{ "type": "genome", "identifier": "GCF_001467505.1", "organism": "Legionella birminghamensis", "title": "Legionella birminghamensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Tel Aviv University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001467505.1", "bioproject": "PRJNA224116", "biosample": "SAMN04274765", "wgs_master": "LNXT00000000.1", "refseq_category": "na", "taxid": "28083", "species_taxid": "28083", "organism_name": "Legionella birminghamensis", "infraspecific_name": "strain=CDC#1407-AL-14", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/12/15", "asm_name": "ASM146750v1", "asm_submitter": "Tel Aviv University", "gbrs_paired_asm": "GCA_001467505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/467/505/GCF_001467505.1_ASM146750v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3737655", "genome_size_ungapped": "3736683", "gc_percent": "43.500000", "replicon_count": "0", "scaffold_count": "54", "contig_count": "54", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001467505.1-RS_2024_03_21", "annotation_date": "2024-03-21", "total_gene_count": "3247", "protein_coding_gene_count": "3157", "non_coding_gene_count": "49", "pubmed_id": "26752266" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-12-15", "dateModified": "2015-12-15", "datePublished": "2015-12-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Legionella birminghamensis" ], "sample_taxid": [ "28083" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "legionellosis", "Cardiac transplantrecipient" ], "sample_host_disease_id": [], "sample_host_location": [ "USA: Alabama" ], "sample_host_location_id": [], "data_size": "1.067 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)": "3737655", "Number of Sequences": "54", "Longest Sequences (bp)": "655066", "N50 (bp)": "202516", "Gap Ratio (%)": "0.026006", "GCcontent (%)": "43.5", "Number of CDSs": "3178", "Average Protein Length": "345.8", "Coding Ratio (%)": "88.2", "Number of rRNAs": "3", "Number of tRNAs": "42", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Legionella birminghamensis", "strain": "strain=CDC#1407-AL-14", "accession": "GCA_001467505.1", "taxid": 28083, "species_taxid": 28083, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1218, "total_fragments": 1221, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella birminghamensis", "strain": "strain=NCTC12437", "accession": "GCA_900452515.1", "taxid": 28083, "species_taxid": 28083, "relation_to_type": "type", "validated": true, "ani": 99.9874, "matched_fragments": 1218, "total_fragments": 1221, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella birminghamensis", "strain": "strain=1407-AL-H", "accession": "GCA_900639775.1", "taxid": 28083, "species_taxid": 28083, "relation_to_type": "type", "validated": true, "ani": 99.9426, "matched_fragments": 1172, "total_fragments": 1221, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella quinlivanii", "strain": "strain=CDC#1442-AUS-E", "accession": "GCA_001467975.1", "taxid": 45073, "species_taxid": 45073, "relation_to_type": "type", "validated": true, "ani": 80.4806, "matched_fragments": 581, "total_fragments": 1221, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Legionella quinlivanii", "strain": "strain=1442-AUS-E", "accession": "GCA_900639995.1", "taxid": 45073, "species_taxid": 45073, "relation_to_type": "type", "validated": true, "ani": 80.3227, "matched_fragments": 577, "total_fragments": 1221, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Legionella clemsonensis", "strain": "strain=CDC-D5610", "accession": "GCA_002240035.1", "taxid": 1867846, "species_taxid": 1867846, "relation_to_type": "type", "validated": true, "ani": 77.6635, "matched_fragments": 95, "total_fragments": 1221, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Legionella massiliensis", "strain": "strain=LegA", "accession": "GCA_000756815.1", "taxid": 1034943, "species_taxid": 1034943, "relation_to_type": "type", "validated": true, "ani": 77.4113, "matched_fragments": 88, "total_fragments": 1221, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900452515.1", "gtdb_species": "s__Legionella_C birminghamensis", "ani": 99.9874, "matched_fragments": 1218, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_003265995.1", "gtdb_species": "s__Legionella_C quinlivanii_A", "ani": 80.7122, "matched_fragments": 597, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.16", "min_intra_species_ani": "96.16", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900461555.1", "gtdb_species": "s__Legionella_C quinlivanii", "ani": 80.468, "matched_fragments": 590, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001467745.1", "gtdb_species": "s__Tatlockia jamestowniensis", "ani": 79.5616, "matched_fragments": 92, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.16", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900637635.1", "gtdb_species": "s__Tatlockia jordanis", "ani": 78.7164, "matched_fragments": 84, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.59", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000162755.2", "gtdb_species": "s__Legionella drancourtii", "ani": 78.2575, "matched_fragments": 78, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "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_001468035.1", "gtdb_species": "s__Legionella tucsonensis", "ani": 77.8793, "matched_fragments": 58, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000621525.1", "gtdb_species": "s__Tatlockia fairfieldensis", "ani": 77.7545, "matched_fragments": 77, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900167045.1", "gtdb_species": "s__Tatlockia maceachernii", "ani": 77.7214, "matched_fragments": 82, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002240035.1", "gtdb_species": "s__Tatlockia clemsonensis", "ani": 77.6635, "matched_fragments": 95, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "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_001467625.1", "gtdb_species": "s__Tatlockia feeleii", "ani": 77.59, "matched_fragments": 90, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000756815.1", "gtdb_species": "s__Tatlockia massiliensis", "ani": 77.4423, "matched_fragments": 87, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001467615.1", "gtdb_species": "s__Legionella_C erythra", "ani": 77.3789, "matched_fragments": 96, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016864235.1", "gtdb_species": "s__Legionella_C sp016864235", "ani": 77.368, "matched_fragments": 101, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C", "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_900639875.1", "gtdb_species": "s__Legionella_A impletisoli", "ani": 77.2258, "matched_fragments": 55, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000308315.1", "gtdb_species": "s__Tatlockia tunisiensis", "ani": 77.0379, "matched_fragments": 88, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia", "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_002786205.1", "gtdb_species": "s__Legionella sp002786205", "ani": 76.5827, "matched_fragments": 54, "total_fragments": 1221, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.324, "cell_length": 0.259, "doubling_h": 0.38, "growth_tmp": 37.0, "optimum_tmp": 33.77, "optimum_ph": 6.9, "genome_size": 3732759.0, "gc_content": 38.268, "coding_genes": 2803.262, "rRNA16S_genes": 3.5, "tRNA_genes": 42.766, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.888, "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": [ "Legionella", "birminghamensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }