{ "type": "genome", "identifier": "GCF_900454835.1", "organism": "Prevotella denticola", "title": "Prevotella denticola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900454835.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4535751", "wgs_master": "UGTM00000000.1", "refseq_category": "na", "taxid": "28129", "species_taxid": "28129", "organism_name": "Prevotella denticola", "infraspecific_name": "strain=NCTC13067", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "52295_A01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900454835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/454/835/GCF_900454835.1_52295_A01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3171703", "genome_size_ungapped": "3171703", "gc_percent": "50.000000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900454835.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "2537", "protein_coding_gene_count": "2423", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Prevotella denticola" ], "sample_taxid": [ "28129" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.900 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)": "3171703", "Number of Sequences": "3", "Longest Sequences (bp)": "1948357", "N50 (bp)": "1948357", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.9", "Number of CDSs": "2448", "Average Protein Length": "358.3", "Coding Ratio (%)": "83.0", "Number of rRNAs": "14", "Number of tRNAs": "52", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Prevotella denticola", "strain": "strain=NCTC13067", "accession": "GCA_900454835.1", "taxid": 28129, "species_taxid": 28129, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1055, "total_fragments": 1056, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Prevotella denticola", "strain": "strain=DSM 20614", "accession": "GCA_000421205.1", "taxid": 28129, "species_taxid": 28129, "relation_to_type": "type", "validated": true, "ani": 99.9534, "matched_fragments": 986, "total_fragments": 1056, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Prevotella multiformis", "strain": "strain=DSM 16608", "accession": "GCA_000191065.1", "taxid": 282402, "species_taxid": 282402, "relation_to_type": "type", "validated": true, "ani": 89.6833, "matched_fragments": 730, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella fusca", "strain": "strain=W1435", "accession": "GCA_018128145.1", "taxid": 589436, "species_taxid": 589436, "relation_to_type": "type", "validated": true, "ani": 81.3406, "matched_fragments": 539, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella fusca", "strain": "strain=W1435", "accession": "GCA_001262015.1", "taxid": 589436, "species_taxid": 589436, "relation_to_type": "type", "validated": true, "ani": 81.1753, "matched_fragments": 545, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella fusca", "strain": "strain=JCM 17724", "accession": "GCA_000614245.1", "taxid": 589436, "species_taxid": 589436, "relation_to_type": "type", "validated": true, "ani": 80.9723, "matched_fragments": 525, "total_fragments": 1056, "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": 77.6469, "matched_fragments": 52, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella mizrahii", "strain": "strain=LKV-178-WT-2A", "accession": "GCA_009695775.1", "taxid": 2606637, "species_taxid": 2606637, "relation_to_type": "type", "validated": true, "ani": 76.8802, "matched_fragments": 106, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hallella faecis", "strain": "strain=CLA-AA-H145", "accession": "GCA_018789675.1", "taxid": 2841596, "species_taxid": 2841596, "relation_to_type": "type", "validated": true, "ani": 76.6728, "matched_fragments": 105, "total_fragments": 1056, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900454835.1", "gtdb_species": "s__Prevotella denticola", "ani": 100.0, "matched_fragments": 1056, "total_fragments": 1056, "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": "conclusive" }, { "accession": "GCF_000191065.1", "gtdb_species": "s__Prevotella multiformis", "ani": 89.6653, "matched_fragments": 732, "total_fragments": 1056, "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_000377625.1", "gtdb_species": "s__Prevotella veroralis", "ani": 81.4075, "matched_fragments": 248, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_018128065.1", "gtdb_species": "s__Prevotella sp000467895", "ani": 81.1815, "matched_fragments": 386, "total_fragments": 1056, "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_001262015.1", "gtdb_species": "s__Prevotella fusca", "ani": 81.1695, "matched_fragments": 547, "total_fragments": 1056, "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": "-" }, { "accession": "GCF_000144405.1", "gtdb_species": "s__Prevotella melaninogenica", "ani": 80.5299, "matched_fragments": 334, "total_fragments": 1056, "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_018127925.1", "gtdb_species": "s__Prevotella melaninogenica_C", "ani": 80.2589, "matched_fragments": 356, "total_fragments": 1056, "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_018127965.1", "gtdb_species": "s__Prevotella 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258, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.82", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_000614065.1", "gtdb_species": "s__Prevotella dentasini", "ani": 78.2253, "matched_fragments": 222, "total_fragments": 1056, "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": "GCA_900762125.1", "gtdb_species": "s__Prevotella sp900762125", "ani": 76.7845, "matched_fragments": 127, "total_fragments": 1056, "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": "GCA_017471245.1", "gtdb_species": "s__Prevotella sp017471245", "ani": 76.443, "matched_fragments": 61, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "98.04", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900543975.1", "gtdb_species": "s__Prevotella sp900543975", "ani": 76.158, "matched_fragments": 84, "total_fragments": 1056, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": -0.155, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 34.75, "optimum_ph": 7.109, "genome_size": 2968632.2, "gc_content": 50.38, "coding_genes": 2295.333, "rRNA16S_genes": 4.0, "tRNA_genes": 49.0, "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": [ "Prevotella", "denticola" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }