{ "type": "genome", "identifier": "GCF_003254335.1", "organism": "Cereibacter changlensis", "title": "Cereibacter changlensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003254335.1", "bioproject": "PRJNA224116", "biosample": "SAMN05661092", "wgs_master": "QKZS00000000.1", "refseq_category": "reference genome", "taxid": "402884", "species_taxid": "402884", "organism_name": "Cereibacter changlensis", "infraspecific_name": "strain=DSM 18774", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/19", "asm_name": "ASM325433v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003254335.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/335/GCF_003254335.1_ASM325433v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4924362", "genome_size_ungapped": "4922069", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "81", "contig_count": "81", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003254335.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "4807", "protein_coding_gene_count": "4658", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-19", "dateModified": "2018-06-19", "datePublished": "2018-06-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Cereibacter changlensis" ], "sample_taxid": [ "402884" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.335 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)": "4924362", "Number of Sequences": "81", "Longest Sequences (bp)": "605698", "N50 (bp)": "277279", "Gap Ratio (%)": "0.046564", "GCcontent (%)": "68.1", "Number of CDSs": "4707", "Average Protein Length": "307.9", "Coding Ratio (%)": "88.3", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cereibacter changlensis", "strain": "strain=DSM 18774", "accession": "GCA_003254335.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1597, "total_fragments": 1601, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cereibacter changlensis", "strain": "strain=JA139", "accession": "GCA_003034985.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 99.8186, "matched_fragments": 1387, "total_fragments": 1601, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cereibacter johrii", "strain": "strain=JA192", "accession": "GCA_001720585.1", "taxid": 445629, "species_taxid": 445629, "relation_to_type": "type", "validated": true, "ani": 82.5685, "matched_fragments": 808, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter johrii", "strain": "strain=JA192", "accession": "GCA_003046325.1", "taxid": 445629, "species_taxid": 445629, "relation_to_type": "type", "validated": true, "ani": 82.5394, "matched_fragments": 884, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sphaeroides", "strain": "strain=2.4.1", "accession": "GCA_000273405.1", "taxid": 1063, "species_taxid": 1063, "relation_to_type": "type", "validated": true, "ani": 82.4426, "matched_fragments": 891, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sphaeroides", "strain": "strain=NBRC 12203", "accession": "GCA_007991035.1", "taxid": 1063, "species_taxid": 1063, "relation_to_type": "type", "validated": true, "ani": 82.4391, "matched_fragments": 882, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 82.3184, "matched_fragments": 815, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter azotoformans", "strain": "strain=KA25", "accession": "GCA_003050905.1", "taxid": 43057, "species_taxid": 43057, "relation_to_type": "type", "validated": true, "ani": 82.2771, "matched_fragments": 840, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter ovatus", "strain": "strain=JA234", "accession": "GCA_900207575.1", "taxid": 439529, "species_taxid": 439529, "relation_to_type": "type", "validated": true, "ani": 81.6168, "matched_fragments": 733, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter albus", "strain": "strain=SP32", "accession": "GCA_009908165.1", "taxid": 1465486, "species_taxid": 1465486, "relation_to_type": "type", "validated": true, "ani": 80.495, "matched_fragments": 744, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter albus", "strain": "strain=SP32", "accession": "GCA_009881095.1", "taxid": 1465486, "species_taxid": 1465486, "relation_to_type": "type", "validated": true, "ani": 80.4518, "matched_fragments": 760, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter mobilis", "strain": "strain=cai42", "accession": "GCA_001620265.1", "taxid": 1335048, "species_taxid": 1335048, "relation_to_type": "type", "validated": true, "ani": 80.326, "matched_fragments": 750, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 80.1381, "matched_fragments": 692, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 80.0536, "matched_fragments": 646, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 79.6334, "matched_fragments": 659, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquarius", "strain": "strain=HYN0069", "accession": "GCA_003060865.1", "taxid": 2169400, "species_taxid": 2169400, "relation_to_type": "type", "validated": true, "ani": 79.1123, "matched_fragments": 568, "total_fragments": 1601, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003034985.1", "gtdb_species": "s__Cereibacter changlensis", "ani": 99.8186, "matched_fragments": 1387, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.78", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_002407205.1", "gtdb_species": "s__Cereibacter_A sp002407205", "ani": 82.8143, "matched_fragments": 867, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_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_001720585.1", "gtdb_species": "s__Cereibacter_A johrii", "ani": 82.5734, "matched_fragments": 807, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A", "ani_circumscription_radius": 95.1736, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "97.86", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_017599285.1", "gtdb_species": "s__Cereibacter_A azotoformans", "ani": 82.4654, "matched_fragments": 738, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "95.54", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000012905.2", "gtdb_species": "s__Cereibacter_A sphaeroides", "ani": 82.463, "matched_fragments": 891, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A", "ani_circumscription_radius": 95.1736, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "96.57", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_900207575.1", "gtdb_species": "s__Cereibacter_A ovatus", "ani": 81.6266, "matched_fragments": 732, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_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_009380135.2", "gtdb_species": "s__Fertoeibacter niger", "ani": 80.5301, "matched_fragments": 750, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter", "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_009908165.1", "gtdb_species": "s__Frigidibacter albus", "ani": 80.5058, "matched_fragments": 742, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter", "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": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001620265.1", "gtdb_species": "s__Frigidibacter mobilis", "ani": 80.3153, "matched_fragments": 750, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter", "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_900110025.1", "gtdb_species": "s__Gemmobacter aquatilis", "ani": 80.1584, "matched_fragments": 690, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_014243445.1", "gtdb_species": "s__Gemmobacter_B straminiformis", "ani": 79.6575, "matched_fragments": 620, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_018798885.1", "gtdb_species": "s__Gemmobacter sp018798885", "ani": 79.648, "matched_fragments": 659, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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": "GCA_003243455.1", "gtdb_species": "s__Rhodobacter_F sphaeroides_A", "ani": 79.3996, "matched_fragments": 557, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F", "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_007859075.1", "gtdb_species": "s__Gemmobacter aquaticus", "ani": 79.1445, "matched_fragments": 515, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_003060865.1", "gtdb_species": "s__Gemmobacter_B sp003060865", "ani": 79.1372, "matched_fragments": 565, "total_fragments": 1601, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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": -0.046, "cell_length": 0.477, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 29.5, "optimum_ph": 6.75, "genome_size": 4924362.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Cereibacter", "changlensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }