{ "type": "genome", "identifier": "GCF_008711285.1", "organism": "Roseibium aquae", "title": "Roseibium aquae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Sun Yat-sen University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008711285.1", "bioproject": "PRJNA224116", "biosample": "SAMN12688460", "wgs_master": "VXDC00000000.1", "refseq_category": "reference genome", "taxid": "1323746", "species_taxid": "1323746", "organism_name": "Roseibium aquae", "infraspecific_name": "strain=CGMCC 1.12426", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/27", "asm_name": "ASM871128v1", "asm_submitter": "Sun Yat-sen University", "gbrs_paired_asm": "GCA_008711285.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/711/285/GCF_008711285.1_ASM871128v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4406902", "genome_size_ungapped": "4406902", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008711285.1-RS_2024_04_25", "annotation_date": "2024-04-25", "total_gene_count": "4112", "protein_coding_gene_count": "4009", "non_coding_gene_count": "53", "pubmed_id": "24867169" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-27", "dateModified": "2019-09-27", "datePublished": "2019-09-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Roseibium aquae" ], "sample_taxid": [ "1323746" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Dasugan Lake" ], "sample_host_location_id": [], "data_size": "1.238 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)": "4406902", "Number of Sequences": "37", "Longest Sequences (bp)": "831453", "N50 (bp)": "344329", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.0", "Number of CDSs": "4075", "Average Protein Length": "316.7", "Coding Ratio (%)": "87.9", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseibium aquae", "strain": "strain=CGMCC 1.12426", "accession": "GCA_008711285.1", "taxid": 1323746, "species_taxid": 1323746, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1447, "total_fragments": 1453, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseibium aquae", "strain": "strain=CGMCC 1.12426", "accession": "GCA_014637575.1", "taxid": 1323746, "species_taxid": 1323746, "relation_to_type": "type", "validated": true, "ani": 99.9971, "matched_fragments": 1433, "total_fragments": 1453, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseibium hamelinense", "strain": "strain=NBRC 16783", "accession": "GCA_009711505.1", "taxid": 150831, "species_taxid": 150831, "relation_to_type": "type", "validated": true, "ani": 78.5659, "matched_fragments": 299, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium hamelinense", "strain": "strain=ATCC BAA-252", "accession": "GCA_007830545.1", "taxid": 150831, "species_taxid": 150831, "relation_to_type": "type", "validated": true, "ani": 78.4606, "matched_fragments": 311, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium denhamense", "strain": "strain=JCM 10543", "accession": "GCA_009711415.1", "taxid": 76305, "species_taxid": 76305, "relation_to_type": "type", "validated": true, "ani": 78.1071, "matched_fragments": 294, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium aestuarii", "strain": "strain=SYSU M00256-3", "accession": "GCA_008477545.1", "taxid": 2600299, "species_taxid": 2600299, "relation_to_type": "type", "validated": true, "ani": 77.9997, "matched_fragments": 355, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium alexandrii", "strain": "strain=DFL-11", "accession": "GCA_000158095.2", "taxid": 388408, "species_taxid": 388408, "relation_to_type": "type", "validated": true, "ani": 77.9321, "matched_fragments": 304, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium sediminis", "strain": "strain=KCTC 52373", "accession": "GCA_008711325.1", "taxid": 1775174, "species_taxid": 1775174, "relation_to_type": "type", "validated": true, "ani": 77.85, "matched_fragments": 354, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001418225.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 77.7829, "matched_fragments": 285, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium litorale", "strain": "strain=4C16A", "accession": "GCA_014842915.1", "taxid": 2803841, "species_taxid": 2803841, "relation_to_type": "type", "validated": true, "ani": 77.7063, "matched_fragments": 323, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium aggregatum", "strain": "strain=IAM 12614", "accession": "GCA_000168975.1", "taxid": 187304, "species_taxid": 187304, "relation_to_type": "suspected-type", "validated": true, "ani": 77.7011, "matched_fragments": 378, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter phragmitetus", "strain": "strain=NCTC13350", "accession": "GCA_900454465.1", "taxid": 121719, "species_taxid": 121719, "relation_to_type": "suspected-type", "validated": true, "ani": 77.68, "matched_fragments": 299, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium marinum", "strain": "strain=DSM 17023", "accession": "GCA_002906165.1", "taxid": 281252, "species_taxid": 281252, "relation_to_type": "type", "validated": true, "ani": 77.6745, "matched_fragments": 381, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter phragmitetus", "strain": "strain=DSM 14782", "accession": "GCA_000382365.1", "taxid": 121719, "species_taxid": 121719, "relation_to_type": "suspected-type", "validated": true, "ani": 77.5375, "matched_fragments": 295, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stappia albiluteola", "strain": "strain=F7233", "accession": "GCA_014050225.1", "taxid": 2758565, "species_taxid": 2758565, "relation_to_type": "type", "validated": true, "ani": 77.4318, "matched_fragments": 247, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jiella sonneratiae", "strain": "strain=MQZ13P-4", "accession": "GCA_017353515.1", "taxid": 2816856, "species_taxid": 2816856, "relation_to_type": "type", "validated": true, "ani": 76.6605, "matched_fragments": 129, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium mongolense", "strain": "strain=USDA 1844", "accession": "GCA_007827505.1", "taxid": 57676, "species_taxid": 57676, "relation_to_type": "type", "validated": true, "ani": 76.6264, "matched_fragments": 98, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium iners", "strain": "strain=DSM 19015", "accession": "GCA_022179305.1", "taxid": 418707, "species_taxid": 418707, "relation_to_type": "type", "validated": true, "ani": 76.2216, "matched_fragments": 83, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium mongolense", "strain": "strain=USDA 1844", "accession": "GCA_000419765.1", "taxid": 57676, "species_taxid": 57676, "relation_to_type": "type", "validated": true, "ani": 76.1859, "matched_fragments": 99, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nonmethylotrophicum", "strain": "strain=6HR-1", "accession": "GCA_004745635.1", "taxid": 1141884, "species_taxid": 1141884, "relation_to_type": "type", "validated": true, "ani": 76.0712, "matched_fragments": 136, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium longum", "strain": "strain=DSM 23933", "accession": "GCA_022179385.1", "taxid": 767694, "species_taxid": 767694, "relation_to_type": "type", "validated": true, "ani": 75.6674, "matched_fragments": 101, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008711285.1", "gtdb_species": "s__Roseibium aquae", "ani": 100.0, "matched_fragments": 1444, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_007830545.1", "gtdb_species": "s__Roseibium hamelinense", "ani": 78.4649, "matched_fragments": 309, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014692675.1", "gtdb_species": "s__Roseibium aggregatum_C", "ani": 78.0916, "matched_fragments": 412, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_002237595.1", "gtdb_species": "s__Roseibium sp002237595", "ani": 78.046, "matched_fragments": 401, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_000192745.1", "gtdb_species": "s__Polymorphum gilvum", "ani": 78.0056, "matched_fragments": 336, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum", "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_001999245.1", "gtdb_species": "s__Roseibium aggregatum_A", "ani": 77.9728, "matched_fragments": 347, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "96.85", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_000158095.2", "gtdb_species": "s__Roseibium alexandrii", "ani": 77.9231, "matched_fragments": 304, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.43", "min_intra_species_ani": "97.43", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008711325.1", "gtdb_species": "s__Roseibium sediminis", "ani": 77.85, "matched_fragments": 354, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_017309185.1", "gtdb_species": "s__Roseibium aggregatum_B", "ani": 77.8483, "matched_fragments": 375, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_017643215.1", "gtdb_species": "s__Roseibium sp017643215", "ani": 77.8384, "matched_fragments": 419, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_009915765.1", "gtdb_species": "s__Pannonibacter sp009915765", "ani": 77.7662, "matched_fragments": 329, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003075075.1", "gtdb_species": "s__Roseibium sp003075075", "ani": 77.7428, "matched_fragments": 396, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_008107695.1", "gtdb_species": "s__Roseibium sp008107695", "ani": 77.7309, "matched_fragments": 357, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_000168975.1", "gtdb_species": "s__Roseibium aggregatum", "ani": 77.7191, "matched_fragments": 375, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_014842915.1", "gtdb_species": "s__Roseibium litorale", "ani": 77.7165, "matched_fragments": 322, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_002906165.1", "gtdb_species": "s__Roseibium marinum", "ani": 77.691, "matched_fragments": 379, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_008107755.1", "gtdb_species": "s__Roseibium sp008107755", "ani": 77.6619, "matched_fragments": 362, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_000382365.1", "gtdb_species": "s__Pannonibacter phragmitetus", "ani": 77.5472, "matched_fragments": 294, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001624695.1", "gtdb_species": "s__Roseibium sp001624695", "ani": 77.529, "matched_fragments": 347, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_000419765.1", "gtdb_species": "s__Rhizobium mongolense", "ani": 76.1457, "matched_fragments": 100, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 96.0481, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "97.63", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.80", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 26.0, "optimum_tmp": 28.0, "optimum_ph": null, "genome_size": 4782713.5, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Roseibium", "aquae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }