{ "type": "genome", "identifier": "GCF_018417475.1", "organism": "Novosphingobium decolorationis", "title": "Novosphingobium decolorationis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang Wanli University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018417475.1", "bioproject": "PRJNA224116", "biosample": "SAMN15143823", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2698673", "species_taxid": "2698673", "organism_name": "Novosphingobium decolorationis", "infraspecific_name": "strain=502str22", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/20", "asm_name": "ASM1841747v1", "asm_submitter": "Zhejiang Wanli University", "gbrs_paired_asm": "GCA_018417475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/417/475/GCF_018417475.1_ASM1841747v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4750375", "genome_size_ungapped": "4750375", "gc_percent": "65.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018417475.1-RS_2024_04_05", "annotation_date": "2024-04-05", "total_gene_count": "4432", "protein_coding_gene_count": "4254", "non_coding_gene_count": "74", "pubmed_id": "34524955" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-20", "dateModified": "2021-05-20", "datePublished": "2021-05-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium decolorationis" ], "sample_taxid": [ "2698673" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean" ], "sample_host_location_id": [], "data_size": "1.305 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)": "4750375", "Number of Sequences": "2", "Longest Sequences (bp)": "4638208", "N50 (bp)": "4638208", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.5", "Number of CDSs": "4432", "Average Protein Length": "317.5", "Coding Ratio (%)": "88.9", "Number of rRNAs": "12", "Number of tRNAs": "67", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium decolorationis", "strain": "strain=502str22", "accession": "GCA_018417475.1", "taxid": 2698673, "species_taxid": 2698673, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1583, "total_fragments": 1583, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Novosphingobium profundi", "strain": "strain=F72", "accession": "GCA_018491765.1", "taxid": 1774954, "species_taxid": 1774954, "relation_to_type": "type", "validated": true, "ani": 84.6244, "matched_fragments": 994, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium aureum", "strain": "strain=YJ-S2-02", "accession": "GCA_015865035.1", "taxid": 2792964, "species_taxid": 2792964, "relation_to_type": "type", "validated": true, "ani": 82.9666, "matched_fragments": 879, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium pentaromativorans", "strain": "strain=US6-1", "accession": "GCA_000767465.1", "taxid": 205844, "species_taxid": 205844, "relation_to_type": "type", "validated": true, "ani": 80.973, "matched_fragments": 607, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium pentaromativorans", "strain": "strain=US6-1", "accession": "GCA_000235975.2", "taxid": 205844, "species_taxid": 205844, "relation_to_type": "type", "validated": true, "ani": 80.9615, "matched_fragments": 589, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium naphthalenivorans", "strain": "strain=NBRC 102051", "accession": "GCA_001590985.1", "taxid": 273168, "species_taxid": 273168, "relation_to_type": "type", "validated": true, "ani": 80.9038, "matched_fragments": 675, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium lindaniclasticum", "strain": "strain=LE124", "accession": "GCA_000445125.1", "taxid": 1329895, "species_taxid": 1329895, "relation_to_type": "type", "validated": true, "ani": 80.8151, "matched_fragments": 612, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium silvae", "strain": "strain=FGD1", "accession": "GCA_009856825.1", "taxid": 2692619, "species_taxid": 2692619, "relation_to_type": "type", "validated": true, "ani": 80.8025, "matched_fragments": 605, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium indicum", "strain": "strain=CGMCC 1.6784", "accession": "GCA_014645195.1", "taxid": 462949, "species_taxid": 462949, "relation_to_type": "type", "validated": true, "ani": 80.7311, "matched_fragments": 644, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium malaysiense", "strain": "strain=MUSC 273", "accession": "GCA_000802225.1", "taxid": 1348853, "species_taxid": 1348853, "relation_to_type": "type", "validated": true, "ani": 80.3512, "matched_fragments": 598, "total_fragments": 1583, "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": 79.9876, "matched_fragments": 528, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium huizhouense", "strain": "strain=c7", "accession": "GCA_020179475.1", "taxid": 2866625, "species_taxid": 2866625, "relation_to_type": "type", "validated": true, "ani": 79.3989, "matched_fragments": 484, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium percolationis", "strain": "strain=c1", "accession": "GCA_020179425.1", "taxid": 2871811, "species_taxid": 2871811, "relation_to_type": "type", "validated": true, "ani": 78.99, "matched_fragments": 487, "total_fragments": 1583, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018417475.1", "gtdb_species": "s__Novosphingobium sp000813185", "ani": 100.0, "matched_fragments": 1583, "total_fragments": 1583, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.53", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_008107685.1", "gtdb_species": "s__Novosphingobium sp008107685", "ani": 91.7105, "matched_fragments": 1159, "total_fragments": 1583, "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": "-" }, { "accession": "GCF_018491765.1", "gtdb_species": "s__Novosphingobium profundi", "ani": 84.6422, "matched_fragments": 992, "total_fragments": 1583, "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": "-" }, { "accession": "GCF_015865035.1", "gtdb_species": "s__Novosphingobium sp015865035", "ani": 82.9571, "matched_fragments": 880, "total_fragments": 1583, "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": "-" }, { "accession": "GCF_006874585.1", "gtdb_species": "s__Novosphingobium sp006874585", "ani": 81.4685, "matched_fragments": 739, "total_fragments": 1583, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001742225.1", "gtdb_species": "s__Novosphingobium resinovorum", "ani": 81.0156, "matched_fragments": 725, "total_fragments": 1583, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000767465.1", "gtdb_species": "s__Novosphingobium pentaromativorans", "ani": 80.9451, "matched_fragments": 612, "total_fragments": 1583, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.84", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.76", "min_intra_species_af": "0.62", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001590985.1", "gtdb_species": "s__Novosphingobium naphthalenivorans", "ani": 80.919, "matched_fragments": 673, "total_fragments": 1583, "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": "-" }, { "accession": "GCF_014645195.1", "gtdb_species": "s__Novosphingobium indicum", "ani": 80.693, "matched_fragments": 648, "total_fragments": 1583, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.77", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000802225.1", "gtdb_species": "s__Novosphingobium malaysiense", "ani": 80.3601, "matched_fragments": 597, "total_fragments": 1583, "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": "-" }, { "accession": "GCF_002556635.1", "gtdb_species": "s__Novosphingobium sp002556635", "ani": 80.3004, "matched_fragments": 603, "total_fragments": 1583, "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": 28.068, "optimum_tmp": 27.333, "optimum_ph": 6.24, "genome_size": 4701696.136, "gc_content": 64.111, "coding_genes": 4956.111, "rRNA16S_genes": 3.0, "tRNA_genes": 56.666, "gram_stain": 0.0, "sporulation": 0.166, "motility": 0.263, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.833, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.166, "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": [ "Novosphingobium", "decolorationis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }