{ "type": "genome", "identifier": "GCF_021403115.1", "organism": "Sphingobium sufflavum", "title": "Sphingobium sufflavum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Huazhong Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021403115.1", "bioproject": "PRJNA224116", "biosample": "SAMN24224721", "wgs_master": "JAJSSH000000000.1", "refseq_category": "reference genome", "taxid": "1129547", "species_taxid": "1129547", "organism_name": "Sphingobium sufflavum", "infraspecific_name": "strain=HL-25", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/01/10", "asm_name": "ASM2140311v1", "asm_submitter": "Huazhong Agricultural University", "gbrs_paired_asm": "GCA_021403115.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/403/115/GCF_021403115.1_ASM2140311v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4430016", "genome_size_ungapped": "4430016", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021403115.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4119", "protein_coding_gene_count": "4008", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-01-10", "dateModified": "2022-01-10", "datePublished": "2022-01-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobium sufflavum" ], "sample_taxid": [ "1129547" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Taiwan" ], "sample_host_location_id": [], "data_size": "1.222 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)": "4430016", "Number of Sequences": "37", "Longest Sequences (bp)": "651675", "N50 (bp)": "243676", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.9", "Number of CDSs": "4076", "Average Protein Length": "316.1", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobium sufflavum", "strain": "strain=HL-25", "accession": "GCA_021403115.1", "taxid": 1129547, "species_taxid": 1129547, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1456, "total_fragments": 1458, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobium fontiphilum", "strain": "strain=DSM 29348", "accession": "GCA_014196635.1", "taxid": 944425, "species_taxid": 944425, "relation_to_type": "type", "validated": true, "ani": 79.5333, "matched_fragments": 441, "total_fragments": 1458, "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": 79.4788, "matched_fragments": 487, "total_fragments": 1458, "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": 79.3326, "matched_fragments": 481, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium amiense", "strain": "strain=NBRC 102518", "accession": "GCA_001591305.1", "taxid": 135719, "species_taxid": 135719, "relation_to_type": "type", "validated": true, "ani": 79.3192, "matched_fragments": 473, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium amiense", "strain": "strain=DSM 16289", "accession": "GCA_003967075.1", "taxid": 135719, "species_taxid": 135719, "relation_to_type": "type", "validated": true, "ani": 79.3127, "matched_fragments": 480, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium phenoxybenzoativorans", "strain": "strain=SC_3", "accession": "GCA_001757355.1", "taxid": 1592790, "species_taxid": 1592790, "relation_to_type": "type", "validated": true, "ani": 79.288, "matched_fragments": 426, "total_fragments": 1458, "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": 79.1798, "matched_fragments": 519, "total_fragments": 1458, "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": 79.1595, "matched_fragments": 502, "total_fragments": 1458, "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": 79.145, "matched_fragments": 485, "total_fragments": 1458, "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": 79.1418, "matched_fragments": 465, "total_fragments": 1458, "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": 79.0385, "matched_fragments": 446, "total_fragments": 1458, "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": 79.0093, "matched_fragments": 447, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium herbicidovorans", "strain": "strain=NBRC 16415", "accession": "GCA_000632125.2", "taxid": 76947, "species_taxid": 76947, "relation_to_type": "type", "validated": true, "ani": 78.7314, "matched_fragments": 365, "total_fragments": 1458, "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": 78.6498, "matched_fragments": 380, "total_fragments": 1458, "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": 78.5668, "matched_fragments": 385, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium xanthum", "strain": "strain=NL9", "accession": "GCA_019737615.1", "taxid": 1387165, "species_taxid": 1387165, "relation_to_type": "type", "validated": true, "ani": 78.5514, "matched_fragments": 390, "total_fragments": 1458, "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": 77.9542, "matched_fragments": 308, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas desiccabilis", "strain": "strain=DSM 16792", "accession": "GCA_014196135.1", "taxid": 429134, "species_taxid": 429134, "relation_to_type": "type", "validated": true, "ani": 77.8684, "matched_fragments": 319, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas turrisvirgatae", "strain": "strain=MCT13", "accession": "GCA_001721295.1", "taxid": 1888892, "species_taxid": 1888892, "relation_to_type": "type", "validated": true, "ani": 77.8275, "matched_fragments": 312, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas desiccabilis", "strain": "strain=CP1D", "accession": "GCA_004135605.1", "taxid": 429134, "species_taxid": 429134, "relation_to_type": "type", "validated": true, "ani": 77.8194, "matched_fragments": 321, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas sanxanigenens", "strain": "strain=NX02", "accession": "GCA_000512205.2", "taxid": 397260, "species_taxid": 397260, "relation_to_type": "type", "validated": true, "ani": 77.7249, "matched_fragments": 414, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas chungangi", "strain": "strain=CGMCC 1.13654", "accession": "GCA_013778325.1", "taxid": 2683589, "species_taxid": 2683589, "relation_to_type": "type", "validated": true, "ani": 77.5807, "matched_fragments": 328, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania proteolytica", "strain": "strain=6B39", "accession": "GCA_019711565.1", "taxid": 2867239, "species_taxid": 2867239, "relation_to_type": "type", "validated": true, "ani": 77.3964, "matched_fragments": 198, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas glacialis", "strain": "strain=CGMCC 1.8957", "accession": "GCA_014653575.1", "taxid": 658225, "species_taxid": 658225, "relation_to_type": "type", "validated": true, "ani": 77.3217, "matched_fragments": 301, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinicella ginsenosidimutans", "strain": "strain=BS-11", "accession": "GCA_007995055.1", "taxid": 1176539, "species_taxid": 1176539, "relation_to_type": "type", "validated": true, "ani": 77.1453, "matched_fragments": 241, "total_fragments": 1458, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014196635.1", "gtdb_species": "s__Sphingobium fontiphilum", "ani": 79.5353, "matched_fragments": 440, "total_fragments": 1458, "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": 79.4871, "matched_fragments": 487, "total_fragments": 1458, "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_012927105.1", "gtdb_species": "s__Sphingobium psychrophilum", "ani": 79.3323, "matched_fragments": 481, "total_fragments": 1458, "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_003967075.1", "gtdb_species": "s__Sphingobium amiense", "ani": 79.3124, "matched_fragments": 480, "total_fragments": 1458, "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": "-" }, { "accession": "GCF_001650725.1", "gtdb_species": "s__Sphingobium sp001650725", "ani": 79.312, "matched_fragments": 506, "total_fragments": 1458, "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_001757355.1", "gtdb_species": "s__Sphingobium phenoxybenzoativorans", "ani": 79.3104, "matched_fragments": 424, "total_fragments": 1458, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.17", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.74", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014203965.1", "gtdb_species": "s__Sphingobium sp014203965", "ani": 79.2647, "matched_fragments": 504, "total_fragments": 1458, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_013375535.1", "gtdb_species": "s__Sphingobium sp013375535", "ani": 79.2534, "matched_fragments": 485, "total_fragments": 1458, "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_002355855.1", "gtdb_species": "s__Sphingobium cloacae", "ani": 79.2384, "matched_fragments": 473, "total_fragments": 1458, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "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_014197035.1", "gtdb_species": "s__Sphingobium scionense", "ani": 79.179, "matched_fragments": 520, "total_fragments": 1458, "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_000722875.1", "gtdb_species": "s__Sphingobium chlorophenolicum", "ani": 79.1692, "matched_fragments": 482, "total_fragments": 1458, "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": "GCA_002457415.1", "gtdb_species": "s__Sphingobium sp002457415", "ani": 79.1611, "matched_fragments": 439, "total_fragments": 1458, "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_013822485.1", "gtdb_species": "s__Sphingobium sp013822485", "ani": 79.1025, "matched_fragments": 375, "total_fragments": 1458, "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_000447205.1", "gtdb_species": "s__Sphingobium ummariense", "ani": 79.0442, "matched_fragments": 446, "total_fragments": 1458, "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, 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