{ "type": "genome", "identifier": "GCF_004366355.1", "organism": "Dinghuibacter silviterrae", "title": "Dinghuibacter silviterrae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004366355.1", "bioproject": "PRJNA224116", "biosample": "SAMN10362790", "wgs_master": "SODV00000000.1", "refseq_category": "reference genome", "taxid": "1539049", "species_taxid": "1539049", "organism_name": "Dinghuibacter silviterrae", "infraspecific_name": "strain=DSM 100059", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436635v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004366355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/366/355/GCF_004366355.1_ASM436635v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6497175", "genome_size_ungapped": "6497175", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004366355.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5476", "protein_coding_gene_count": "5414", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Dinghuibacter silviterrae" ], "sample_taxid": [ "1539049" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.840 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)": "6497175", "Number of Sequences": "4", "Longest Sequences (bp)": "4001322", "N50 (bp)": "4001322", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.8", "Number of CDSs": "5412", "Average Protein Length": "374.5", "Coding Ratio (%)": "93.6", "Number of rRNAs": "3", "Number of tRNAs": "44", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Dinghuibacter silviterrae", "strain": "strain=DSM 100059", "accession": "GCA_004366355.1", "taxid": 1539049, "species_taxid": 1539049, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2163, "total_fragments": 2163, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Puia dinghuensis", "strain": "strain=CGMCC 1.15448", "accession": "GCA_014642875.1", "taxid": 1792502, "species_taxid": 1792502, "relation_to_type": "type", "validated": true, "ani": 76.8885, "matched_fragments": 140, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flaviaesturariibacter flavus", "strain": "strain=17J68-12", "accession": "GCA_004337505.1", "taxid": 2502780, "species_taxid": 2502780, "relation_to_type": "type", "validated": true, "ani": 76.7448, "matched_fragments": 65, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga chungangae", "strain": "strain=MAH-28", "accession": "GCA_017742215.1", "taxid": 2821488, "species_taxid": 2821488, "relation_to_type": "type", "validated": true, "ani": 76.1492, "matched_fragments": 78, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga lutea", "strain": "strain=ZY74", "accession": "GCA_003813775.1", "taxid": 2488634, "species_taxid": 2488634, "relation_to_type": "type", "validated": true, "ani": 75.9888, "matched_fragments": 85, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flaviaesturariibacter aridisoli", "strain": "strain=17J68-15", "accession": "GCA_004343705.1", "taxid": 2545761, "species_taxid": 2545761, "relation_to_type": "type", "validated": true, "ani": 75.9789, "matched_fragments": 92, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga parva", "strain": "strain=LY-1", "accession": "GCA_003071345.1", "taxid": 2169414, "species_taxid": 2169414, "relation_to_type": "type", "validated": true, "ani": 75.9563, "matched_fragments": 67, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavisolibacter nicotianae", "strain": "strain=X7X", "accession": "GCA_003628535.1", "taxid": 2364882, "species_taxid": 2364882, "relation_to_type": "type", "validated": true, "ani": 75.9267, "matched_fragments": 67, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga agrisoli", "strain": "strain=BN140078", "accession": "GCA_008386695.1", "taxid": 2607653, "species_taxid": 2607653, "relation_to_type": "type", "validated": true, "ani": 75.8512, "matched_fragments": 69, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga varians", "strain": "strain=KACC 19415", "accession": "GCA_014529945.1", "taxid": 2202339, "species_taxid": 2202339, "relation_to_type": "type", "validated": true, "ani": 75.7262, "matched_fragments": 53, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga fulva", "strain": "strain=G-6-1-13", "accession": "GCA_012927205.1", "taxid": 2728842, "species_taxid": 2728842, "relation_to_type": "type", "validated": true, "ani": 75.5452, "matched_fragments": 59, "total_fragments": 2163, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004366355.1", "gtdb_species": "s__Dinghuibacter silviterrae", "ani": 100.0, "matched_fragments": 2163, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Dinghuibacter", "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": "conclusive" }, { "accession": "GCF_014642875.1", "gtdb_species": "s__Puia dinghuensis", "ani": 76.9065, "matched_fragments": 139, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia", "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_004337505.1", "gtdb_species": "s__Flaviaesturariibacter flavus", "ani": 76.7816, "matched_fragments": 64, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter", "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_903970475.1", "gtdb_species": "s__Dinghuibacter sp903970475", "ani": 76.7729, "matched_fragments": 189, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Dinghuibacter", "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_018267545.1", "gtdb_species": "s__Puia sp018267545", "ani": 76.0886, "matched_fragments": 101, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia", "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_001898505.1", "gtdb_species": "s__Puia sp001898505", "ani": 76.0666, "matched_fragments": 103, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004343705.1", "gtdb_species": "s__Flaviaesturariibacter aridisoli", "ani": 75.9964, "matched_fragments": 91, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter", "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_003167015.1", "gtdb_species": "s__Puia sp003167015", "ani": 75.9901, "matched_fragments": 84, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia", "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_003813775.1", "gtdb_species": "s__Chitinophaga lutea", "ani": 75.9888, "matched_fragments": 85, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_003628535.1", "gtdb_species": "s__Flavisolibacter nicotianae", "ani": 75.95, "matched_fragments": 66, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter", "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_018267585.1", "gtdb_species": "s__Puia sp018267585", "ani": 75.9228, "matched_fragments": 105, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia", "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_008386695.1", "gtdb_species": "s__Chitinophaga agrisoli", "ani": 75.8512, "matched_fragments": 69, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_014529945.1", "gtdb_species": "s__Chitinophaga varians", "ani": 75.7262, "matched_fragments": 53, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_007830125.1", "gtdb_species": "s__Chitinophaga japonensis", "ani": 75.717, "matched_fragments": 91, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_015654595.1", "gtdb_species": "s__Puia sp015654595", "ani": 75.703, "matched_fragments": 67, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia", "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_017849455.1", "gtdb_species": "s__Pseudobacter sp017849455", "ani": 75.6221, "matched_fragments": 54, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter", "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_015069695.1", "gtdb_species": "s__JADCRZ01 sp015069695", "ani": 75.6142, "matched_fragments": 59, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JADCRZ01", "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_016192105.1", "gtdb_species": "s__JJ008 sp016192105", "ani": 75.5449, "matched_fragments": 52, "total_fragments": 2163, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008", "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": 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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Dinghuibacter", "silviterrae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }