{ "type": "genome", "identifier": "GCF_900102105.1", "organism": "Agrobacterium pusense", "title": "Agrobacterium pusense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900102105.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421750", "wgs_master": "FNBB00000000.1", "refseq_category": "na", "taxid": "648995", "species_taxid": "648995", "organism_name": "Agrobacterium pusense", "infraspecific_name": "strain=LMG 25623", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/21", "asm_name": "IMG-taxon 2671180227 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900102105.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/102/105/GCF_900102105.1_IMG-taxon_2671180227_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": "5283618", "genome_size_ungapped": "5283301", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-16", "total_gene_count": "5074", "protein_coding_gene_count": "4943", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-21", "dateModified": "2016-10-21", "datePublished": "2016-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Agrobacterium pusense" ], "sample_taxid": [ "648995" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.485 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)": "5283618", "Number of Sequences": "28", "Longest Sequences (bp)": "913562", "N50 (bp)": "405057", "Gap Ratio (%)": "0.006000", "GCcontent (%)": "59.2", "Number of CDSs": "5061", "Average Protein Length": "304.0", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium pusense", "strain": "strain=LMG 25623", "accession": "GCA_900102105.1", "taxid": 648995, "species_taxid": 648995, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1742, "total_fragments": 1748, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium pusense", "strain": "strain=NRCPB10", "accession": "GCA_002008275.1", "taxid": 648995, "species_taxid": 648995, "relation_to_type": "type", "validated": true, "ani": 99.9943, "matched_fragments": 1739, "total_fragments": 1748, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Agrobacterium leguminum", "strain": "strain=MOPV5", "accession": "GCA_015704895.1", "taxid": 2792015, "species_taxid": 2792015, "relation_to_type": "type", "validated": true, "ani": 89.0727, "matched_fragments": 1367, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium tumefaciens", "strain": "strain=ICMP 5856T", "accession": "GCA_009498475.1", "taxid": 358, "species_taxid": 358, "relation_to_type": "suspected-type", "validated": true, "ani": 88.5413, "matched_fragments": 1394, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium tumefaciens", "strain": "strain=B6", "accession": "GCA_001541315.1", "taxid": 358, "species_taxid": 358, "relation_to_type": "suspected-type", "validated": true, "ani": 88.4919, "matched_fragments": 1406, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium tumefaciens", "strain": "strain=B6", "accession": "GCA_900045375.1", "taxid": 358, "species_taxid": 358, "relation_to_type": "suspected-type", "validated": true, "ani": 88.4639, "matched_fragments": 1413, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium salinitolerans", "strain": "strain=YIC 5082", "accession": "GCA_002008225.1", "taxid": 1183413, "species_taxid": 1183413, "relation_to_type": "type", "validated": true, "ani": 88.2732, "matched_fragments": 1320, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella zoogloeoides", "strain": "strain=ATCC 19623", "accession": "GCA_020883495.1", "taxid": 352475, "species_taxid": 352475, "relation_to_type": "type", "validated": true, "ani": 79.2959, "matched_fragments": 561, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium redzepovicii", "strain": "strain=18T", "accession": "GCA_019793435.1", "taxid": 2867518, "species_taxid": 2867518, "relation_to_type": "type", "validated": true, "ani": 78.8845, "matched_fragments": 617, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium dioscoreae", "strain": "strain=S-93", "accession": "GCA_009176305.1", "taxid": 2653122, "species_taxid": 2653122, "relation_to_type": "type", "validated": true, "ani": 78.8219, "matched_fragments": 528, "total_fragments": 1748, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900102105.1", "gtdb_species": "s__Agrobacterium pusense", "ani": 100.0, "matched_fragments": 1742, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.74", "num_clustered_genomes": 79, "status": "conclusive" }, { "accession": "GCF_002943835.1", "gtdb_species": "s__Agrobacterium deltaense", "ani": 89.0011, "matched_fragments": 1361, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.77", "num_clustered_genomes": 64, "status": "-" }, { "accession": "GCF_001541315.1", "gtdb_species": "s__Agrobacterium tumefaciens", "ani": 88.502, "matched_fragments": 1405, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 248, "status": "-" }, { "accession": "GCF_002008225.1", "gtdb_species": "s__Agrobacterium salinitolerans", "ani": 88.2836, "matched_fragments": 1319, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.86", "min_intra_species_ani": "95.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_002005205.3", "gtdb_species": "s__Agrobacterium rhizogenes_A", "ani": 88.0915, "matched_fragments": 1351, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_017744915.1", "gtdb_species": "s__Agrobacterium tumefaciens_I", "ani": 87.9442, "matched_fragments": 1321, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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_003241215.1", "gtdb_species": "s__Agrobacterium fabrum_A", "ani": 87.7389, "matched_fragments": 947, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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_017726655.1", "gtdb_species": "s__Agrobacterium tumefaciens_B", "ani": 87.5673, "matched_fragments": 1271, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.01", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900012615.1", "gtdb_species": "s__Agrobacterium sp900012615", "ani": 87.4607, "matched_fragments": 1331, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.47", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000092025.1", "gtdb_species": "s__Agrobacterium fabrum", "ani": 87.3936, "matched_fragments": 1398, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.52", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCF_007002745.1", "gtdb_species": "s__Agrobacterium rhizogenes_B", "ani": 87.3187, "matched_fragments": 1361, "total_fragments": 1748, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium", "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": null, "cell_length": null, "doubling_h": 0.322, "growth_tmp": 27.25, "optimum_tmp": 28.016, "optimum_ph": null, "genome_size": 5686926.776, "gc_content": 58.629, "coding_genes": 5349.095, "rRNA16S_genes": 3.5, "tRNA_genes": 54.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.8, "range_salinity": 0.5, "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": [ "Agrobacterium", "pusense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }