{ "type": "genome", "identifier": "GCF_900108245.1", "organism": "Bosea lathyri", "title": "Bosea lathyri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900108245.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488115", "wgs_master": "FNUY00000000.1", "refseq_category": "reference genome", "taxid": "1036778", "species_taxid": "1036778", "organism_name": "Bosea lathyri", "infraspecific_name": "strain=DSM 26656", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/24", "asm_name": "IMG-taxon 2622736433 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900108245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/108/245/GCF_900108245.1_IMG-taxon_2622736433_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5918613", "genome_size_ungapped": "5917888", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900108245.1-RS_2024_04_25", "annotation_date": "2024-04-25", "total_gene_count": "5582", "protein_coding_gene_count": "5444", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-24", "dateModified": "2016-10-24", "datePublished": "2016-10-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Bosea lathyri" ], "sample_taxid": [ "1036778" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.630 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)": "5918613", "Number of Sequences": "25", "Longest Sequences (bp)": "971284", "N50 (bp)": "399699", "Gap Ratio (%)": "0.012249", "GCcontent (%)": "64.8", "Number of CDSs": "5524", "Average Protein Length": "312.8", "Coding Ratio (%)": "87.6", "Number of rRNAs": "12", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bosea lathyri", "strain": "strain=DSM 26656", "accession": "GCA_900108245.1", "taxid": 1036778, "species_taxid": 1036778, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1956, "total_fragments": 1960, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bosea vaviloviae", "strain": "strain=Vaf18", "accession": "GCA_001741865.1", "taxid": 1526658, "species_taxid": 1526658, "relation_to_type": "type", "validated": true, "ani": 84.4785, "matched_fragments": 1271, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea psychrotolerans", "strain": "strain=1131", "accession": "GCA_002917105.1", "taxid": 1871628, "species_taxid": 1871628, "relation_to_type": "type", "validated": true, "ani": 84.2423, "matched_fragments": 1227, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea caraganae", "strain": "strain=RCAM 04680", "accession": "GCA_003351345.1", "taxid": 2763117, "species_taxid": 2763117, "relation_to_type": "type", "validated": true, "ani": 83.6351, "matched_fragments": 1149, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea robiniae", "strain": "strain=DSM 26672", "accession": "GCA_900102525.1", "taxid": 1036780, "species_taxid": 1036780, "relation_to_type": "type", "validated": true, "ani": 83.1881, "matched_fragments": 1084, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea thiooxidans", "strain": "strain=DSM 9653", "accession": "GCA_900168195.1", "taxid": 53254, "species_taxid": 53254, "relation_to_type": "type", "validated": true, "ani": 83.045, "matched_fragments": 1110, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium oryzihabitans", "strain": "strain=TER-1", "accession": "GCA_004004555.2", "taxid": 2499852, "species_taxid": 2499852, "relation_to_type": "type", "validated": true, "ani": 77.7811, "matched_fragments": 517, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nonmethylotrophicum", "strain": "strain=6HR-1", "accession": "GCA_004745635.1", "taxid": 1141884, "species_taxid": 1141884, "relation_to_type": "type", "validated": true, "ani": 77.7541, "matched_fragments": 550, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terricola", "strain": "strain=17Sr1-39", "accession": "GCA_006151805.1", "taxid": 2583531, "species_taxid": 2583531, "relation_to_type": "type", "validated": true, "ani": 77.7455, "matched_fragments": 566, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium gnaphalii", "strain": "strain=DSM 24027", "accession": "GCA_022179205.1", "taxid": 1010610, "species_taxid": 1010610, "relation_to_type": "type", "validated": true, "ani": 77.7282, "matched_fragments": 317, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium tardum", "strain": "strain=NBRC 103632", "accession": "GCA_022179585.1", "taxid": 374432, "species_taxid": 374432, "relation_to_type": "type", "validated": true, "ani": 77.4795, "matched_fragments": 400, "total_fragments": 1960, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900108245.1", "gtdb_species": "s__Bosea lathyri", "ani": 100.0, "matched_fragments": 1956, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_001741865.1", "gtdb_species": "s__Bosea vaviloviae", "ani": 84.4776, "matched_fragments": 1269, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_900470775.1", "gtdb_species": "s__Bosea sp900470775", "ani": 84.2992, "matched_fragments": 1163, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_002917105.1", "gtdb_species": "s__Bosea psychrotolerans", "ani": 84.2647, "matched_fragments": 1224, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_900113835.1", "gtdb_species": "s__Bosea sp900113835", "ani": 84.2105, "matched_fragments": 1204, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_003046175.1", "gtdb_species": "s__Bosea sp003046175", "ani": 84.081, "matched_fragments": 1159, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_001298265.1", "gtdb_species": "s__Bosea vaviloviae_B", "ani": 83.813, "matched_fragments": 1112, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_001713455.1", "gtdb_species": "s__Bosea sp001713455", "ani": 83.6721, "matched_fragments": 1073, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.00", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003351345.1", "gtdb_species": "s__Bosea caraganae", "ani": 83.6348, "matched_fragments": 1150, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_003241815.1", "gtdb_species": "s__Bosea sp003241815", "ani": 83.4875, "matched_fragments": 977, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_002279705.1", "gtdb_species": "s__Bosea sp002279705", "ani": 83.4169, "matched_fragments": 876, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "99.41", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001429395.1", "gtdb_species": "s__Bosea sp001429395", "ani": 83.3466, "matched_fragments": 1129, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_001295925.1", "gtdb_species": "s__Bosea sp001295925", "ani": 83.1971, "matched_fragments": 960, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_900466745.1", "gtdb_species": "s__Bosea sp900466745", "ani": 83.1372, "matched_fragments": 947, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000745475.1", "gtdb_species": "s__Bosea vestrisii", "ani": 83.0531, "matched_fragments": 1101, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_004341515.1", "gtdb_species": "s__Bosea sp004341515", "ani": 82.9531, "matched_fragments": 1215, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_001426225.1", "gtdb_species": "s__Bosea sp001426225", "ani": 82.685, "matched_fragments": 942, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_017308075.1", "gtdb_species": "s__Bosea sp017308075", "ani": 82.4766, "matched_fragments": 1037, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001898115.1", "gtdb_species": "s__Bosea sp001898115", "ani": 82.1846, "matched_fragments": 992, "total_fragments": 1960, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.43", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.204, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 31.0, "optimum_ph": null, "genome_size": 5918613.0, "gc_content": 65.367, "coding_genes": 6103.0, "rRNA16S_genes": 2.0, "tRNA_genes": 49.0, "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": [ "Bosea", "lathyri" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }