{ "type": "genome", "identifier": "GCF_023051225.1", "organism": "Sphingobium agri", "title": "Sphingobium agri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chung-Ang University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023051225.1", "bioproject": "PRJNA224116", "biosample": "SAMN27409403", "wgs_master": "JALKHS000000000.1", "refseq_category": "reference genome", "taxid": "2933566", "species_taxid": "2933566", "organism_name": "Sphingobium agri", "infraspecific_name": "strain=MAH-33", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/18", "asm_name": "ASM2305122v1", "asm_submitter": "Chung-Ang University", "gbrs_paired_asm": "GCA_023051225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/051/225/GCF_023051225.1_ASM2305122v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3908768", "genome_size_ungapped": "3908768", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023051225.1-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "3794", "protein_coding_gene_count": "3714", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-18", "dateModified": "2022-04-18", "datePublished": "2022-04-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobium agri" ], "sample_taxid": [ "2933566" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Anseong" ], "sample_host_location_id": [], "data_size": "1.092 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)": "3908768", "Number of Sequences": "28", "Longest Sequences (bp)": "1457875", "N50 (bp)": "292691", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.2", "Number of CDSs": "3728", "Average Protein Length": "312.9", "Coding Ratio (%)": "89.5", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobium herbicidovorans", "strain": "strain=NBRC 16415", "accession": "GCA_000632125.2", "taxid": 76947, "species_taxid": 76947, "relation_to_type": "type", "validated": true, "ani": 83.2998, "matched_fragments": 770, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium herbicidovorans", "strain": "strain=MH", "accession": "GCA_002080435.1", "taxid": 76947, "species_taxid": 76947, "relation_to_type": "type", "validated": true, "ani": 83.2997, "matched_fragments": 784, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium herbicidovorans", "strain": "strain=NBRC 16415", "accession": "GCA_001598535.1", "taxid": 76947, "species_taxid": 76947, "relation_to_type": "type", "validated": true, "ani": 83.265, "matched_fragments": 765, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium quisquiliarum", "strain": "strain=P25", "accession": "GCA_000445065.1", "taxid": 538379, "species_taxid": 538379, "relation_to_type": "type", "validated": true, "ani": 83.1996, "matched_fragments": 687, "total_fragments": 1288, "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": 82.4806, "matched_fragments": 652, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium fuliginis", "strain": "strain=DSM 18781", "accession": "GCA_004152845.1", "taxid": 336203, "species_taxid": 336203, "relation_to_type": "type", "validated": true, "ani": 82.413, "matched_fragments": 649, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium estronivorans", "strain": "strain=AXB", "accession": "GCA_008692605.1", "taxid": 1577690, "species_taxid": 1577690, "relation_to_type": "type", "validated": true, "ani": 82.4112, "matched_fragments": 634, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium fuliginis", "strain": "strain=CCM 7327", "accession": "GCA_014636045.1", "taxid": 336203, "species_taxid": 336203, "relation_to_type": "type", "validated": true, "ani": 82.3823, "matched_fragments": 658, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chungbukense", "strain": "strain=DJ77", "accession": "GCA_001005725.1", "taxid": 56193, "species_taxid": 56193, "relation_to_type": "type", "validated": true, "ani": 82.3375, "matched_fragments": 645, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium vermicomposti", "strain": "strain=DSM 21299", "accession": "GCA_011762025.1", "taxid": 529005, "species_taxid": 529005, "relation_to_type": "type", "validated": true, "ani": 82.3299, "matched_fragments": 727, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chlorophenolicum", "strain": "strain=NBRC 16172", "accession": "GCA_001598515.1", "taxid": 46429, "species_taxid": 46429, "relation_to_type": "type", "validated": true, "ani": 82.317, "matched_fragments": 569, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chlorophenolicum", "strain": "strain=NBRC 16172", "accession": "GCA_000722875.1", "taxid": 46429, "species_taxid": 46429, "relation_to_type": "type", "validated": true, "ani": 82.3164, "matched_fragments": 622, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium bisphenolivorans", "strain": "strain=YL23", "accession": "GCA_000412635.1", "taxid": 1335760, "species_taxid": 1335760, "relation_to_type": "type", "validated": true, "ani": 81.8867, "matched_fragments": 660, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium baderi", "strain": "strain=LL03", "accession": "GCA_000445145.1", "taxid": 1332080, "species_taxid": 1332080, "relation_to_type": "type", "validated": true, "ani": 81.5422, "matched_fragments": 551, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium cloacae", "strain": "strain=JCM 10874", "accession": "GCA_002355855.1", "taxid": 120107, "species_taxid": 120107, "relation_to_type": "type", "validated": true, "ani": 81.5389, "matched_fragments": 564, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium baderi", "strain": "strain=LL03", "accession": "GCA_001046655.1", "taxid": 1332080, "species_taxid": 1332080, "relation_to_type": "type", "validated": true, "ani": 81.5117, "matched_fragments": 542, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium scionense", "strain": "strain=DSM 19371", "accession": "GCA_014197035.1", "taxid": 1404341, "species_taxid": 1404341, "relation_to_type": "type", "validated": true, "ani": 81.0064, "matched_fragments": 593, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas changnyeongensis", "strain": "strain=C33", "accession": "GCA_009913435.1", "taxid": 2698679, "species_taxid": 2698679, "relation_to_type": "type", "validated": true, "ani": 77.9202, "matched_fragments": 277, "total_fragments": 1288, "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": 77.7871, "matched_fragments": 253, "total_fragments": 1288, "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": 77.7682, "matched_fragments": 296, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citri", "strain": "strain=RRHST34", "accession": "GCA_019429485.1", "taxid": 2862499, "species_taxid": 2862499, "relation_to_type": "type", "validated": true, "ani": 77.5515, "matched_fragments": 252, "total_fragments": 1288, "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": 77.4066, "matched_fragments": 290, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900218065.1", "gtdb_species": "s__Sphingobium sp900218065", "ani": 97.2475, "matched_fragments": 1023, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.42", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_015693305.1", "gtdb_species": "s__Sphingobium sp015693305", "ani": 86.5573, "matched_fragments": 960, "total_fragments": 1288, "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_001658005.1", "gtdb_species": "s__Sphingobium sp001658005", "ani": 83.4028, "matched_fragments": 802, "total_fragments": 1288, "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_002080435.1", "gtdb_species": "s__Sphingobium herbicidovorans", "ani": 83.3111, "matched_fragments": 783, "total_fragments": 1288, "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": 3, "status": "-" }, { "accession": "GCF_000445065.1", "gtdb_species": "s__Sphingobium quisquiliarum", "ani": 83.1996, "matched_fragments": 687, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "97.93", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001563285.1", "gtdb_species": "s__Sphingobium sp001563285", "ani": 82.9985, "matched_fragments": 681, "total_fragments": 1288, "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_000264945.2", "gtdb_species": "s__Sphingobium indicum", "ani": 82.4683, "matched_fragments": 653, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.64", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_008692605.1", "gtdb_species": "s__Sphingobium estronivorans", "ani": 82.4176, "matched_fragments": 633, "total_fragments": 1288, "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": 82.3807, "matched_fragments": 654, "total_fragments": 1288, "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_004152845.1", "gtdb_species": "s__Sphingobium fuliginis", "ani": 82.3772, "matched_fragments": 652, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_001005725.1", "gtdb_species": "s__Sphingobium chungbukense", "ani": 82.3112, "matched_fragments": 648, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.72", "min_intra_species_af": "0.72", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000722875.1", "gtdb_species": "s__Sphingobium chlorophenolicum", "ani": 82.3105, "matched_fragments": 622, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "95.89", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.76", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_011762025.1", "gtdb_species": "s__Sphingobium vermicomposti", "ani": 82.3084, "matched_fragments": 729, "total_fragments": 1288, "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_013375555.1", "gtdb_species": "s__Sphingobium sp013375555", "ani": 82.0699, "matched_fragments": 663, "total_fragments": 1288, "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_014873695.1", "gtdb_species": "s__Sphingobium sp014873695", "ani": 81.773, "matched_fragments": 720, "total_fragments": 1288, "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_014197035.1", "gtdb_species": "s__Sphingobium scionense", "ani": 81.0101, "matched_fragments": 592, "total_fragments": 1288, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.278, "cell_length": 0.094, "doubling_h": null, "growth_tmp": 28.352, "optimum_tmp": 28.868, "optimum_ph": 7.125, "genome_size": 4749227.887, "gc_content": 63.812, "coding_genes": 4211.023, "rRNA16S_genes": 2.333, "tRNA_genes": 53.785, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.347, "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", "agri" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }