{ "type": "genome", "identifier": "GCF_009467825.1", "organism": "Cyclobacterium xiamenense", "title": "Cyclobacterium xiamenense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Xinjiang Institute of Ecology and Geography", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009467825.1", "bioproject": "PRJNA224116", "biosample": "SAMN13053028", "wgs_master": "WIOK00000000.1", "refseq_category": "na", "taxid": "1297121", "species_taxid": "1297121", "organism_name": "Cyclobacterium xiamenense", "infraspecific_name": "strain=CGMCC 1.12432", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/11/01", "asm_name": "ASM946782v1", "asm_submitter": "Xinjiang Institute of Ecology and Geography", "gbrs_paired_asm": "GCA_009467825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/467/825/GCF_009467825.1_ASM946782v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5784474", "genome_size_ungapped": "5783706", "gc_percent": "48.500000", "replicon_count": "0", "scaffold_count": "98", "contig_count": "98", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009467825.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4612", "protein_coding_gene_count": "4534", "non_coding_gene_count": "49", "pubmed_id": "24277859" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-11-01", "dateModified": "2019-11-01", "datePublished": "2019-11-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Cyclobacterium xiamenense" ], "sample_taxid": [ "1297121" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Xiamen" ], "sample_host_location_id": [], "data_size": "1.652 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.62, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5784474", "Number of Sequences": "98", "Longest Sequences (bp)": "354620", "N50 (bp)": "154225", "Gap Ratio (%)": "0.013277", "GCcontent (%)": "48.5", "Number of CDSs": "4495", "Average Protein Length": "373.1", "Coding Ratio (%)": "87.0", "Number of rRNAs": "3", "Number of tRNAs": "41", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1880, "total_fragments": 1886, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cyclobacterium roseum", "strain": "strain=SYSU L10180", "accession": "GCA_010119225.1", "taxid": 2666137, "species_taxid": 2666137, "relation_to_type": "type", "validated": true, "ani": 80.7925, "matched_fragments": 858, "total_fragments": 1886, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium salsum", "strain": "strain=SYSU L10167", "accession": "GCA_010119245.1", "taxid": 2666329, "species_taxid": 2666329, "relation_to_type": "type", "validated": true, "ani": 80.2466, "matched_fragments": 841, "total_fragments": 1886, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium jeungdonense", "strain": "strain=KCTC 23150", "accession": "GCA_010994275.1", "taxid": 708087, "species_taxid": 708087, "relation_to_type": "type", "validated": true, "ani": 79.4002, "matched_fragments": 809, "total_fragments": 1886, "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": 79.114, "matched_fragments": 576, "total_fragments": 1886, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cyclobacterium lianum", "strain": "strain=CGMCC 1.6102", "accession": "GCA_900143075.1", "taxid": 388280, "species_taxid": 388280, "relation_to_type": "type", "validated": true, "ani": 78.3718, "matched_fragments": 503, "total_fragments": 1886, "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": 77.4596, "matched_fragments": 143, "total_fragments": 1886, "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": 77.3734, "matched_fragments": 180, "total_fragments": 1886, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.62, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009467825.1", "gtdb_species": "s__Cyclobacterium xiamenense", "ani": 100.0, "matched_fragments": 1880, "total_fragments": 1886, "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": "conclusive" }, { "accession": "GCF_010119225.1", "gtdb_species": "s__Cyclobacterium sp010119225", "ani": 80.7923, "matched_fragments": 857, "total_fragments": 1886, "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_010119245.1", "gtdb_species": "s__Cyclobacterium sp010119245", "ani": 80.2423, "matched_fragments": 842, "total_fragments": 1886, "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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79.1006, "matched_fragments": 579, "total_fragments": 1886, "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": "GCA_014762705.1", "gtdb_species": "s__Cyclobacterium sp014762705", "ani": 78.4874, "matched_fragments": 518, "total_fragments": 1886, "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_900143075.1", "gtdb_species": "s__Cyclobacterium lianum", "ani": 78.3795, "matched_fragments": 503, 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"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": "-" } ] }, "_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", "xiamenense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }