{ "type": "genome", "identifier": "GCF_008629685.1", "organism": "Adhaeribacter rhizoryzae", "title": "Adhaeribacter rhizoryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Dongguk University, Biomedi Campus", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008629685.1", "bioproject": "PRJNA224116", "biosample": "SAMN12687949", "wgs_master": "VWSF00000000.1", "refseq_category": "reference genome", "taxid": "2607907", "species_taxid": "2607907", "organism_name": "Adhaeribacter rhizoryzae", "infraspecific_name": "strain=DK36", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/20", "asm_name": "ASM862968v1", "asm_submitter": "Dongguk University, Biomedi Campus", "gbrs_paired_asm": "GCA_008629685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/629/685/GCF_008629685.1_ASM862968v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6518791", "genome_size_ungapped": "6518398", "gc_percent": "43.500000", "replicon_count": "0", "scaffold_count": "53", "contig_count": "53", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008629685.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5287", "protein_coding_gene_count": "5197", "non_coding_gene_count": "43", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-20", "dateModified": "2019-09-20", "datePublished": "2019-09-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Adhaeribacter rhizoryzae" ], "sample_taxid": [ "2607907" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.834 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)": "6518791", "Number of Sequences": "53", "Longest Sequences (bp)": "787700", "N50 (bp)": "217801", "Gap Ratio (%)": "0.006029", "GCcontent (%)": "43.3", "Number of CDSs": "5174", "Average Protein Length": "347.2", "Coding Ratio (%)": "82.7", "Number of rRNAs": "3", "Number of tRNAs": "38", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Adhaeribacter rhizoryzae", "strain": "strain=DK36", "accession": "GCA_008629685.1", "taxid": 2607907, "species_taxid": 2607907, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2142, "total_fragments": 2144, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Adhaeribacter aerolatus", "strain": "strain=NBRC 106133", "accession": "GCA_007991635.1", "taxid": 670289, "species_taxid": 670289, "relation_to_type": "type", "validated": true, "ani": 84.8993, "matched_fragments": 1488, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Adhaeribacter swui", "strain": "strain=KCTC 52873", "accession": "GCA_014217805.1", "taxid": 2086471, "species_taxid": 2086471, "relation_to_type": "type", "validated": true, "ani": 77.4892, "matched_fragments": 506, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Adhaeribacter aquaticus", "strain": "strain=DSM 16391", "accession": "GCA_000473365.1", "taxid": 299567, "species_taxid": 299567, "relation_to_type": "type", "validated": true, "ani": 77.4109, "matched_fragments": 352, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Adhaeribacter pallidiroseus", "strain": "strain=HMF7616", "accession": "GCA_003340495.1", "taxid": 2072847, "species_taxid": 2072847, "relation_to_type": "type", "validated": true, "ani": 77.1408, "matched_fragments": 414, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Adhaeribacter radiodurans", "strain": "strain=KUDC8001", "accession": "GCA_014075995.1", "taxid": 2745197, "species_taxid": 2745197, "relation_to_type": "type", "validated": true, "ani": 77.0221, "matched_fragments": 445, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Adhaeribacter arboris", "strain": "strain=HMF7605", "accession": "GCA_003023845.1", "taxid": 2072846, "species_taxid": 2072846, "relation_to_type": "type", "validated": true, "ani": 76.9592, "matched_fragments": 405, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter silvestris", "strain": "strain=XAAS-R86T", "accession": "GCA_020907275.1", "taxid": 2305183, "species_taxid": 2305183, "relation_to_type": "type", "validated": true, "ani": 76.5679, "matched_fragments": 73, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Adhaeribacter soli", "strain": "strain=MA2", "accession": "GCA_008727925.1", "taxid": 2607655, "species_taxid": 2607655, "relation_to_type": "type", "validated": true, "ani": 76.5085, "matched_fragments": 212, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter ruber", "strain": "strain=JC213", "accession": "GCA_023630205.1", "taxid": 1343895, "species_taxid": 1343895, "relation_to_type": "type", "validated": true, "ani": 76.23, "matched_fragments": 104, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter deserti", "strain": "strain=JC215", "accession": "GCA_023630255.1", "taxid": 1343896, "species_taxid": 1343896, "relation_to_type": "type", "validated": true, "ani": 76.1326, "matched_fragments": 106, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rufibacter sediminis", "strain": "strain=CGMCC 1.16289", "accession": "GCA_024436355.1", "taxid": 2762756, "species_taxid": 2762756, "relation_to_type": "type", "validated": true, "ani": 76.0225, "matched_fragments": 130, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter arcticus", "strain": "strain=2b14", "accession": "GCA_003284895.1", "taxid": 2080288, "species_taxid": 2080288, "relation_to_type": "type", "validated": true, "ani": 75.9855, "matched_fragments": 136, "total_fragments": 2144, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008629685.1", "gtdb_species": "s__Adhaeribacter rhizoryzae", "ani": 100.0, "matched_fragments": 2142, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_007991635.1", "gtdb_species": "s__Adhaeribacter aerolatus", "ani": 84.904, "matched_fragments": 1488, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_014217805.1", "gtdb_species": "s__Adhaeribacter swui", "ani": 77.4955, "matched_fragments": 505, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_000473365.1", "gtdb_species": "s__Adhaeribacter aquaticus", "ani": 77.3868, "matched_fragments": 355, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_003340495.1", "gtdb_species": "s__Adhaeribacter pallidiroseus", "ani": 77.1451, "matched_fragments": 415, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_014075995.1", "gtdb_species": "s__Adhaeribacter radiodurans", "ani": 77.0166, "matched_fragments": 446, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_003023845.1", "gtdb_species": "s__Adhaeribacter arboris", "ani": 76.9584, "matched_fragments": 406, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter", "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_008727925.1", "gtdb_species": "s__Adhaeribacter_A soli", "ani": 76.5085, "matched_fragments": 212, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter_A", "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_001310085.1", "gtdb_species": "s__Rufibacter tibetensis", "ani": 76.2205, "matched_fragments": 104, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter", "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_003284895.1", "gtdb_species": "s__Pontibacter sp003284895", "ani": 75.9855, "matched_fragments": 136, "total_fragments": 2144, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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": -0.101, "cell_length": 0.306, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 30.375, "optimum_ph": 7.083, "genome_size": 5167491.0, "gc_content": 39.6, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "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": [ "Adhaeribacter", "rhizoryzae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }