{ "type": "genome", "identifier": "GCF_003149515.1", "organism": "Hymenobacter nivis", "title": "Hymenobacter nivis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hokkaido University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003149515.1", "bioproject": "PRJNA224116", "biosample": "SAMN08984992", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1850093", "species_taxid": "1850093", "organism_name": "Hymenobacter nivis", "infraspecific_name": "strain=NBRC 111535", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/23", "asm_name": "ASM314951v1", "asm_submitter": "Hokkaido University", "gbrs_paired_asm": "GCA_003149515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/149/515/GCF_003149515.1_ASM314951v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5027597", "genome_size_ungapped": "5027597", "gc_percent": "62.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003149515.1-RS_2024_08_04", "annotation_date": "2024-08-04", "total_gene_count": "4592", "protein_coding_gene_count": "4445", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-23", "dateModified": "2018-05-23", "datePublished": "2018-05-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Hymenobacter nivis" ], "sample_taxid": [ "1850093" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Yatude Valley" ], "sample_host_location_id": [], "data_size": "1.396 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.02, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5027597", "Number of Sequences": "1", "Longest Sequences (bp)": "5027597", "N50 (bp)": "5027597", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.5", "Number of CDSs": "4516", "Average Protein Length": "314.4", "Coding Ratio (%)": "84.7", "Number of rRNAs": "6", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Hymenobacter nivis", "strain": "strain=NBRC 111535", "accession": "GCA_003149515.1", "taxid": 1850093, "species_taxid": 1850093, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1675, "total_fragments": 1675, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Hymenobacter coccineus", "strain": "strain=CCM 8649", "accession": "GCA_001816125.1", "taxid": 1908235, "species_taxid": 1908235, "relation_to_type": "type", "validated": true, "ani": 88.9905, "matched_fragments": 1184, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter caeli", "strain": "strain=9A", "accession": "GCA_013294115.1", "taxid": 2735894, "species_taxid": 2735894, "relation_to_type": "type", "validated": true, "ani": 87.2161, "matched_fragments": 1210, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter armeniacus", "strain": "strain=BT189", "accession": "GCA_014699055.1", "taxid": 2771358, "species_taxid": 2771358, "relation_to_type": "type", "validated": true, "ani": 81.1229, "matched_fragments": 958, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter terricola", "strain": "strain=3F2", "accession": "GCA_017921975.2", "taxid": 2819236, "species_taxid": 2819236, "relation_to_type": "type", "validated": true, "ani": 81.05, "matched_fragments": 959, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter properus", "strain": "strain=BT439", "accession": "GCA_015694735.1", "taxid": 2791026, "species_taxid": 2791026, "relation_to_type": "type", "validated": true, "ani": 80.7864, "matched_fragments": 919, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter lapidarius", "strain": "strain=CCM 8643", "accession": "GCA_001816145.1", "taxid": 1908237, "species_taxid": 1908237, "relation_to_type": "type", "validated": true, "ani": 80.6132, "matched_fragments": 823, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter sedentarius", "strain": "strain=DG5B", "accession": "GCA_001507645.1", "taxid": 1411621, "species_taxid": 1411621, "relation_to_type": "type", "validated": true, "ani": 80.5591, "matched_fragments": 875, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter rubidus", "strain": "strain=DG7B", "accession": "GCA_016734815.1", "taxid": 1441626, "species_taxid": 1441626, "relation_to_type": "type", "validated": true, "ani": 80.4142, "matched_fragments": 876, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter frigidus", "strain": "strain=CGMCC 1.14966", "accession": "GCA_014640435.1", "taxid": 1524095, "species_taxid": 1524095, "relation_to_type": "type", "validated": true, "ani": 80.2757, "matched_fragments": 874, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter montanus", "strain": "strain=BT664", "accession": "GCA_014699115.1", "taxid": 2771359, "species_taxid": 2771359, "relation_to_type": "type", "validated": true, "ani": 79.4299, "matched_fragments": 714, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter terrenus", "strain": "strain=MIMtkLc17", "accession": "GCA_000972495.1", "taxid": 1629124, "species_taxid": 1629124, "relation_to_type": "type", "validated": true, "ani": 79.1763, "matched_fragments": 725, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter setariae", "strain": "strain=Fur1", "accession": "GCA_007713685.1", "taxid": 2594794, "species_taxid": 2594794, "relation_to_type": "type", "validated": true, "ani": 78.8155, "matched_fragments": 724, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter guriensis", "strain": "strain=BT594", "accession": "GCA_015773195.1", "taxid": 2793065, "species_taxid": 2793065, "relation_to_type": "type", "validated": true, "ani": 78.4599, "matched_fragments": 629, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter metallicola", "strain": "strain=9PBR-1", "accession": "GCA_004745645.1", "taxid": 2563114, "species_taxid": 2563114, "relation_to_type": "type", "validated": true, "ani": 78.2738, "matched_fragments": 586, "total_fragments": 1675, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.02, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003149515.1", "gtdb_species": "s__Hymenobacter nivis", "ani": 100.0, "matched_fragments": 1675, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_001562275.1", "gtdb_species": "s__Hymenobacter sp001562275", "ani": 89.5516, "matched_fragments": 1343, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_001816125.1", "gtdb_species": "s__Hymenobacter coccineus", "ani": 88.9836, "matched_fragments": 1184, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_006439025.1", "gtdb_species": "s__Hymenobacter nivis_A", "ani": 88.9392, "matched_fragments": 1266, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_013294115.1", "gtdb_species": "s__Hymenobacter caeli", "ani": 87.1924, "matched_fragments": 1212, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_016427455.1", "gtdb_species": "s__Hymenobacter sp016427455", "ani": 80.9597, "matched_fragments": 943, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.46", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001507645.1", "gtdb_species": "s__Hymenobacter sedentarius", "ani": 80.5477, "matched_fragments": 878, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_000715495.1", "gtdb_species": "s__Hymenobacter sp000715495", "ani": 80.4421, "matched_fragments": 855, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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_000972495.1", "gtdb_species": "s__Hymenobacter terrenus", "ani": 79.1894, "matched_fragments": 723, "total_fragments": 1675, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "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": -0.222, "cell_length": 0.338, "doubling_h": null, "growth_tmp": 25.583, "optimum_tmp": 23.888, "optimum_ph": 7.3, "genome_size": 5027600.0, "gc_content": 62.5, "coding_genes": 4252.0, "rRNA16S_genes": 3.0, "tRNA_genes": 43.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Hymenobacter", "nivis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }