{ "type": "genome", "identifier": "GCA_004963685.1", "organism": "Mesorhizobium sp.", "title": "Mesorhizobium sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "Cook Lab - University of California at Davis", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004963685.1", "bioproject": "PRJNA453501", "biosample": "SAMN11348847", "wgs_master": "SUHD00000000.1", "refseq_category": "na", "taxid": "1871066", "species_taxid": "1871066", "organism_name": "Mesorhizobium sp.", "infraspecific_name": "", "isolate": "N.Ca.IN.010.05.1", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/30", "asm_name": "ASM496368v1", "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/004/963/685/GCA_004963685.1_ASM496368v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-30", "dateModified": "2019-04-30", "datePublished": "2019-04-30", "_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: Jharkhand, Bokaro, Khetko" ], "sample_host_location_id": [], "data_size": "1.351 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 57.72, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4644904", "Number of Sequences": "2757", "Longest Sequences (bp)": "28539", "N50 (bp)": "2543", "Gap Ratio (%)": "1.243449", "GCcontent (%)": "62.8", "Number of CDSs": "3132", "Average Protein Length": "223.4", "Coding Ratio (%)": "45.2", "Number of rRNAs": "3", "Number of tRNAs": "33", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mesorhizobium atlanticum", "strain": "strain=CNPSo 3140", "accession": "GCA_003289965.1", "taxid": 2233532, "species_taxid": 2233532, "relation_to_type": "type", "validated": true, "ani": 90.3363, "matched_fragments": 338, "total_fragments": 521, "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": 87.7688, "matched_fragments": 346, "total_fragments": 521, "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": 85.5996, "matched_fragments": 343, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium silamurunense", "strain": "strain=CCBAU 01550", "accession": "GCA_014843825.1", "taxid": 499528, "species_taxid": 499528, "relation_to_type": "type", "validated": true, "ani": 85.4196, "matched_fragments": 351, "total_fragments": 521, "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": 84.1292, "matched_fragments": 295, "total_fragments": 521, "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": 83.8253, "matched_fragments": 325, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium japonicum", "strain": "strain=MAFF 303099", "accession": "GCA_000009625.1", "taxid": 2066070, "species_taxid": 2066070, "relation_to_type": "type", "validated": true, "ani": 83.7206, "matched_fragments": 319, "total_fragments": 521, "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": 83.7163, "matched_fragments": 279, "total_fragments": 521, "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": 83.5942, "matched_fragments": 291, "total_fragments": 521, "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": 83.591, "matched_fragments": 319, "total_fragments": 521, "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": 83.0433, "matched_fragments": 282, "total_fragments": 521, "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": 82.9049, "matched_fragments": 291, "total_fragments": 521, "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": 79.307, "matched_fragments": 159, "total_fragments": 521, "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": 79.2765, "matched_fragments": 160, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelativorans intermedius", "strain": "strain=LMG 28482", "accession": "GCA_025398255.1", "taxid": 515947, "species_taxid": 515947, "relation_to_type": "type", "validated": true, "ani": 78.839, "matched_fragments": 120, "total_fragments": 521, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 57.72, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_004020875.1", "gtdb_species": "s__Mesorhizobium sp004020875", "ani": 99.6963, "matched_fragments": 515, "total_fragments": 521, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.89", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCA_004017535.1", "gtdb_species": "s__Mesorhizobium sp004017535", "ani": 92.7346, "matched_fragments": 420, "total_fragments": 521, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003952425.1", "gtdb_species": "s__Mesorhizobium sp003952425", "ani": 91.9844, "matched_fragments": 390, "total_fragments": 521, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.51", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_004016445.2", "gtdb_species": "s__Mesorhizobium sp004016445", "ani": 91.664, "matched_fragments": 384, "total_fragments": 521, "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": "96.92", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003289965.1", "gtdb_species": "s__Mesorhizobium atlanticum", "ani": 90.3363, "matched_fragments": 338, "total_fragments": 521, "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_000824845.1", "gtdb_species": "s__Mesorhizobium sp000824845", "ani": 90.001, "matched_fragments": 349, "total_fragments": 521, "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_002295065.1", "gtdb_species": "s__Mesorhizobium sp002295065", "ani": 89.758, "matched_fragments": 349, "total_fragments": 521, "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_019091085.1", "gtdb_species": "s__Mesorhizobium sp019091085", "ani": 88.9713, "matched_fragments": 302, "total_fragments": 521, "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_000824785.1", "gtdb_species": "s__Mesorhizobium plurifarium", "ani": 88.6908, "matched_fragments": 351, "total_fragments": 521, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.23", "min_intra_species_ani": "96.62", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_016591715.1", "gtdb_species": "s__Mesorhizobium sp016591715", "ani": 88.3451, "matched_fragments": 357, "total_fragments": 521, "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_003963455.1", "gtdb_species": "s__Mesorhizobium sp003963455", "ani": 86.8205, "matched_fragments": 314, "total_fragments": 521, "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 sp004020875" ], "_genome_taxon": [ "Mesorhizobium", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Rhizobiaceae", "g__Mesorhizobium", "s__Mesorhizobium sp004020875", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Rhizobiaceae", "Mesorhizobium", "Mesorhizobium", "sp004020875" ], "_meo": [ { "id": "MEO_0000055", "label": "rhizosphere" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }