{ "type": "genome", "identifier": "GCF_000614245.1", "organism": "Prevotella fusca JCM 17724", "title": "Prevotella fusca JCM 17724", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000614245.1", "bioproject": "PRJNA224116", "biosample": "SAMD00011176", "wgs_master": "BAKO00000000.1", "refseq_category": "na", "taxid": "1236517", "species_taxid": "589436", "organism_name": "Prevotella fusca JCM 17724", "infraspecific_name": "strain=JCM 17724", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/03/31", "asm_name": "ASM61424v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_000614245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/614/245/GCF_000614245.1_ASM61424v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3173817", "genome_size_ungapped": "3173817", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "116", "contig_count": "116", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000614245.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "2670", "protein_coding_gene_count": "2119", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-03-31", "dateModified": "2014-03-31", "datePublished": "2014-03-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Prevotella fusca JCM 17724" ], "sample_taxid": [ "1236517" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.904 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.45, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3173817", "Number of Sequences": "116", "Longest Sequences (bp)": "212133", "N50 (bp)": "77483", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.0", "Number of CDSs": "2794", "Average Protein Length": "290.4", "Coding Ratio (%)": "76.7", "Number of rRNAs": "4", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Prevotella fusca", "strain": "strain=JCM 17724", "accession": "GCA_000614245.1", "taxid": 589436, "species_taxid": 589436, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1000, "total_fragments": 1006, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Prevotella fusca", "strain": "strain=W1435", "accession": "GCA_001262015.1", "taxid": 589436, "species_taxid": 589436, "relation_to_type": "type", "validated": true, "ani": 99.9673, "matched_fragments": 1005, "total_fragments": 1006, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Prevotella fusca", "strain": "strain=W1435", "accession": "GCA_018128145.1", "taxid": 589436, "species_taxid": 589436, "relation_to_type": "type", "validated": true, "ani": 99.9658, "matched_fragments": 1006, "total_fragments": 1006, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Prevotella melaninogenica", "strain": "strain=ATCC 25845", "accession": "GCA_000144405.1", "taxid": 28132, "species_taxid": 28132, "relation_to_type": "suspected-type", "validated": true, "ani": 83.2364, "matched_fragments": 666, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella melaninogenica", "strain": "strain=FDAARGOS_1566", "accession": "GCA_020735785.1", "taxid": 28132, "species_taxid": 28132, "relation_to_type": "suspected-type", "validated": true, "ani": 83.2343, "matched_fragments": 666, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella scopos", "strain": "strain=W2052", "accession": "GCA_018127785.1", "taxid": 589437, "species_taxid": 589437, "relation_to_type": "type", "validated": true, "ani": 82.9033, "matched_fragments": 607, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella scopos", "strain": "strain=W2052", "accession": "GCA_001683355.1", "taxid": 589437, "species_taxid": 589437, "relation_to_type": "type", "validated": true, "ani": 82.7531, "matched_fragments": 622, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella jejuni", "strain": "strain=DSM 26989", "accession": "GCA_900187995.1", "taxid": 1177574, "species_taxid": 1177574, "relation_to_type": "type", "validated": true, "ani": 81.7935, "matched_fragments": 585, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella denticola", "strain": "strain=NCTC13067", "accession": "GCA_900454835.1", "taxid": 28129, "species_taxid": 28129, "relation_to_type": "type", "validated": true, "ani": 81.1967, "matched_fragments": 508, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella denticola", "strain": "strain=DSM 20614", "accession": "GCA_000421205.1", "taxid": 28129, "species_taxid": 28129, "relation_to_type": "type", "validated": true, "ani": 80.9829, "matched_fragments": 510, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella veroralis", "strain": "strain=DSM 19559", "accession": "GCA_000377625.1", "taxid": 28137, "species_taxid": 28137, "relation_to_type": "type", "validated": true, "ani": 80.1052, "matched_fragments": 350, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella veroralis", "strain": "strain=JCM 6290", "accession": "GCA_000613325.1", "taxid": 28137, "species_taxid": 28137, "relation_to_type": "type", "validated": true, "ani": 80.0612, "matched_fragments": 345, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella falsenii", "strain": "strain=JCM 15124", "accession": "GCA_000613945.1", "taxid": 515414, "species_taxid": 515414, "relation_to_type": "type", "validated": true, "ani": 79.207, "matched_fragments": 122, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Palleniella intestinalis", "strain": "strain=PINT", "accession": "GCA_013166595.1", "taxid": 2736291, "species_taxid": 2736291, "relation_to_type": "type", "validated": true, "ani": 77.2308, "matched_fragments": 53, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.45, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001262015.1", "gtdb_species": "s__Prevotella fusca", "ani": 99.9673, "matched_fragments": 1005, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_018128065.1", "gtdb_species": "s__Prevotella sp000467895", "ani": 83.9623, "matched_fragments": 667, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.71", "min_intra_species_ani": "96.42", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_018127965.1", "gtdb_species": "s__Prevotella melaninogenica_B", "ani": 83.4813, "matched_fragments": 649, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.77", "min_intra_species_ani": "95.72", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003609775.1", "gtdb_species": "s__Prevotella melaninogenica_A", "ani": 83.3696, "matched_fragments": 635, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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_018127925.1", "gtdb_species": "s__Prevotella melaninogenica_C", "ani": 83.3555, "matched_fragments": 643, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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_000144405.1", "gtdb_species": "s__Prevotella melaninogenica", "ani": 83.2302, "matched_fragments": 666, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.46", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_018127785.1", "gtdb_species": "s__Prevotella scopos", "ani": 82.9066, "matched_fragments": 606, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900187995.1", "gtdb_species": "s__Prevotella jejuni", "ani": 81.7832, "matched_fragments": 586, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.22", "min_intra_species_ani": "96.57", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_900454835.1", "gtdb_species": "s__Prevotella denticola", "ani": 81.2058, "matched_fragments": 507, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_000191065.1", "gtdb_species": "s__Prevotella multiformis", "ani": 80.5424, "matched_fragments": 482, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000257925.1", 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79.2231, "matched_fragments": 121, "total_fragments": 1006, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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": -0.226, "cell_length": 0.114, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 35.219, "optimum_ph": 7.109, "genome_size": 3244209.0, "gc_content": 44.092, "coding_genes": 2467.667, "rRNA16S_genes": 4.0, "tRNA_genes": 48.0, "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": 0.975, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.025, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Prevotella", "fusca", "JCM", "17724" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }