{ "type": "genome", "identifier": "GCF_900639775.1", "organism": "Legionella birminghamensis", "title": "Legionella birminghamensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "INSTITUT PASTEUR", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900639775.1", "bioproject": "PRJNA224116", "biosample": "SAMEA5198042", "wgs_master": "CAAAHV000000000.1", "refseq_category": "na", "taxid": "28083", "species_taxid": "28083", "organism_name": "Legionella birminghamensis", "infraspecific_name": "strain=1407-AL-H", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/04", "asm_name": "Leg_birminghamensis_1407-AL-H.v1", "asm_submitter": "INSTITUT PASTEUR", "gbrs_paired_asm": "GCA_900639775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/639/775/GCF_900639775.1_Leg_birminghamensis_1407-AL-H.v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3733558", "genome_size_ungapped": "3730558", "gc_percent": "43.500000", "replicon_count": "0", "scaffold_count": "125", "contig_count": "125", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900639775.1-RS_2024_04_10", "annotation_date": "2024-04-10", "total_gene_count": "3243", "protein_coding_gene_count": "3153", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-04", "dateModified": "2019-02-04", "datePublished": "2019-02-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Legionella birminghamensis" ], "sample_taxid": [ "28083" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.068 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)": "3733558", "Number of Sequences": "125", "Longest Sequences (bp)": "185320", "N50 (bp)": "78276", "Gap Ratio (%)": "0.080620", "GCcontent (%)": "43.4", "Number of CDSs": "3157", "Average Protein Length": "346.3", "Coding Ratio (%)": "87.8", "Number of rRNAs": "3", "Number of tRNAs": "41", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1181, "total_fragments": 1185, "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": 99.9758, "matched_fragments": 1184, "total_fragments": 1185, "ani_threshold": 95, "status": "conclusive" }, { "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": 99.971, "matched_fragments": 1177, "total_fragments": 1185, "ani_threshold": 95, "status": "conclusive" }, { "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": 80.3967, "matched_fragments": 568, "total_fragments": 1185, "ani_threshold": 95, "status": "below_threshold" }, { 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0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900452515.1", "gtdb_species": "s__Legionella_C birminghamensis", "ani": 99.9758, "matched_fragments": 1184, "total_fragments": 1185, "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": 80.7915, "matched_fragments": 585, "total_fragments": 1185, "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", 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"status": "-" }, { "accession": "GCF_900637635.1", "gtdb_species": "s__Tatlockia jordanis", "ani": 78.4556, "matched_fragments": 82, "total_fragments": 1185, "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_900167045.1", "gtdb_species": "s__Tatlockia maceachernii", "ani": 78.0633, "matched_fragments": 75, "total_fragments": 1185, "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": 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77.5755, "matched_fragments": 76, "total_fragments": 1185, "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_002240035.1", "gtdb_species": "s__Tatlockia clemsonensis", "ani": 77.4776, "matched_fragments": 87, "total_fragments": 1185, "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_001468035.1", "gtdb_species": "s__Legionella tucsonensis", "ani": 77.2999, "matched_fragments": 59, 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"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" }