{ "type": "genome", "identifier": "GCF_012396015.1", "organism": "Tsukamurella spumae", "title": "Tsukamurella spumae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bacterial Special Pathogens Branch (CDC)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012396015.1", "bioproject": "PRJNA224116", "biosample": "SAMN14517875", "wgs_master": "JAAXOQ000000000.1", "refseq_category": "reference genome", "taxid": "44753", "species_taxid": "44753", "organism_name": "Tsukamurella spumae", "infraspecific_name": "strain=DSM 44113", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/15", "asm_name": "ASM1239601v1", "asm_submitter": "Bacterial Special Pathogens Branch (CDC)", "gbrs_paired_asm": "GCA_012396015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/396/015/GCF_012396015.1_ASM1239601v1", 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"sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.206 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)": "4461018", "Number of Sequences": "79", "Longest Sequences (bp)": "304131", "N50 (bp)": "126579", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.2", "Number of CDSs": "4390", "Average Protein Length": "311.9", "Coding Ratio (%)": "92.1", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Tsukamurella spumae", "strain": "strain=DSM 44113", "accession": "GCA_012396015.1", "taxid": 44753, "species_taxid": 44753, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1443, 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"status": "below_threshold" }, { "organism_name": "Tsukamurella tyrosinosolvens", "strain": "strain=DSM 44234", "accession": "GCA_900104775.1", "taxid": 57704, "species_taxid": 57704, "relation_to_type": "type", "validated": true, "ani": 86.8195, "matched_fragments": 1170, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tsukamurella conjunctivitidis", "strain": "strain=HKU72", "accession": "GCA_007858475.1", "taxid": 2592068, "species_taxid": 2592068, "relation_to_type": "type", "validated": true, "ani": 86.3094, "matched_fragments": 1151, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tsukamurella asaccharolytica", "strain": "strain=HKU71", "accession": "GCA_007858435.1", "taxid": 2592067, "species_taxid": 2592067, "relation_to_type": "type", "validated": true, "ani": 85.7829, "matched_fragments": 1014, "total_fragments": 1448, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012396015.1", "gtdb_species": "s__Tsukamurella spumae", "ani": 100.0, "matched_fragments": 1443, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella", "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_001575205.1", "gtdb_species": "s__Tsukamurella pseudospumae", "ani": 91.9055, "matched_fragments": 1202, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "98.07", "mean_intra_species_af": 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"num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_900103175.1", "gtdb_species": "s__Tsukamurella pulmonis", "ani": 86.21, "matched_fragments": 1097, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "98.89", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_007858435.1", "gtdb_species": "s__Tsukamurella asaccharolytica", "ani": 85.7718, "matched_fragments": 1015, "total_fragments": 1448, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella", "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": -0.113, "cell_length": 0.336, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.625, "optimum_ph": 7.0, "genome_size": 4816553.391, "gc_content": 69.644, "coding_genes": 4430.333, "rRNA16S_genes": 2.0, "tRNA_genes": 48.0, "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": [ "Tsukamurella", "spumae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }