{ "type": "genome", "identifier": "GCF_003860345.1", "organism": "Caenibius tardaugens NBRC 16725", "title": "Caenibius tardaugens NBRC 16725", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003860345.1", "bioproject": "PRJNA224116", "biosample": "SAMD00041832", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1219035", "species_taxid": "169176", "organism_name": "Caenibius tardaugens NBRC 16725", "infraspecific_name": "strain=NBRC 16725", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/04", "asm_name": "ASM386034v1", "asm_submitter": "CSIC", "gbrs_paired_asm": "GCA_003860345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/860/345/GCF_003860345.1_ASM386034v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4358096", "genome_size_ungapped": "4358096", "gc_percent": "61.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003860345.1-RS_2024_05_21", "annotation_date": "2024-05-21", "total_gene_count": "4126", "protein_coding_gene_count": "4007", "non_coding_gene_count": "58", "pubmed_id": "30938330" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-04", "dateModified": "2018-12-04", "datePublished": "2018-12-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Caenibius tardaugens NBRC 16725" ], "sample_taxid": [ "1219035" ], "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": "1.209 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)": "4358096", "Number of Sequences": "1", "Longest Sequences (bp)": "4358096", "N50 (bp)": "4358096", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.2", "Number of CDSs": "4094", "Average Protein Length": "318.9", "Coding Ratio (%)": "89.9", "Number of rRNAs": "6", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Caenibius tardaugens", "strain": "strain=NBRC 16725", "accession": "GCA_003860345.1", "taxid": 169176, "species_taxid": 169176, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1449, "total_fragments": 1452, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Caenibius tardaugens", "strain": "strain=NBRC 16725", "accession": "GCA_000466945.1", "taxid": 169176, "species_taxid": 169176, "relation_to_type": "type", "validated": true, "ani": 99.9653, "matched_fragments": 1403, "total_fragments": 1452, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Novosphingobium arvoryzae", "strain": "strain=KCTC 32422", "accession": "GCA_014652615.1", "taxid": 1256514, "species_taxid": 1256514, "relation_to_type": "type", "validated": true, "ani": 78.2997, "matched_fragments": 326, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium kunmingense", "strain": "strain=CGMCC 1.12274", "accession": "GCA_002813245.1", "taxid": 1211806, "species_taxid": 1211806, "relation_to_type": "type", "validated": true, "ani": 78.2321, "matched_fragments": 278, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium olei", "strain": "strain=TW-4", "accession": "GCA_012927405.1", "taxid": 2728851, "species_taxid": 2728851, "relation_to_type": "type", "validated": true, "ani": 78.1021, "matched_fragments": 313, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium jiangmenense", "strain": "strain=1Y9A", "accession": "GCA_015694345.1", "taxid": 2791981, "species_taxid": 2791981, "relation_to_type": "type", "validated": true, "ani": 78.0881, "matched_fragments": 300, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania soli", "strain": "strain=6D36", "accession": "GCA_015529805.1", "taxid": 2782568, "species_taxid": 2782568, "relation_to_type": "type", "validated": true, "ani": 78.0353, "matched_fragments": 199, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania gaetbuli", "strain": "strain=DSM 16225", "accession": "GCA_009827315.1", "taxid": 266952, "species_taxid": 266952, "relation_to_type": "type", "validated": true, "ani": 77.99, "matched_fragments": 233, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter aerophilus", "strain": "strain=Ery1", "accession": "GCA_003581645.1", "taxid": 2306995, "species_taxid": 2306995, "relation_to_type": "type", "validated": true, "ani": 77.9871, "matched_fragments": 229, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter marensis", "strain": "strain=DSM 21428", "accession": "GCA_001461885.1", "taxid": 543877, "species_taxid": 543877, "relation_to_type": "type", "validated": true, "ani": 77.9368, "matched_fragments": 260, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania pacifica", "strain": "strain=NZ-96", "accession": "GCA_019857205.1", "taxid": 2860199, "species_taxid": 2860199, "relation_to_type": "type", "validated": true, "ani": 77.9165, "matched_fragments": 212, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium subterraneum", "strain": "strain=DSM 12447", "accession": "GCA_000807925.1", "taxid": 48936, "species_taxid": 48936, "relation_to_type": "type", "validated": true, "ani": 77.9164, "matched_fragments": 284, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter marensis", "strain": "strain=KCTC 22370", "accession": "GCA_001028625.1", "taxid": 543877, "species_taxid": 543877, "relation_to_type": "type", "validated": true, "ani": 77.9123, "matched_fragments": 265, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter marinus", "strain": "strain=H32", "accession": "GCA_009827515.1", "taxid": 538382, "species_taxid": 538382, "relation_to_type": "type", "validated": true, "ani": 77.9021, "matched_fragments": 268, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium subterraneum", "strain": "strain=NBRC 16086", "accession": "GCA_001598575.1", "taxid": 48936, "species_taxid": 48936, "relation_to_type": "type", "validated": true, "ani": 77.8931, "matched_fragments": 272, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium nitrogenifigens", "strain": "strain=DSM 19370", "accession": "GCA_000375445.1", "taxid": 378548, "species_taxid": 378548, "relation_to_type": "type", "validated": true, "ani": 77.8269, "matched_fragments": 254, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania qiaonensis", "strain": "strain=6D47A", "accession": "GCA_019711515.1", "taxid": 2867240, "species_taxid": 2867240, "relation_to_type": "type", "validated": true, "ani": 77.8141, "matched_fragments": 210, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium colocasiae", "strain": "strain=KCTC 32255", "accession": "GCA_014652555.1", "taxid": 1256513, "species_taxid": 1256513, "relation_to_type": "type", "validated": true, "ani": 77.7794, "matched_fragments": 301, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium huizhouense", "strain": "strain=c7", "accession": "GCA_020179475.1", "taxid": 2866625, "species_taxid": 2866625, "relation_to_type": "type", "validated": true, "ani": 77.757, "matched_fragments": 286, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania aestuarii", "strain": "strain=GH1", "accession": "GCA_019711535.1", "taxid": 2867241, "species_taxid": 2867241, "relation_to_type": "type", "validated": true, "ani": 77.7507, "matched_fragments": 207, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Croceicoccus bisphenolivorans", "strain": "strain=H4", "accession": "GCA_001634625.1", "taxid": 1783232, "species_taxid": 1783232, "relation_to_type": "type", "validated": true, "ani": 77.7261, "matched_fragments": 244, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tsuneonella suprasediminis", "strain": "strain=Ery12", "accession": "GCA_003605755.1", "taxid": 2306996, "species_taxid": 2306996, "relation_to_type": "type", "validated": true, "ani": 77.7127, "matched_fragments": 270, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania gelatinilytica", "strain": "strain=1NDH1", "accession": "GCA_019711315.1", "taxid": 2867231, "species_taxid": 2867231, "relation_to_type": "type", "validated": true, "ani": 77.6965, "matched_fragments": 223, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania aerophila", "strain": "strain=GH25", "accession": "GCA_019711555.1", "taxid": 2867242, "species_taxid": 2867242, "relation_to_type": "type", "validated": true, "ani": 77.6458, "matched_fragments": 211, "total_fragments": 1452, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003860345.1", "gtdb_species": "s__Caenibius tardaugens", "ani": 100.0, "matched_fragments": 1450, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001305965.1", "gtdb_species": "s__Caenibius sp001305965", "ani": 78.9291, "matched_fragments": 350, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius", "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_001625325.1", "gtdb_species": "s__Caenibius estronivorus", "ani": 78.7459, "matched_fragments": 428, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius", "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_005145025.1", "gtdb_species": "s__Novosphingobium sp005145025", "ani": 78.512, "matched_fragments": 345, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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_014652615.1", "gtdb_species": "s__Novosphingobium arvoryzae", "ani": 78.2743, "matched_fragments": 328, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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_014763545.1", "gtdb_species": "s__JACXVD01 sp014763545", "ani": 78.1291, 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"matched_fragments": 300, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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_017302615.1", "gtdb_species": "s__Novosphingobium sp017302615", "ani": 78.0801, "matched_fragments": 289, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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_017744735.1", "gtdb_species": "s__Caenibius sp017744735", "ani": 78.0695, "matched_fragments": 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1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009827315.1", "gtdb_species": "s__Qipengyuania gaetbuli", "ani": 77.9745, "matched_fragments": 234, "total_fragments": 1452, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania", "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_000807925.1", "gtdb_species": "s__Novosphingobium subterraneum", "ani": 77.9406, "matched_fragments": 282, "total_fragments": 1452, 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