{ "type": "genome", "identifier": "GCF_001519075.1", "organism": "Novosphingobium fuchskuhlense", "title": "Novosphingobium fuchskuhlense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bielefeld University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001519075.1", "bioproject": "PRJNA224116", "biosample": "SAMN04193360", "wgs_master": "LLZS00000000.1", "refseq_category": "reference genome", "taxid": "1117702", "species_taxid": "1117702", "organism_name": "Novosphingobium fuchskuhlense", "infraspecific_name": "strain=FNE08-7", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/01/20", "asm_name": "ASM151907v1", "asm_submitter": "Bielefeld University", "gbrs_paired_asm": "GCA_001519075.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/519/075/GCF_001519075.1_ASM151907v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3968408", "genome_size_ungapped": "3963850", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "14", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001519075.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3664", "protein_coding_gene_count": "3589", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-01-20", "dateModified": "2016-01-20", "datePublished": "2016-01-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium fuchskuhlense" ], "sample_taxid": [ "1117702" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Northeast-basin of Lake Grosse Fuchskuhle" ], "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)": "3968408", "Number of Sequences": "7", "Longest Sequences (bp)": "2093241", "N50 (bp)": "2093241", "Gap Ratio (%)": "0.114857", "GCcontent (%)": "65.4", "Number of CDSs": "3629", "Average Protein Length": "335.1", "Coding Ratio (%)": "91.9", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium fuchskuhlense", "strain": "strain=FNE08-7", "accession": "GCA_001519075.1", "taxid": 1117702, "species_taxid": 1117702, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1319, "total_fragments": 1319, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Novosphingobium sediminis", "strain": "strain=NBRC 106119", "accession": "GCA_007991615.1", "taxid": 707214, "species_taxid": 707214, "relation_to_type": "type", "validated": true, "ani": 85.7795, "matched_fragments": 971, "total_fragments": 1319, "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": 80.9473, "matched_fragments": 634, "total_fragments": 1319, "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": 80.6132, "matched_fragments": 650, "total_fragments": 1319, "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": 80.5072, "matched_fragments": 621, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium jiangmenense", "strain": "strain=1Y9A", "accession": "GCA_015694345.1", "taxid": 2791981, "species_taxid": 2791981, "relation_to_type": "type", "validated": true, "ani": 80.3798, "matched_fragments": 598, "total_fragments": 1319, "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": 80.254, "matched_fragments": 565, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium subterraneum", "strain": "strain=DSM 12447", "accession": "GCA_000807925.1", "taxid": 48936, "species_taxid": 48936, "relation_to_type": "type", "validated": true, "ani": 80.1355, "matched_fragments": 539, "total_fragments": 1319, "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": 80.0967, "matched_fragments": 578, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium pokkalii", "strain": "strain=KCTC 42224", "accession": "GCA_014652855.1", "taxid": 1770194, "species_taxid": 1770194, "relation_to_type": "type", "validated": true, "ani": 79.8681, "matched_fragments": 579, "total_fragments": 1319, "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": 79.6068, "matched_fragments": 541, "total_fragments": 1319, "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": 78.2635, "matched_fragments": 371, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Croceicoccus gelatinilyticus", "strain": "strain=1NDH52", "accession": "GCA_018398395.1", "taxid": 2835536, "species_taxid": 2835536, "relation_to_type": "type", "validated": true, "ani": 78.0791, "matched_fragments": 324, "total_fragments": 1319, "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": 77.9814, "matched_fragments": 291, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pituitosa", "strain": "strain=NBRC 102491", "accession": "GCA_001598435.1", "taxid": 99597, "species_taxid": 99597, "relation_to_type": "type", "validated": true, "ani": 77.8378, "matched_fragments": 312, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001519075.1", "gtdb_species": "s__Novosphingobium fuchskuhlense", "ani": 100.0, "matched_fragments": 1319, "total_fragments": 1319, "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": "conclusive" }, { "accession": "GCF_900117425.1", "gtdb_species": "s__Novosphingobium sp900117425", "ani": 85.9226, "matched_fragments": 977, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.26", "min_intra_species_ani": "96.76", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_007991615.1", "gtdb_species": "s__Novosphingobium sediminis", "ani": 85.7719, "matched_fragments": 972, "total_fragments": 1319, "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": "GCA_903834285.1", "gtdb_species": "s__Novosphingobium sp903834285", "ani": 85.495, "matched_fragments": 821, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903828025.1", "gtdb_species": "s__Novosphingobium sp903828025", "ani": 82.8359, "matched_fragments": 600, "total_fragments": 1319, "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_012927405.1", "gtdb_species": "s__Novosphingobium olei", "ani": 80.5279, "matched_fragments": 618, "total_fragments": 1319, "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_001014975.1", "gtdb_species": "s__Novosphingobium sp002336885", "ani": 80.5272, "matched_fragments": 592, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.80", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_005145025.1", "gtdb_species": "s__Novosphingobium sp005145025", "ani": 80.524, "matched_fragments": 594, "total_fragments": 1319, "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_003454795.1", "gtdb_species": "s__Novosphingobium sp003454795", "ani": 80.1292, "matched_fragments": 567, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.02", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900176395.1", "gtdb_species": "s__Novosphingobium sp900176395", "ani": 79.9626, "matched_fragments": 527, "total_fragments": 1319, "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": -0.097, "cell_length": 0.23, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 26.5, "optimum_ph": 6.5, "genome_size": 3969204.0, "gc_content": 65.28, "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, "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": [ "Novosphingobium", "fuchskuhlense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }