{ "type": "genome", "identifier": "GCF_001598375.1", "organism": "Novosphingobium capsulatum NBRC 12533", "title": "Novosphingobium capsulatum NBRC 12533", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001598375.1", "bioproject": "PRJNA224116", "biosample": "SAMD00046742", "wgs_master": "BCYV00000000.1", "refseq_category": "reference genome", "taxid": "1219042", "species_taxid": "13688", "organism_name": "Novosphingobium capsulatum NBRC 12533", "infraspecific_name": "strain=NBRC 12533", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/03/11", "asm_name": "ASM159837v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001598375.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/598/375/GCF_001598375.1_ASM159837v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4836455", "genome_size_ungapped": "4836455", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "70", "contig_count": "70", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001598375.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "4432", "protein_coding_gene_count": "4332", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-03-11", "dateModified": "2016-03-11", "datePublished": "2016-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium capsulatum NBRC 12533" ], "sample_taxid": [ "1219042" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.325 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)": "4836455", "Number of Sequences": "70", "Longest Sequences (bp)": "443791", "N50 (bp)": "250928", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.7", "Number of CDSs": "4316", "Average Protein Length": "337.4", "Coding Ratio (%)": "90.3", "Number of rRNAs": "1", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium capsulatum", "strain": "strain=NBRC 12533", "accession": "GCA_001598375.1", "taxid": 13688, "species_taxid": 13688, 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80.701, "matched_fragments": 603, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium olei", "strain": "strain=TW-4", "accession": "GCA_012927405.1", "taxid": 2728851, "species_taxid": 2728851, "relation_to_type": "type", "validated": true, "ani": 80.4435, "matched_fragments": 634, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium arvoryzae", "strain": "strain=KCTC 32422", "accession": "GCA_014652615.1", "taxid": 1256514, "species_taxid": 1256514, "relation_to_type": "type", "validated": true, "ani": 79.8465, "matched_fragments": 466, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium aromaticivorans", "strain": "strain=DSM 12444", "accession": "GCA_000013325.1", "taxid": 48935, "species_taxid": 48935, "relation_to_type": "type", "validated": true, "ani": 79.7486, "matched_fragments": 556, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium taihuense", "strain": "strain=DSM 17507", "accession": "GCA_014199635.1", "taxid": 260085, "species_taxid": 260085, "relation_to_type": "type", "validated": true, "ani": 79.6072, "matched_fragments": 587, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium taihuense", "strain": "strain=CGMCC 1.3432", "accession": "GCA_007830315.1", "taxid": 260085, "species_taxid": 260085, "relation_to_type": "type", "validated": true, "ani": 79.5884, "matched_fragments": 583, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium nitrogenifigens", "strain": "strain=DSM 19370", "accession": "GCA_000192575.1", "taxid": 378548, "species_taxid": 378548, "relation_to_type": "type", "validated": true, "ani": 79.4928, "matched_fragments": 515, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium nitrogenifigens", "strain": "strain=DSM 19370", "accession": "GCA_000375445.1", "taxid": 378548, "species_taxid": 378548, "relation_to_type": "type", "validated": true, "ani": 79.4911, "matched_fragments": 514, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium decolorationis", "strain": "strain=502str22", "accession": "GCA_018417475.1", "taxid": 2698673, "species_taxid": 2698673, "relation_to_type": "type", "validated": true, "ani": 79.4807, "matched_fragments": 436, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium hassiacum", "strain": "strain=DSM 14552", "accession": "GCA_014196055.1", "taxid": 173676, "species_taxid": 173676, "relation_to_type": "type", "validated": true, "ani": 79.3879, "matched_fragments": 504, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium rosa", "strain": "strain=NBRC 15208", "accession": "GCA_001598555.1", "taxid": 76978, "species_taxid": 76978, "relation_to_type": "type", "validated": true, "ani": 78.7178, "matched_fragments": 531, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium umbonatum", "strain": "strain=FSY-9", "accession": "GCA_004005905.1", "taxid": 1908524, "species_taxid": 1908524, "relation_to_type": "type", "validated": true, "ani": 78.5313, "matched_fragments": 407, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium aquimarinum", "strain": "strain=M24A2M", "accession": "GCA_009746585.1", "taxid": 2682494, "species_taxid": 2682494, "relation_to_type": "type", "validated": true, "ani": 78.3657, "matched_fragments": 366, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_014652615.1", "gtdb_species": "s__Novosphingobium arvoryzae", "ani": 79.8463, "matched_fragments": 466, "total_fragments": 1578, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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": -0.185, "cell_length": 0.172, "doubling_h": null, "growth_tmp": 27.0, "optimum_tmp": 27.333, "optimum_ph": 6.24, "genome_size": 4832846.5, "gc_content": 65.72, "coding_genes": 4956.111, "rRNA16S_genes": 3.0, "tRNA_genes": 56.666, "gram_stain": 0.0, "sporulation": 0.166, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, 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