{ "type": "genome", "identifier": "GCF_003967075.1", "organism": "Sphingobium amiense", "title": "Sphingobium amiense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ibaraki University College of Agriculture", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003967075.1", "bioproject": "PRJNA224116", "biosample": "SAMD00116355", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "135719", "species_taxid": "135719", "organism_name": "Sphingobium amiense", "infraspecific_name": "strain=DSM 16289", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/13", "asm_name": "ASM396707v1", "asm_submitter": "Ibaraki University College of Agriculture", "gbrs_paired_asm": "GCA_003967075.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/967/075/GCF_003967075.1_ASM396707v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4773922", "genome_size_ungapped": "4773922", "gc_percent": "64.500000", "replicon_count": "7", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003967075.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "4680", "protein_coding_gene_count": "4545", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-13", "dateModified": "2018-10-13", "datePublished": "2018-10-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobium amiense" ], "sample_taxid": [ "135719" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.312 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)": "4773922", "Number of Sequences": "7", "Longest Sequences (bp)": "4221764", "N50 (bp)": "4221764", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.6", "Number of CDSs": "4642", "Average Protein Length": "312.1", "Coding Ratio (%)": "91.1", "Number of rRNAs": "6", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobium amiense", "strain": "strain=DSM 16289", "accession": "GCA_003967075.1", "taxid": 135719, "species_taxid": 135719, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1580, "total_fragments": 1588, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobium amiense", "strain": "strain=NBRC 102518", "accession": "GCA_001591305.1", "taxid": 135719, "species_taxid": 135719, "relation_to_type": "type", "validated": true, "ani": 99.9195, "matched_fragments": 1448, "total_fragments": 1588, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobium cloacae", "strain": "strain=JCM 10874", "accession": "GCA_002355855.1", "taxid": 120107, "species_taxid": 120107, "relation_to_type": "type", "validated": true, "ani": 84.6322, "matched_fragments": 782, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium cloacae", "strain": "strain=NBRC 102517", "accession": "GCA_001591285.1", "taxid": 120107, "species_taxid": 120107, "relation_to_type": "type", "validated": true, "ani": 84.5293, "matched_fragments": 734, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium indicum", "strain": "strain=B90A", "accession": "GCA_000264945.2", "taxid": 332055, "species_taxid": 332055, "relation_to_type": "type", "validated": true, "ani": 83.5158, "matched_fragments": 708, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium cupriresistens", "strain": "strain=CCTCC AB 2011146", "accession": "GCA_004152865.1", "taxid": 1132417, "species_taxid": 1132417, "relation_to_type": "type", "validated": true, "ani": 83.3878, "matched_fragments": 760, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium limneticum", "strain": "strain=DSM 25076", "accession": "GCA_008710155.1", "taxid": 1007511, "species_taxid": 1007511, "relation_to_type": "type", "validated": true, "ani": 83.2094, "matched_fragments": 782, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium yanoikuyae", "strain": "strain=ATCC 51230", "accession": "GCA_000315525.1", "taxid": 13690, "species_taxid": 13690, "relation_to_type": "suspected-type", "validated": true, "ani": 83.1894, "matched_fragments": 785, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium ummariense", "strain": "strain=RL-3", "accession": "GCA_000447205.1", "taxid": 420994, "species_taxid": 420994, "relation_to_type": "type", "validated": true, "ani": 83.0652, "matched_fragments": 726, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium lactosutens", "strain": "strain=DS20", "accession": "GCA_000445105.1", "taxid": 522773, "species_taxid": 522773, "relation_to_type": "type", "validated": true, "ani": 83.0078, "matched_fragments": 771, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium psychrophilum", "strain": "strain=AR-3-1", "accession": "GCA_012927105.1", "taxid": 2728834, "species_taxid": 2728834, "relation_to_type": "type", "validated": true, "ani": 82.7068, "matched_fragments": 779, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium abikonense", "strain": "strain=NBRC 16140", "accession": "GCA_001598335.1", "taxid": 86193, "species_taxid": 86193, "relation_to_type": "type", "validated": true, "ani": 82.4579, "matched_fragments": 699, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium terrigena", "strain": "strain=EO9", "accession": "GCA_003591655.1", "taxid": 2304063, "species_taxid": 2304063, "relation_to_type": "type", "validated": true, "ani": 82.1875, "matched_fragments": 728, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas cavernae", "strain": "strain=K2R01-6", "accession": "GCA_003590775.1", "taxid": 2320861, "species_taxid": 2320861, "relation_to_type": "type", "validated": true, "ani": 78.5271, "matched_fragments": 359, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas flavalba", "strain": "strain=ZLT-5", "accession": "GCA_004796535.1", "taxid": 2559804, "species_taxid": 2559804, "relation_to_type": "type", "validated": true, "ani": 78.2409, "matched_fragments": 372, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas aracearum", "strain": "strain=WZY 27", "accession": "GCA_003345355.1", "taxid": 2283317, "species_taxid": 2283317, "relation_to_type": "type", "validated": true, "ani": 78.2035, "matched_fragments": 369, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas profundi", "strain": "strain=LMO-1", "accession": "GCA_009739515.1", "taxid": 2681549, "species_taxid": 2681549, "relation_to_type": "type", "validated": true, "ani": 77.9862, "matched_fragments": 425, "total_fragments": 1588, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003967075.1", "gtdb_species": "s__Sphingobium amiense", "ani": 100.0, "matched_fragments": 1577, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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": "conclusive" }, { "accession": "GCA_003248505.1", "gtdb_species": "s__Sphingobium sp003248505", "ani": 85.4517, "matched_fragments": 738, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_013911745.1", "gtdb_species": "s__Sphingobium sp013911745", "ani": 85.2411, "matched_fragments": 567, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_001556865.1", "gtdb_species": "s__Sphingobium sp001556865", "ani": 84.6814, "matched_fragments": 741, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_009720145.1", "gtdb_species": "s__Sphingobium sp009720145", "ani": 84.1633, "matched_fragments": 779, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_002457415.1", "gtdb_species": "s__Sphingobium sp002457415", "ani": 83.8729, "matched_fragments": 638, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_001650725.1", "gtdb_species": "s__Sphingobium sp001650725", "ani": 83.8253, "matched_fragments": 766, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008710155.1", "gtdb_species": "s__Sphingobium limneticum", "ani": 83.1957, "matched_fragments": 784, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000445105.1", "gtdb_species": "s__Sphingobium lactosutens", "ani": 83.0356, "matched_fragments": 771, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.3976, "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_000508185.1", "gtdb_species": "s__Sphingobium sp000508185", "ani": 82.9935, "matched_fragments": 724, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_013375535.1", "gtdb_species": "s__Sphingobium sp013375535", "ani": 82.7072, "matched_fragments": 763, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_001598335.1", "gtdb_species": "s__Sphingobium abikonense", "ani": 82.4688, "matched_fragments": 698, "total_fragments": 1588, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.3976, "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": -0.278, "cell_length": 0.094, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 28.868, "optimum_ph": 7.125, "genome_size": 4539760.0, "gc_content": 64.739, "coding_genes": 4211.023, "rRNA16S_genes": 2.333, "tRNA_genes": 53.785, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Sphingobium", "amiense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }