{ "type": "genome", "identifier": "GCF_021922985.1", "organism": "Clavibacter michiganensis subsp. tessellarius", "title": "Clavibacter michiganensis subsp. tessellarius", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Hawaii", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021922985.1", "bioproject": "PRJNA224116", "biosample": "SAMN11854497", "wgs_master": "na", "refseq_category": "na", "taxid": "31965", "species_taxid": "28447", "organism_name": "Clavibacter michiganensis subsp. tessellarius", "infraspecific_name": "strain=ATCC 33566", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/02/03", "asm_name": "ASM2192298v1", "asm_submitter": "University of Hawaii", "gbrs_paired_asm": "GCA_021922985.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/922/985/GCF_021922985.1_ASM2192298v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3366694", "genome_size_ungapped": "3366694", "gc_percent": "73.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021922985.1-RS_2024_03_17", "annotation_date": "2024-03-17", "total_gene_count": "3221", "protein_coding_gene_count": "3143", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-02-03", "dateModified": "2022-02-03", "datePublished": "2022-02-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Clavibacter michiganensis subsp. tessellarius" ], "sample_taxid": [ "31965" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.875 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)": "3366694", "Number of Sequences": "4", "Longest Sequences (bp)": "3254008", "N50 (bp)": "3254008", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.6", "Number of CDSs": "3191", "Average Protein Length": "320.1", "Coding Ratio (%)": "91.0", "Number of rRNAs": "6", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_021922985.1", "taxid": 31965, "species_taxid": 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"matched_fragments": 921, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002240635.1", "gtdb_species": "s__Clavibacter tessellarius", "ani": 99.9983, "matched_fragments": 1097, "total_fragments": 1120, "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": "conclusive" }, { "accession": "GCF_001618005.1", "gtdb_species": "s__Clavibacter tessellarius_A", "ani": 93.6465, "matched_fragments": 936, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", 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"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_016907085.1", "gtdb_species": "s__Clavibacter michiganensis_O", "ani": 91.3874, "matched_fragments": 941, "total_fragments": 1120, "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_014775655.1", "gtdb_species": "s__Clavibacter zhangzhiyongii", "ani": 91.3824, "matched_fragments": 917, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000069225.1", "gtdb_species": "s__Clavibacter sepedonicus", "ani": 90.58, "matched_fragments": 928, "total_fragments": 1120, "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": "-" } ] }, "_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, 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