{ "type": "genome", "identifier": "GCF_000069225.1", "organism": "Clavibacter sepedonicus", "title": "Clavibacter sepedonicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Sanger Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000069225.1", "bioproject": "PRJNA224116", "biosample": "SAMEA1705948", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "31964", "species_taxid": "31964", "organism_name": "Clavibacter sepedonicus", "infraspecific_name": "strain=ATCC 33113", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2008/02/29", "asm_name": "ASM6922v1", "asm_submitter": "Sanger Institute", "gbrs_paired_asm": "GCA_000069225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/069/225/GCF_000069225.1_ASM6922v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3403786", "genome_size_ungapped": "3403786", "gc_percent": "72.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000069225.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3311", "protein_coding_gene_count": "3188", "non_coding_gene_count": "54", "pubmed_id": "18192393" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2008-02-29", "dateModified": "2008-02-29", "datePublished": "2008-02-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Clavibacter sepedonicus" ], "sample_taxid": [ "31964" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada" ], "sample_host_location_id": [], "data_size": "0.892 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)": "3403786", "Number of Sequences": "3", "Longest Sequences (bp)": "3258645", "N50 (bp)": "3258645", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.4", "Number of CDSs": "3314", "Average Protein Length": "309.6", "Coding Ratio (%)": "90.4", "Number of rRNAs": "6", "Number of tRNAs": "46", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clavibacter michiganensis subsp. michiganensis", "strain": "strain=LMG 7333", "accession": "GCA_002240575.1", "taxid": 33013, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 92.6996, "matched_fragments": 939, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis", "strain": "strain=VKM Ac-1403", "accession": "GCA_900168345.1", "taxid": 28447, "species_taxid": 28447, "relation_to_type": "suspected-type", "validated": true, "ani": 92.6643, "matched_fragments": 938, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis", "strain": "strain=LMG7333", "accession": "GCA_021216655.1", "taxid": 28447, "species_taxid": 28447, "relation_to_type": "suspected-type", "validated": true, "ani": 92.6471, "matched_fragments": 935, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter phaseoli", "strain": "strain=LPPA 982", "accession": "GCA_021922925.1", "taxid": 1734031, "species_taxid": 1734031, "relation_to_type": "type", "validated": true, "ani": 92.6129, "matched_fragments": 899, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=CFBP 2404", "accession": "GCA_003693415.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 92.5814, "matched_fragments": 924, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=ATCC 10253", "accession": "GCA_003076355.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 92.556, "matched_fragments": 945, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=LMG 3663", "accession": "GCA_002240565.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 92.5483, "matched_fragments": 958, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter californiensis", "strain": "strain=CFBP 8216", "accession": "GCA_003576155.1", "taxid": 1401995, "species_taxid": 1401995, "relation_to_type": "type", "validated": true, "ani": 92.5301, "matched_fragments": 614, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter californiensis", "strain": "strain=CFBP 8216", "accession": "GCA_021952865.1", "taxid": 1401995, "species_taxid": 1401995, "relation_to_type": "type", "validated": true, "ani": 92.488, "matched_fragments": 920, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter zhangzhiyongii", "strain": "strain=DM1", "accession": "GCA_014775655.1", "taxid": 2768071, "species_taxid": 2768071, "relation_to_type": "type", "validated": true, "ani": 90.7162, "matched_fragments": 888, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_002240635.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 90.6254, "matched_fragments": 920, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_021922985.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 90.5516, "matched_fragments": 927, "total_fragments": 1133, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000069225.1", "gtdb_species": "s__Clavibacter sepedonicus", "ani": 100.0, "matched_fragments": 1133, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_016907085.1", "gtdb_species": "s__Clavibacter michiganensis_O", "ani": 93.0911, "matched_fragments": 934, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "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_900168345.1", "gtdb_species": "s__Clavibacter michiganensis", "ani": 92.645, "matched_fragments": 939, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "95.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.88", "num_clustered_genomes": 49, "status": "-" }, { "accession": "GCF_000355695.1", "gtdb_species": "s__Clavibacter nebraskensis", "ani": 92.5311, "matched_fragments": 918, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.1408, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002240565.1", "gtdb_species": "s__Clavibacter insidiosus", "ani": 92.5213, "matched_fragments": 960, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.1408, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "95.88", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002931175.1", "gtdb_species": "s__Clavibacter californiensis", "ani": 92.5159, "matched_fragments": 897, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "98.71", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003576185.1", "gtdb_species": "s__Clavibacter phaseoli", "ani": 92.2898, "matched_fragments": 572, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.97", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003576405.1", "gtdb_species": "s__Clavibacter sp003576405", "ani": 92.1077, "matched_fragments": 680, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_015351075.1", "gtdb_species": "s__Clavibacter sp015351075", "ani": 92.0545, "matched_fragments": 926, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "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_015351105.1", "gtdb_species": "s__Clavibacter sp015351105", "ani": 92.0415, "matched_fragments": 953, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "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_002151125.1", "gtdb_species": "s__Clavibacter michiganensis_C", "ani": 92.0147, "matched_fragments": 883, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "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_001280205.1", "gtdb_species": "s__Clavibacter capsici", "ani": 91.1769, "matched_fragments": 918, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002240635.1", "gtdb_species": "s__Clavibacter tessellarius", "ani": 90.6027, "matched_fragments": 923, "total_fragments": 1133, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.95", "min_intra_species_ani": "95.37", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.2, "optimum_tmp": 26.333, "optimum_ph": null, "genome_size": 3287966.286, "gc_content": 70.856, "coding_genes": 3004.583, "rRNA16S_genes": 2.0, "tRNA_genes": 45.375, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "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 }, "_genome_taxon": [ "Clavibacter", "sepedonicus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }