fragments": 1981, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.32", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.76", "num_clustered_genomes": 62, "status": "conclusive" }, { "accession": "GCF_002294995.1", "gtdb_species": "s__Mesorhizobium sp002294995", "ani": 94.2348, "matched_fragments": 1692, "total_fragments": 1981, "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": "GCA_004963905.1", "gtdb_species": "s__Mesorhizobium sp004963905", "ani": 90.0325, "matched_fragments": 1539, "total_fragments": 1981, "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_003952385.1", "gtdb_species": "s__Mesorhizobium sp003952385", "ani": 89.9771, "matched_fragments": 1524, "total_fragments": 1981, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.01", "min_intra_species_ani": "97.50", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_004020545.1", "gtdb_species": "s__Mesorhizobium sp004020545", "ani": 89.7743, "matched_fragments": 1518, "total_fragments": 1981, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "97.54", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_003952485.1", "gtdb_species": "s__Mesorhizobium sp003952485", "ani": 89.7146, "matched_fragments": 1553, "total_fragments": 1981, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.21", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_014843825.1", "gtdb_species": "s__Mesorhizobium silamurunense", "ani": 89.6786, "matched_fragments": 1423, "total_fragments": 1981, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "99.52", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003863365.1", "gtdb_species": "s__Mesorhizobium tamadayense", "ani": 89.405, "matched_fragments": 1506, "total_fragments": 1981, "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_004791585.1", "gtdb_species": "s__Mesorhizobium sp004791585", "ani": 89.3359, "matched_fragments": 1560, "total_fragments": 1981, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "98.11", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCA_001510895.1", "gtdb_species": "s__Mesorhizobium loti_A", "ani": 89.0489, "matched_fragments": 1482, "total_fragments": 1981, "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": "GCA_000824825.2", "gtdb_species": "s__Mesorhizobium sp000824825", "ani": 88.7397, "matched_fragments": 1471, "total_fragments": 1981, "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": "-" } ] }, "_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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Rhizobiaceae", "g__Mesorhizobium", "s__Mesorhizobium sp002294985" ], "_genome_taxon": [ "Mesorhizobium", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Rhizobiaceae", "g__Mesorhizobium", "s__Mesorhizobium sp002294985", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Rhizobiaceae", "Mesorhizobium", "Mesorhizobium", "sp002294985" ], "_meo": [ { "id": "MEO_0000055", "label": "rhizosphere" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }