{ "type": "genome", "identifier": "GCF_000174755.1", "organism": "Capnocytophaga gingivalis ATCC 33624", "title": "Capnocytophaga gingivalis ATCC 33624", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000174755.1", "bioproject": "PRJNA224116", "biosample": "SAMN00001917", "wgs_master": "ACLQ00000000.1", "refseq_category": "na", "taxid": "553178", "species_taxid": "1017", "organism_name": "Capnocytophaga gingivalis ATCC 33624", "infraspecific_name": "strain=ATCC 33624", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/04/29", "asm_name": "ASM17475v1", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000174755.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/174/755/GCF_000174755.1_ASM17475v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2667138", "genome_size_ungapped": "2667138", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000174755.1-RS_2024_05_15", "annotation_date": "2024-05-15", "total_gene_count": "2520", "protein_coding_gene_count": "2417", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-04-29", "dateModified": "2009-04-29", "datePublished": "2009-04-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Capnocytophaga gingivalis ATCC 33624" ], "sample_taxid": [ "553178" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "0.754 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)": "2667138", "Number of Sequences": "37", "Longest Sequences (bp)": "337980", "N50 (bp)": "152766", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.5", "Number of CDSs": "2422", "Average Protein Length": "320.4", "Coding Ratio (%)": "87.3", "Number of rRNAs": "6", "Number of tRNAs": "48", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Capnocytophaga gingivalis", "strain": "strain=ATCC 33624", "accession": "GCA_000174755.1", "taxid": 1017, "species_taxid": 1017, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 874, "total_fragments": 874, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Capnocytophaga sputigena", "strain": "strain=NCTC11653", "accession": "GCA_900446695.1", "taxid": 1019, "species_taxid": 1019, "relation_to_type": "type", "validated": true, "ani": 84.1484, "matched_fragments": 161, "total_fragments": 874, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Capnocytophaga granulosa", "strain": "strain=DSM 11449", "accession": "GCA_900106575.1", "taxid": 45242, "species_taxid": 45242, "relation_to_type": "type", "validated": true, "ani": 81.6327, "matched_fragments": 503, "total_fragments": 874, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Capnocytophaga granulosa", "strain": "strain=NCTC12948", "accession": "GCA_900446675.1", "taxid": 45242, "species_taxid": 45242, "relation_to_type": "type", "validated": true, "ani": 81.6326, "matched_fragments": 507, "total_fragments": 874, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Capnocytophaga granulosa", "strain": "strain=ATCC 51502", "accession": "GCA_000411115.1", "taxid": 45242, "species_taxid": 45242, "relation_to_type": "type", "validated": true, "ani": 81.6172, "matched_fragments": 505, "total_fragments": 874, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000174755.1", "gtdb_species": "s__Capnocytophaga gingivalis", "ani": 100.0, "matched_fragments": 874, "total_fragments": 874, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000411115.1", "gtdb_species": "s__Capnocytophaga granulosa", "ani": 81.6229, "matched_fragments": 504, "total_fragments": 874, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.31", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000466425.1", "gtdb_species": "s__Capnocytophaga sp000466425", "ani": 81.2934, "matched_fragments": 467, "total_fragments": 874, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga", "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_000192225.1", "gtdb_species": "s__Capnocytophaga sp000192225", "ani": 80.6135, "matched_fragments": 376, "total_fragments": 874, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_905372595.1", "gtdb_species": "s__Capnocytophaga sp905372595", "ani": 80.1599, "matched_fragments": 168, "total_fragments": 874, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga", "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": -0.388, "cell_length": 0.5, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 2752884.0, "gc_content": 40.3, "coding_genes": 2574.0, "rRNA16S_genes": 3.0, "tRNA_genes": 50.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": [ "Capnocytophaga", "gingivalis", "ATCC", "33624" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }