{ "type": "genome", "identifier": "GCF_900240215.1", "organism": "Raoultibacter timonensis", "title": "Raoultibacter timonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900240215.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104414112", "wgs_master": "OEPT00000000.1", "refseq_category": "na", "taxid": "1907662", "species_taxid": "1907662", "organism_name": "Raoultibacter timonensis", "infraspecific_name": "strain=Marseille-P3277", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/02", "asm_name": "PRJEB23748", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900240215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/240/215/GCF_900240215.1_PRJEB23748", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3936881", "genome_size_ungapped": "3914867", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "84", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900240215.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3248", "protein_coding_gene_count": "3141", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-02", "dateModified": "2018-01-02", "datePublished": "2018-01-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Raoultibacter timonensis" ], "sample_taxid": [ "1907662" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.092 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3936881", "Number of Sequences": "21", "Longest Sequences (bp)": "2852076", "N50 (bp)": "2852076", "Gap Ratio (%)": "0.564432", "GCcontent (%)": "59.9", "Number of CDSs": "3218", "Average Protein Length": "350.2", "Coding Ratio (%)": "85.9", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Raoultibacter timonensis", "strain": "strain=Marseille-P3277", "accession": "GCA_900240215.1", "taxid": 1907662, "species_taxid": 1907662, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 1302, "total_fragments": 1303, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Raoultibacter massiliensis", "strain": "strain=Marseille-P2849", "accession": "GCA_900199545.1", "taxid": 1852371, "species_taxid": 1852371, "relation_to_type": "type", "validated": true, "ani": 82.2207, "matched_fragments": 784, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella timonensis", "strain": "strain=Marseille-P3135", "accession": "GCA_900184265.1", "taxid": 1871008, "species_taxid": 1871008, "relation_to_type": "type", "validated": true, "ani": 79.0482, "matched_fragments": 399, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella sinensis", "strain": "strain=DSM 16107", "accession": "GCA_003725965.1", "taxid": 242230, "species_taxid": 242230, "relation_to_type": "type", "validated": true, "ani": 79.0127, "matched_fragments": 407, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella lenta", "strain": "strain=DSM 2243", "accession": "GCA_000024265.1", "taxid": 84112, "species_taxid": 84112, "relation_to_type": "type", "validated": true, "ani": 78.9732, "matched_fragments": 368, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella lenta", "strain": "strain=UCSF2243", "accession": "GCA_003339945.1", "taxid": 84112, "species_taxid": 84112, "relation_to_type": "type", "validated": true, "ani": 78.9538, "matched_fragments": 360, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella sinensis", "strain": "strain=DSM 16107", "accession": "GCA_003339815.1", "taxid": 242230, "species_taxid": 242230, "relation_to_type": "type", "validated": true, "ani": 78.942, "matched_fragments": 418, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella lenta", "strain": "strain=ATCC 25559", "accession": "GCA_003340105.1", "taxid": 84112, "species_taxid": 84112, "relation_to_type": "type", "validated": true, "ani": 78.8924, "matched_fragments": 364, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella lenta", "strain": "strain=DSM 2243", "accession": "GCA_003339975.1", "taxid": 84112, "species_taxid": 84112, "relation_to_type": "type", "validated": true, "ani": 78.8913, "matched_fragments": 367, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eggerthella guodeyinii", "strain": "strain=HF-1101", "accession": "GCA_009834925.2", "taxid": 2690837, "species_taxid": 2690837, "relation_to_type": "type", "validated": true, "ani": 78.8215, "matched_fragments": 451, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900240215.1", "gtdb_species": "s__Raoultibacter timonensis", "ani": 99.9999, "matched_fragments": 1302, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_900199545.1", "gtdb_species": "s__Raoultibacter massiliensis", "ani": 82.211, "matched_fragments": 785, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter", "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_901411515.1", "gtdb_species": "s__Raoultibacter sp901411515", "ani": 81.6492, "matched_fragments": 782, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter", "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_900170005.1", "gtdb_species": "s__Gordonibacter massiliensis", "ani": 79.0776, "matched_fragments": 417, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "97.12", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900184265.1", "gtdb_species": "s__Eggerthella timonensis", "ani": 79.058, "matched_fragments": 397, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella", "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_000024265.1", "gtdb_species": "s__Eggerthella lenta", "ani": 78.979, "matched_fragments": 369, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 72, "status": "-" }, { "accession": "GCF_003339815.1", "gtdb_species": "s__Eggerthella sinensis", "ani": 78.9357, "matched_fragments": 418, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009834925.2", "gtdb_species": "s__Eggerthella sp014287365", "ani": 78.8356, "matched_fragments": 449, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "96.91", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003340345.1", "gtdb_species": "s__Paraeggerthella hongkongensis_A", "ani": 78.5355, "matched_fragments": 298, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.26", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900754955.1", "gtdb_species": "s__CAAEEV01 sp900754955", "ani": 78.4985, "matched_fragments": 196, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.85", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900754495.1", "gtdb_species": "s__Aphodovivens avicola", "ani": 77.9275, "matched_fragments": 187, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.28", "min_intra_species_ani": "95.91", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.73", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900550385.1", "gtdb_species": "s__Aphodovivens sp900550385", "ani": 77.7232, "matched_fragments": 177, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "99.66", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_905203045.1", "gtdb_species": "s__CAG-1427 sp900555755", "ani": 76.8896, "matched_fragments": 87, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Raoultibacter", "timonensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }