{ "type": "genome", "identifier": "GCF_030409895.1", "organism": "Cyclobacterium jeungdonense", "title": "Cyclobacterium jeungdonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The Institute of Microbiology of the Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030409895.1", "bioproject": "PRJNA224116", "biosample": "SAMN35653676", "wgs_master": "JAUFQS000000000.1", "refseq_category": "na", "taxid": "708087", "species_taxid": "708087", "organism_name": "Cyclobacterium jeungdonense", "infraspecific_name": "strain=CECT 7706", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/07/05", "asm_name": "ASM3040989v1", "asm_submitter": "The Institute of Microbiology of the Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_030409895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/409/895/GCF_030409895.1_ASM3040989v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5801294", "genome_size_ungapped": "5800720", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "51", "contig_count": "51", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030409895.1-RS_2024_07_07", "annotation_date": "2024-07-07", "total_gene_count": "4689", "protein_coding_gene_count": "4602", "non_coding_gene_count": "54", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-07-05", "dateModified": "2023-07-05", "datePublished": "2023-07-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Cyclobacterium jeungdonense" ], "sample_taxid": [ "708087" ], "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": "1.649 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)": "5801294", "Number of Sequences": "51", "Longest Sequences (bp)": "1341920", "N50 (bp)": "381090", "Gap Ratio (%)": "0.009894", "GCcontent (%)": "44.0", "Number of CDSs": "4572", "Average Protein Length": "369.3", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cyclobacterium jeungdonense", "strain": "strain=KCTC 23150", "accession": "GCA_010994275.1", "taxid": 708087, "species_taxid": 708087, "relation_to_type": "type", "validated": true, "ani": 99.9991, "matched_fragments": 1903, "total_fragments": 1911, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cyclobacterium salsum", "strain": "strain=SYSU L10167", "accession": "GCA_010119245.1", "taxid": 2666329, "species_taxid": 2666329, "relation_to_type": "type", "validated": true, "ani": 86.3282, "matched_fragments": 1505, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium roseum", "strain": "strain=SYSU L10180", "accession": "GCA_010119225.1", "taxid": 2666137, "species_taxid": 2666137, "relation_to_type": "type", "validated": true, "ani": 86.0451, "matched_fragments": 1470, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium plantarum", "strain": "strain=GBPx2", "accession": "GCA_011290685.1", "taxid": 2716263, "species_taxid": 2716263, "relation_to_type": "type", "validated": true, "ani": 80.0529, "matched_fragments": 760, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium xiamenense", "strain": "strain=CGMCC 1.12432", "accession": "GCA_009467825.1", "taxid": 1297121, "species_taxid": 1297121, "relation_to_type": "type", "validated": true, "ani": 79.5911, "matched_fragments": 797, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium marinum", "strain": "strain=DSM 745", "accession": "GCA_000222485.1", "taxid": 104, "species_taxid": 104, "relation_to_type": "type", "validated": true, "ani": 77.1262, "matched_fragments": 257, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lunatimonas salinarum", "strain": "strain=KCTC 42988", "accession": "GCA_017811155.1", "taxid": 1774590, "species_taxid": 1774590, "relation_to_type": "type", "validated": true, "ani": 76.2101, "matched_fragments": 138, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Echinicola salinicaeni", "strain": "strain=P51", "accession": "GCA_014280965.1", "taxid": 2762757, "species_taxid": 2762757, "relation_to_type": "type", "validated": true, "ani": 75.4545, "matched_fragments": 72, "total_fragments": 1911, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010994275.1", "gtdb_species": "s__Cyclobacterium jeungdonense", "ani": 99.9991, "matched_fragments": 1903, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010119245.1", "gtdb_species": "s__Cyclobacterium sp010119245", "ani": 86.3317, "matched_fragments": 1505, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010119225.1", "gtdb_species": "s__Cyclobacterium sp010119225", "ani": 86.0486, "matched_fragments": 1469, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_010993705.1", "gtdb_species": 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"matched_fragments": 729, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "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_009467825.1", "gtdb_species": "s__Cyclobacterium xiamenense", "ani": 79.5849, "matched_fragments": 798, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000222485.1", "gtdb_species": "s__Cyclobacterium marinum", "ani": 77.127, "matched_fragments": 256, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017811155.1", "gtdb_species": "s__Lunatimonas salinarum", "ani": 76.2101, "matched_fragments": 138, "total_fragments": 1911, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas", "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": -0.437, "cell_length": -0.013, "doubling_h": null, "growth_tmp": 24.333, "optimum_tmp": 25.666, "optimum_ph": 7.5, "genome_size": 5929341.875, "gc_content": 38.202, "coding_genes": 4875.833, "rRNA16S_genes": 3.5, "tRNA_genes": 39.0, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Cyclobacterium", "jeungdonense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }