{ "type": "genome", "identifier": "GCF_000614025.1", "organism": "Prevotella aurantiaca JCM 15754", "title": "Prevotella aurantiaca JCM 15754", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000614025.1", "bioproject": "PRJNA224116", "biosample": "SAMD00012187", "wgs_master": "BAKF00000000.1", "refseq_category": "na", "taxid": "1236508", "species_taxid": "596085", "organism_name": "Prevotella aurantiaca JCM 15754", "infraspecific_name": "strain=JCM 15754", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/03/31", "asm_name": "ASM61402v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_000614025.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/614/025/GCF_000614025.1_ASM61402v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3002170", "genome_size_ungapped": "3002170", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "148", "contig_count": "148", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000614025.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "2638", "protein_coding_gene_count": "2290", "non_coding_gene_count": "48", "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 aurantiaca JCM 15754" ], "sample_taxid": [ "1236508" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.852 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)": "3002170", "Number of Sequences": "148", "Longest Sequences (bp)": "216539", "N50 (bp)": "59497", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.9", "Number of CDSs": "2572", "Average Protein Length": "309.2", "Coding Ratio (%)": "79.5", "Number of rRNAs": "3", "Number of tRNAs": "42", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Prevotella aurantiaca", "strain": "strain=JCM 15754", "accession": "GCA_000614025.1", "taxid": 596085, "species_taxid": 596085, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 926, "total_fragments": 930, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Prevotella intermedia", "strain": "strain=ATCC 25611", "accession": "GCA_001953955.1", "taxid": 28131, "species_taxid": 28131, "relation_to_type": "type", "validated": true, "ani": 83.3553, "matched_fragments": 597, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella intermedia", "strain": "strain=DSM 20706", "accession": "GCA_000439065.1", "taxid": 28131, "species_taxid": 28131, "relation_to_type": "type", "validated": true, "ani": 83.3249, "matched_fragments": 592, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella intermedia", "strain": "strain=ATCC 25611", "accession": "GCA_000519165.1", "taxid": 28131, "species_taxid": 28131, "relation_to_type": "type", "validated": true, "ani": 83.3243, "matched_fragments": 593, "total_fragments": 930, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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"min_intra_species_ani": "96.89", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 40, "status": "-" }, { "accession": "GCF_000613945.1", "gtdb_species": "s__Prevotella falsenii", "ani": 82.17, "matched_fragments": 550, "total_fragments": 930, "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_000220235.1", "gtdb_species": "s__Prevotella nigrescens", "ani": 81.4902, "matched_fragments": 523, "total_fragments": 930, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.14", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.78", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_000377625.1", "gtdb_species": "s__Prevotella veroralis", "ani": 80.71, "matched_fragments": 123, "total_fragments": 930, "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_000613345.1", "gtdb_species": "s__Prevotella disiens", "ani": 79.9909, "matched_fragments": 329, "total_fragments": 930, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_900155655.1", "gtdb_species": "s__Prevotella ihumii", "ani": 79.9016, "matched_fragments": 252, "total_fragments": 930, "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": -0.188, "cell_length": 0.135, "doubling_h": null, "growth_tmp": 36.755, "optimum_tmp": 37.0, "optimum_ph": 7.109, "genome_size": 3002170.0, "gc_content": 45.137, "coding_genes": 2508.172, "rRNA16S_genes": 4.0, "tRNA_genes": 50.875, "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, 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