{ "type": "genome", "identifier": "GCF_007990915.1", "organism": "Sphingomonas aquatilis NBRC 16722", "title": "Sphingomonas aquatilis NBRC 16722", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007990915.1", "bioproject": "PRJNA224116", "biosample": "SAMD00169727", "wgs_master": "BJXI00000000.1", "refseq_category": "na", "taxid": "1219039", "species_taxid": "93063", "organism_name": "Sphingomonas aquatilis NBRC 16722", "infraspecific_name": "strain=NBRC 16722", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/08/01", "asm_name": "ASM799091v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_007990915.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/990/915/GCF_007990915.1_ASM799091v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3932334", "genome_size_ungapped": "3932334", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "244", "contig_count": "244", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007990915.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "3900", "protein_coding_gene_count": "3761", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-08-01", "dateModified": "2019-08-01", "datePublished": "2019-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas aquatilis NBRC 16722" ], "sample_taxid": [ "1219039" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.080 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)": "3932334", "Number of Sequences": "244", "Longest Sequences (bp)": "124279", "N50 (bp)": "28249", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.1", "Number of CDSs": "3655", "Average Protein Length": "305.4", "Coding Ratio (%)": "85.2", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas aquatilis", "strain": "strain=NBRC 16722", "accession": "GCA_007990915.1", "taxid": 93063, "species_taxid": 93063, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1179, "total_fragments": 1193, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Sphingomonas aquatilis", "strain": "strain=DSM 15581", "accession": "GCA_014196115.1", "taxid": 93063, "species_taxid": 93063, "relation_to_type": "type", "validated": true, "ani": 99.9998, "matched_fragments": 1193, "total_fragments": 1193, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Sphingomonas melonis", "strain": "strain=DAPP-PG 224", "accession": "GCA_000379045.1", "taxid": 152682, "species_taxid": 152682, "relation_to_type": "type", "validated": true, "ani": 95.9338, "matched_fragments": 1011, "total_fragments": 1193, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Sphingomonas taxi", "strain": "strain=ATCC 55669", "accession": "GCA_000764535.1", "taxid": 1549858, "species_taxid": 1549858, "relation_to_type": "type", "validated": true, "ani": 84.4216, "matched_fragments": 764, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas insulae", "strain": "strain=KCTC 12872", "accession": "GCA_010450875.1", "taxid": 424800, "species_taxid": 424800, "relation_to_type": "type", "validated": true, "ani": 83.9455, "matched_fragments": 736, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas jinjuensis", "strain": "strain=YC6723", "accession": "GCA_014197105.1", "taxid": 535907, "species_taxid": 535907, "relation_to_type": "type", "validated": true, "ani": 81.2717, "matched_fragments": 656, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas ginsenosidivorax", "strain": "strain=KHI67", "accession": "GCA_007995065.1", "taxid": 862135, "species_taxid": 862135, "relation_to_type": "type", "validated": true, "ani": 81.1275, "matched_fragments": 619, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas carotinifaciens", "strain": "strain=DSM 27347", "accession": "GCA_009789535.1", "taxid": 1166323, "species_taxid": 1166323, "relation_to_type": "type", "validated": true, "ani": 81.1023, "matched_fragments": 606, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas metalli", "strain": "strain=CGMCC 1.15330", "accession": "GCA_014641735.1", "taxid": 1779358, "species_taxid": 1779358, "relation_to_type": "type", "validated": true, "ani": 81.0283, "matched_fragments": 615, "total_fragments": 1193, "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": 80.2499, "matched_fragments": 594, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas folli", "strain": "strain=RHCKR7", "accession": "GCA_019429525.1", "taxid": 2862497, "species_taxid": 2862497, "relation_to_type": "type", "validated": true, "ani": 80.2304, "matched_fragments": 586, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yunnanensis", "strain": "strain=YIM 3", "accession": "GCA_019898765.1", "taxid": 310400, "species_taxid": 310400, "relation_to_type": "type", "validated": true, "ani": 80.2072, "matched_fragments": 584, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hylomeconis", "strain": "strain=CCTCC AB 2013304", "accession": "GCA_025370105.1", "taxid": 1395958, "species_taxid": 1395958, "relation_to_type": "type", "validated": true, "ani": 79.9257, "matched_fragments": 522, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hankookensis", "strain": "strain=KCTC 22579", "accession": "GCA_022664465.1", "taxid": 563996, "species_taxid": 563996, "relation_to_type": "type", "validated": true, "ani": 79.8665, "matched_fragments": 553, "total_fragments": 1193, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014196115.1", "gtdb_species": "s__Sphingomonas aquatilis", "ani": 99.9998, "matched_fragments": 1193, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.36", "min_intra_species_ani": "95.86", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCA_003075315.1", "gtdb_species": "s__Sphingomonas sp003075315", "ani": 93.7914, "matched_fragments": 1010, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "96.53", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002292295.1", "gtdb_species": "s__Sphingomonas sp002292295", "ani": 84.8734, "matched_fragments": 764, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_013409985.1", "gtdb_species": "s__Sphingomonas melonis_A", "ani": 84.4627, "matched_fragments": 742, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_000764535.1", "gtdb_species": "s__Sphingomonas taxi", "ani": 84.4274, "matched_fragments": 763, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "97.55", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003355005.1", "gtdb_species": "s__Sphingomonas sp003355005", "ani": 84.0649, "matched_fragments": 741, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_000632225.1", "gtdb_species": "s__Sphingomonas sp000632225", "ani": 84.0049, "matched_fragments": 746, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_016107325.1", "gtdb_species": "s__Sphingomonas sp016107325", "ani": 83.0739, "matched_fragments": 774, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_014197105.1", "gtdb_species": "s__Sphingomonas jinjuensis", "ani": 81.3302, "matched_fragments": 651, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_007995065.1", "gtdb_species": "s__Sphingomonas ginsenosidivorax", "ani": 81.0803, "matched_fragments": 625, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_001476905.1", "gtdb_species": "s__Sphingomonas sanguinis_B", "ani": 80.9954, "matched_fragments": 579, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "96.11", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014196255.1", "gtdb_species": "s__Sphingomonas pseudosanguinis", "ani": 80.9831, "matched_fragments": 608, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_004340945.1", "gtdb_species": "s__Sphingomonas sp004340945", "ani": 80.0519, "matched_fragments": 593, "total_fragments": 1193, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.25", "min_intra_species_ani": "95.25", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.288, "cell_length": 0.14, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 28.407, "optimum_ph": 7.016, "genome_size": 3932334.0, "gc_content": 67.072, "coding_genes": 4592.69, "rRNA16S_genes": 2.285, "tRNA_genes": 51.0, "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": [ "Sphingomonas", "aquatilis", "NBRC", "16722" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }