{ "type": "genome", "identifier": "GCF_007990545.2", "organism": "Leptotrichia wadei", "title": "Leptotrichia wadei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007990545.2", "bioproject": "PRJNA224116", "biosample": "SAMD00156224", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "157687", "species_taxid": "157687", "organism_name": "Leptotrichia wadei", "infraspecific_name": "strain=JCM16777", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/09", "asm_name": "ASM799054v2", "asm_submitter": "Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University", "gbrs_paired_asm": "GCA_007990545.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/990/545/GCF_007990545.2_ASM799054v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2337418", "genome_size_ungapped": "2337418", "gc_percent": "29.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007990545.2-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "2177", "protein_coding_gene_count": "2087", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-01-09", "dateModified": "2020-01-09", "datePublished": "2020-01-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptotrichia wadei" ], "sample_taxid": [ "157687" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Norway" ], "sample_host_location_id": [], "data_size": "0.632 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)": "2337418", "Number of Sequences": "2", "Longest Sequences (bp)": "2305216", "N50 (bp)": "2305216", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.5", "Number of CDSs": "2135", "Average Protein Length": "310.0", "Coding Ratio (%)": "85.0", "Number of rRNAs": "15", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptotrichia wadei", "strain": "strain=JCM16777", "accession": "GCA_007990545.2", "taxid": 157687, "species_taxid": 157687, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 777, "total_fragments": 778, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptotrichia wadei", "strain": "strain=DSM 19758", "accession": "GCA_000373345.1", "taxid": 157687, "species_taxid": 157687, "relation_to_type": "type", "validated": true, "ani": 99.9167, "matched_fragments": 730, "total_fragments": 778, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptotrichia shahii", "strain": "strain=DSM 19757", "accession": "GCA_000373045.1", "taxid": 157691, "species_taxid": 157691, "relation_to_type": "type", "validated": true, "ani": 90.9499, "matched_fragments": 589, "total_fragments": 778, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia shahii", "strain": "strain=JCM16776", "accession": "GCA_008327825.1", "taxid": 157691, "species_taxid": 157691, "relation_to_type": "type", "validated": true, "ani": 90.8589, "matched_fragments": 597, "total_fragments": 778, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia hofstadii", "strain": "strain=DSM 21651", "accession": "GCA_000428965.1", "taxid": 157688, "species_taxid": 157688, "relation_to_type": "type", "validated": true, "ani": 85.3909, "matched_fragments": 574, "total_fragments": 778, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia massiliensis", "strain": "strain=Marseille-P3007", "accession": "GCA_900104625.1", "taxid": 1852388, "species_taxid": 1852388, "relation_to_type": "type", "validated": true, "ani": 85.2688, "matched_fragments": 553, "total_fragments": 778, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia buccalis", "strain": "strain=DSM 1135", "accession": "GCA_000023905.1", "taxid": 40542, "species_taxid": 40542, "relation_to_type": "type", "validated": true, "ani": 85.2026, "matched_fragments": 546, "total_fragments": 778, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia trevisanii", "strain": "strain=DSM 22070", "accession": "GCA_000482505.1", "taxid": 109328, "species_taxid": 109328, "relation_to_type": "type", "validated": true, "ani": 85.0894, "matched_fragments": 546, "total_fragments": 778, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007990545.2", "gtdb_species": "s__Leptotrichia wadei", "ani": 100.0, "matched_fragments": 777, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "96.88", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_007990445.1", "gtdb_species": "s__Leptotrichia wadei_A", "ani": 92.3158, "matched_fragments": 606, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.03", "min_intra_species_ani": "96.85", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_008327825.1", "gtdb_species": "s__Leptotrichia shahii", "ani": 90.8605, "matched_fragments": 597, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002240055.1", "gtdb_species": "s__Leptotrichia sp002240055", "ani": 86.1293, "matched_fragments": 407, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007990635.1", "gtdb_species": "s__Leptotrichia hongkongensis", "ani": 85.5834, "matched_fragments": 551, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "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_007990525.1", "gtdb_species": "s__Leptotrichia hofstadii", "ani": 85.4786, "matched_fragments": 575, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900104625.1", "gtdb_species": "s__Leptotrichia massiliensis", "ani": 85.284, "matched_fragments": 553, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.80", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000469385.1", "gtdb_species": "s__Leptotrichia sp000469385", "ani": 85.2818, "matched_fragments": 521, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "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_000023905.1", "gtdb_species": "s__Leptotrichia buccalis", "ani": 85.1271, "matched_fragments": 553, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "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_000482505.1", "gtdb_species": "s__Leptotrichia trevisanii", "ani": 85.0785, "matched_fragments": 547, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.58", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_018128245.1", "gtdb_species": "s__JABCPH02 sp013333235", "ani": 83.7042, "matched_fragments": 365, "total_fragments": 778, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__JABCPH02", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.39", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.426, "cell_length": 0.64, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2369937.5, "gc_content": 29.603, "coding_genes": 2196.333, "rRNA16S_genes": 5.0, "tRNA_genes": 46.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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": [ "Leptotrichia", "wadei" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }