{ "type": "genome", "identifier": "GCF_014640435.1", "organism": "Hymenobacter frigidus", "title": "Hymenobacter frigidus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014640435.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245003", "wgs_master": "BMGY00000000.1", "refseq_category": "reference genome", "taxid": "1524095", "species_taxid": "1524095", "organism_name": "Hymenobacter frigidus", "infraspecific_name": "strain=CGMCC 1.14966", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1464043v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014640435.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/640/435/GCF_014640435.1_ASM1464043v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4775043", "genome_size_ungapped": "4774931", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "116", "contig_count": "116", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014640435.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "4190", "protein_coding_gene_count": "4081", "non_coding_gene_count": "48", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Hymenobacter frigidus" ], "sample_taxid": [ "1524095" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.344 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)": "4775043", "Number of Sequences": "116", "Longest Sequences (bp)": "257525", "N50 (bp)": "94527", "Gap Ratio (%)": "0.002346", "GCcontent (%)": "60.5", "Number of CDSs": "4082", "Average Protein Length": "332.5", "Coding Ratio (%)": "85.3", "Number of rRNAs": "0", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1526, "total_fragments": 1535, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Hymenobacter terricola", "strain": "strain=3F2", "accession": "GCA_017921975.2", "taxid": 2819236, "species_taxid": 2819236, "relation_to_type": "type", "validated": true, "ani": 84.1024, "matched_fragments": 1111, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter artigasi", "strain": "strain=1B", "accession": "GCA_012275535.1", "taxid": 2719616, "species_taxid": 2719616, "relation_to_type": "type", "validated": true, "ani": 83.9261, "matched_fragments": 1133, "total_fragments": 1535, "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": 83.4422, "matched_fragments": 1072, "total_fragments": 1535, "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": 83.0408, "matched_fragments": 1001, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter glacialis", "strain": "strain=CCM 8648", "accession": "GCA_001816165.1", "taxid": 1908236, "species_taxid": 1908236, "relation_to_type": "type", "validated": true, "ani": 82.9357, "matched_fragments": 970, "total_fragments": 1535, "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": 82.897, "matched_fragments": 1042, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter jeongseonensis", "strain": "strain=BT683", "accession": "GCA_015694725.1", "taxid": 2791027, "species_taxid": 2791027, "relation_to_type": "type", "validated": true, "ani": 82.3384, "matched_fragments": 1021, "total_fragments": 1535, "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": 81.3703, "matched_fragments": 918, "total_fragments": 1535, "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": 80.9537, "matched_fragments": 882, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter piscis", "strain": "strain=NST-14", "accession": "GCA_018760735.1", "taxid": 2839984, "species_taxid": 2839984, "relation_to_type": "type", "validated": true, "ani": 79.1877, "matched_fragments": 692, "total_fragments": 1535, "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": 78.7419, "matched_fragments": 619, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014640435.1", "gtdb_species": "s__Hymenobacter frigidus", "ani": 100.0, "matched_fragments": 1526, "total_fragments": 1535, "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_012275535.1", "gtdb_species": "s__Hymenobacter artigasi", "ani": 83.9314, "matched_fragments": 1131, "total_fragments": 1535, "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_018967845.1", "gtdb_species": "s__Hymenobacter sp018967845", "ani": 83.7567, "matched_fragments": 1118, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015694525.1", "gtdb_species": "s__Hymenobacter ruricola", "ani": 83.4783, "matched_fragments": 1055, "total_fragments": 1535, "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": 83.337, "matched_fragments": 1061, "total_fragments": 1535, "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_001816145.1", "gtdb_species": "s__Hymenobacter lapidarius", "ani": 83.033, "matched_fragments": 1004, "total_fragments": 1535, "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_001816165.1", "gtdb_species": "s__Hymenobacter glacialis", "ani": 82.9457, "matched_fragments": 969, "total_fragments": 1535, "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_001507645.1", "gtdb_species": "s__Hymenobacter sedentarius", "ani": 82.8794, "matched_fragments": 1046, "total_fragments": 1535, "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": 82.699, "matched_fragments": 1024, "total_fragments": 1535, "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_015694725.1", "gtdb_species": "s__Hymenobacter jeongseonensis", "ani": 82.3285, "matched_fragments": 1022, "total_fragments": 1535, "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_900115775.1", "gtdb_species": "s__Hymenobacter arizonensis", "ani": 81.9782, "matched_fragments": 1033, "total_fragments": 1535, "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_017571495.1", "gtdb_species": "s__Hymenobacter negativus", "ani": 81.8179, "matched_fragments": 1000, "total_fragments": 1535, "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": 81.3778, "matched_fragments": 917, "total_fragments": 1535, "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": 5095981.0, "gc_content": 60.5, "coding_genes": 4057.5, "rRNA16S_genes": 3.0, "tRNA_genes": 43.5, "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", "frigidus" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }