{ "type": "genome", "identifier": "GCF_003634345.1", "organism": "Coprobacter fastidiosus NSB1 = JCM 33896", "title": "Coprobacter fastidiosus NSB1 = JCM 33896", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003634345.1", "bioproject": "PRJNA224116", "biosample": "SAMN05444348", "wgs_master": "RBXN00000000.1", "refseq_category": "na", "taxid": "1349822", "species_taxid": "1099853", "organism_name": "Coprobacter fastidiosus NSB1 = JCM 33896", "infraspecific_name": "strain=NSB1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/11", "asm_name": "ASM363434v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003634345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/634/345/GCF_003634345.1_ASM363434v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3411820", "genome_size_ungapped": "3411820", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003634345.1-RS_2024_06_10", "annotation_date": "2024-06-10", "total_gene_count": "2709", "protein_coding_gene_count": "2613", "non_coding_gene_count": "62", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-11", "dateModified": "2018-10-11", "datePublished": "2018-10-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Coprobacter fastidiosus NSB1 = JCM 33896" ], "sample_taxid": [ "1349822" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: Moscow" ], "sample_host_location_id": [], "data_size": "0.963 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)": "3411820", "Number of Sequences": "19", "Longest Sequences (bp)": "738067", "N50 (bp)": "312965", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.3", "Number of CDSs": "2631", "Average Protein Length": "380.4", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Coprobacter fastidiosus", "strain": "strain=NSB1", "accession": "GCA_003634345.1", "taxid": 1099853, "species_taxid": 1099853, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1128, "total_fragments": 1128, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Coprobacter fastidiosus", "strain": "strain=NSB1", "accession": "GCA_000473955.1", "taxid": 1099853, "species_taxid": 1099853, "relation_to_type": "type", "validated": true, "ani": 99.9705, "matched_fragments": 1105, "total_fragments": 1128, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Coprobacter secundus subsp. similis", "strain": "strain=2CBH44", "accession": "GCA_015097275.1", "taxid": 2751153, "species_taxid": 1501392, "relation_to_type": "type", "validated": true, "ani": 77.8813, "matched_fragments": 158, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides thetaiotaomicron", "strain": "strain=VPI 5482", "accession": "GCA_022453665.1", "taxid": 818, "species_taxid": 818, "relation_to_type": "type", "validated": true, "ani": 77.329, "matched_fragments": 55, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Barnesiella intestinihominis", "strain": "strain=YIT 11860", "accession": "GCA_000296465.1", "taxid": 487174, "species_taxid": 487174, "relation_to_type": "type", "validated": true, "ani": 77.2112, "matched_fragments": 74, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_013009555.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 76.807, "matched_fragments": 50, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_025146415.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 76.7818, "matched_fragments": 52, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parabacteroides pacaensis", "strain": "strain=Marseille-P4001", "accession": "GCA_900292045.1", "taxid": 2086575, "species_taxid": 2086575, "relation_to_type": "type", "validated": true, "ani": 76.5796, "matched_fragments": 53, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parabacteroides timonensis", "strain": "strain=Marseille-P3236", "accession": "GCA_900128505.1", "taxid": 1871013, "species_taxid": 1871013, "relation_to_type": "type", "validated": true, "ani": 76.2964, "matched_fragments": 58, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003634345.1", "gtdb_species": "s__Coprobacter fastidiosus", "ani": 100.0, "matched_fragments": 1128, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.46", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.59", "num_clustered_genomes": 13, "status": "conclusive" }, { "accession": "GCA_900545915.1", "gtdb_species": "s__Coprobacter sp900545915", "ani": 93.3979, "matched_fragments": 950, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.49", "min_intra_species_ani": "96.20", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_000803105.1", "gtdb_species": "s__Coprobacter secundus", "ani": 77.8285, "matched_fragments": 159, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "96.86", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_019114445.1", "gtdb_species": "s__Barnesiella excrementigallinarum", "ani": 77.5007, "matched_fragments": 70, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella", "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_000296465.1", "gtdb_species": "s__Barnesiella intestinihominis", "ani": 77.2834, "matched_fragments": 72, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 27, "status": "-" }, { "accession": "GCA_017467745.1", "gtdb_species": "s__Gallibacteroides sp017467745", "ani": 77.0945, "matched_fragments": 65, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CHK158-818;g__Gallibacteroides", "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_000434215.1", "gtdb_species": "s__UBA11471 sp000434215", "ani": 76.7199, "matched_fragments": 70, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "98.64", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_015550595.1", "gtdb_species": "s__Parabacteroides sp900540715", "ani": 76.1833, "matched_fragments": 51, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900541965.1", "gtdb_species": "s__Parabacteroides sp900541965", "ani": 76.161, "matched_fragments": 54, "total_fragments": 1128, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.603, "cell_length": 0.096, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 33.5, "optimum_ph": null, "genome_size": 3412407.0, "gc_content": 38.3, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "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": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Coprobacter", "fastidiosus", "NSB1", "=", "JCM", "33896" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }