{ "type": "genome", "identifier": "GCF_006364635.1", "organism": "Legionella pneumophila", "title": "Legionella pneumophila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006364635.1", "bioproject": "PRJNA224116", "biosample": "SAMN11056494", "wgs_master": "na", "refseq_category": "na", "taxid": "446", "species_taxid": "446", "organism_name": "Legionella pneumophila", "infraspecific_name": "strain=FDAARGOS_779", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/19", "asm_name": "ASM636463v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_006364635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/364/635/GCF_006364635.1_ASM636463v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3409192", "genome_size_ungapped": "3409192", "gc_percent": "38.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006364635.1-RS_2025_01_06", "annotation_date": "2025-01-06", "total_gene_count": "3060", "protein_coding_gene_count": "2981", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-19", "dateModified": "2019-06-19", "datePublished": "2019-06-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Legionella pneumophila" ], "sample_taxid": [ "446" ], "sample_host_organism": [ "NIST Mixed Microbial RM strain" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "USA:VA" ], "sample_host_location_id": [], "data_size": "0.962 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)": "3409192", "Number of Sequences": "1", "Longest Sequences (bp)": "3409192", "N50 (bp)": "3409192", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.3", "Number of CDSs": "2994", "Average Protein Length": "332.7", "Coding Ratio (%)": "87.6", "Number of rRNAs": "9", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Legionella pneumophila", "strain": "strain=FDAARGOS_779", "accession": "GCA_006364635.1", "taxid": 446, "species_taxid": 446, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1136, "total_fragments": 1136, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella pneumophila subsp. pneumophila", "strain": "strain=FDAARGOS_202", "accession": "GCA_002082955.2", "taxid": 91891, "species_taxid": 446, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 1135, "total_fragments": 1136, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella pneumophila subsp. pneumophila", "strain": "strain=PartS-Lpneumophila-RM8376", "accession": "GCA_022870105.1", "taxid": 91891, "species_taxid": 446, "relation_to_type": "type", "validated": true, "ani": 99.9974, "matched_fragments": 1135, "total_fragments": 1136, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella pneumophila subsp. pneumophila", "strain": "strain=ATCC 33152", "accession": "GCA_000586375.1", "taxid": 91891, "species_taxid": 446, "relation_to_type": "type", "validated": true, "ani": 99.975, "matched_fragments": 1121, "total_fragments": 1136, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella pneumophila", "strain": "strain=NCTC11192", "accession": "GCA_900452735.1", "taxid": 446, "species_taxid": 446, "relation_to_type": "type", "validated": true, "ani": 99.932, "matched_fragments": 1134, "total_fragments": 1136, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella pneumophila", "strain": "strain=ATCC 33152", "accession": "GCA_001582475.1", "taxid": 446, "species_taxid": 446, "relation_to_type": "type", "validated": true, "ani": 99.9182, "matched_fragments": 1089, "total_fragments": 1136, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Legionella rowbothamii", "strain": "strain=LLAP6", "accession": "GCA_900639985.1", "taxid": 96229, "species_taxid": 96229, "relation_to_type": "type", "validated": true, "ani": 78.3164, "matched_fragments": 136, "total_fragments": 1136, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000008485.1", "gtdb_species": "s__Legionella pneumophila", "ani": 99.9293, "matched_fragments": 1133, "total_fragments": 1136, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.85", "min_intra_species_ani": "95.56", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 789, "status": "conclusive" }, { "accession": "GCA_000586315.1", "gtdb_species": "s__Legionella fraseri", "ani": 92.0561, "matched_fragments": 977, "total_fragments": 1136, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "96.27", "mean_intra_species_af": 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"num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000770585.1", "gtdb_species": "s__Legionella norrlandica", "ani": 80.0577, "matched_fragments": 531, "total_fragments": 1136, "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_016786215.1", "gtdb_species": "s__Legionella sp016786215", "ani": 79.3661, "matched_fragments": 258, "total_fragments": 1136, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": 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"s__Legionella saoudiensis", "ani": 77.806, "matched_fragments": 137, "total_fragments": 1136, "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": "GCA_004283175.1", "gtdb_species": "s__Legionella longbeachae", "ani": 77.4552, "matched_fragments": 164, "total_fragments": 1136, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.77", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.324, "cell_length": 0.259, 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