{ "type": "genome", "identifier": "GCF_001541345.2", "organism": "Agrobacterium vitis", "title": "Agrobacterium vitis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Monash University Malaysia", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001541345.2", "bioproject": "PRJNA224116", "biosample": "SAMN04223557", "wgs_master": "LMVL00000000.2", "refseq_category": "reference genome", "taxid": "373", "species_taxid": "373", "organism_name": "Agrobacterium vitis", "infraspecific_name": "strain=NCPPB 3554", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/23", "asm_name": "ASM154134v2", "asm_submitter": "Monash University Malaysia", "gbrs_paired_asm": "GCA_001541345.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/541/345/GCF_001541345.2_ASM154134v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5754491", "genome_size_ungapped": "5754491", "gc_percent": "57.500000", "replicon_count": "1", "scaffold_count": "22", "contig_count": "22", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001541345.2-RS_2024_03_19", "annotation_date": "2024-03-19", "total_gene_count": "5177", "protein_coding_gene_count": "5019", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-23", "dateModified": "2018-07-23", "datePublished": "2018-07-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Agrobacterium vitis" ], "sample_taxid": [ "373" ], "sample_host_organism": [ "Grapevine" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia" ], "sample_host_location_id": [], "data_size": "1.621 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)": "5754491", "Number of Sequences": "22", "Longest Sequences (bp)": "1134217", "N50 (bp)": "999201", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.5", "Number of CDSs": "5152", "Average Protein Length": "321.9", "Coding Ratio (%)": "86.5", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium taibaishanense", "strain": "strain=DSM 100021", "accession": "GCA_014196735.1", "taxid": 887144, "species_taxid": 887144, "relation_to_type": "type", "validated": true, "ani": 82.2221, "matched_fragments": 1189, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium taibaishanense", "strain": "strain=14971", "accession": "GCA_001938985.1", "taxid": 887144, "species_taxid": 887144, "relation_to_type": "type", "validated": true, "ani": 82.2208, "matched_fragments": 1186, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter selenitireducens", "strain": "strain=ATCC BAA-1503", "accession": "GCA_000518785.1", "taxid": 448181, "species_taxid": 448181, "relation_to_type": "type", "validated": true, "ani": 78.9916, "matched_fragments": 551, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium wuzhouense", "strain": "strain=W44", "accession": "GCA_003205195.1", "taxid": 1986026, "species_taxid": 1986026, "relation_to_type": "type", "validated": true, "ani": 78.6473, "matched_fragments": 531, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium halophytocola", "strain": "strain=DSM 21600", "accession": "GCA_017873095.1", "taxid": 735519, "species_taxid": 735519, "relation_to_type": "type", "validated": true, "ani": 78.6419, "matched_fragments": 554, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium rosettiformans", "strain": "strain=DSM 26376", "accession": "GCA_014202175.1", "taxid": 1368430, "species_taxid": 1368430, "relation_to_type": "type", "validated": true, "ani": 78.5136, "matched_fragments": 506, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium rosettiformans", "strain": "strain=W3", "accession": "GCA_004912135.1", "taxid": 1368430, "species_taxid": 1368430, "relation_to_type": "type", "validated": true, "ani": 78.4937, "matched_fragments": 500, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium vignae", "strain": "strain=CCBAU 05176", "accession": "GCA_000732195.1", "taxid": 690585, "species_taxid": 690585, "relation_to_type": "type", "validated": true, "ani": 78.3542, "matched_fragments": 480, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium galegae", "strain": "strain=HAMBI 540", "accession": "GCA_000731315.1", "taxid": 399, "species_taxid": 399, "relation_to_type": "suspected-type", "validated": true, "ani": 78.1502, "matched_fragments": 524, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium giardinii", "strain": "strain=H152", "accession": "GCA_000379605.1", "taxid": 56731, "species_taxid": 56731, "relation_to_type": "type", "validated": true, "ani": 78.0938, "matched_fragments": 457, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella kummerowiae", "strain": "strain=CCBAU 25048", "accession": "GCA_009827055.1", "taxid": 417745, "species_taxid": 417745, "relation_to_type": "type", "validated": true, "ani": 78.0893, "matched_fragments": 433, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium hainanense", "strain": "strain=CCBAU 57015", "accession": "GCA_900094555.1", "taxid": 52131, "species_taxid": 52131, "relation_to_type": "type", "validated": true, "ani": 78.0708, "matched_fragments": 475, "total_fragments": 1908, "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": 78.0447, "matched_fragments": 443, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium vallis", "strain": "strain=CCBAU 65647", "accession": "GCA_003985155.1", "taxid": 634290, "species_taxid": 634290, "relation_to_type": "type", "validated": true, "ani": 78.0353, "matched_fragments": 474, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium alkalisoli", "strain": "strain=DSM 21826", "accession": "GCA_002968635.1", "taxid": 528178, "species_taxid": 528178, "relation_to_type": "type", "validated": true, "ani": 77.9743, "matched_fragments": 432, "total_fragments": 1908, "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": 77.9617, "matched_fragments": 466, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium skierniewicense", "strain": "strain=Ch11", "accession": "GCA_023757665.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 77.9132, "matched_fragments": 395, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter ferrooxidans", "strain": "strain=F8825", "accession": "GCA_004137355.1", "taxid": 2509717, "species_taxid": 2509717, "relation_to_type": "type", "validated": true, "ani": 77.8918, "matched_fragments": 407, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium skierniewicense", "strain": "strain=DSM 26438", "accession": "GCA_014196515.1", "taxid": 984260, "species_taxid": 984260, "relation_to_type": "type", "validated": true, "ani": 77.8562, "matched_fragments": 392, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella sumterensis", "strain": "strain=MEC087", "accession": "GCA_004514425.2", "taxid": 1967501, "species_taxid": 1967501, "relation_to_type": "type", "validated": true, "ani": 77.7706, "matched_fragments": 429, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001541345.2", "gtdb_species": "s__Allorhizobium vitis", "ani": 100.0, "matched_fragments": 1904, "total_fragments": 1908, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "96.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_001758275.2", "gtdb_species": "s__Allorhizobium vitis_B", "ani": 93.9619, "matched_fragments": 1656, "total_fragments": 1908, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_009744025.1", "gtdb_species": "s__Allorhizobium vitis_A", "ani": 93.4332, "matched_fragments": 1654, "total_fragments": 1908, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.14", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_009744115.1", "gtdb_species": "s__Allorhizobium vitis_E", "ani": 93.2835, "matched_fragments": 1583, "total_fragments": 1908, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "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_013426735.1", "gtdb_species": "s__Allorhizobium vitis_D", "ani": 92.8542, "matched_fragments": 1553, "total_fragments": 1908, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.49", "min_intra_species_ani": "97.49", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.322, "growth_tmp": 26.5, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 6224131.167, "gc_content": 57.119, "coding_genes": 5508.667, "rRNA16S_genes": 4.0, "tRNA_genes": 54.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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", "vitis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }