{ "type": "genome", "identifier": "GCF_001590965.1", "organism": "Novosphingobium lentum NBRC 107847", "title": "Novosphingobium lentum NBRC 107847", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001590965.1", "bioproject": "PRJNA224116", "biosample": "SAMD00046709", "wgs_master": "BCTW00000000.1", "refseq_category": "reference genome", "taxid": "1219033", "species_taxid": "145287", "organism_name": "Novosphingobium lentum NBRC 107847", "infraspecific_name": "strain=NBRC 107847", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/02/23", "asm_name": "ASM159096v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001590965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/590/965/GCF_001590965.1_ASM159096v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4407848", "genome_size_ungapped": "4407848", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "53", "contig_count": "53", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001590965.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "4183", "protein_coding_gene_count": "4104", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-02-23", "dateModified": "2016-02-23", "datePublished": "2016-02-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium lentum NBRC 107847" ], "sample_taxid": [ "1219033" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.210 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)": "4407848", "Number of Sequences": "53", "Longest Sequences (bp)": "301613", "N50 (bp)": "198605", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.7", "Number of CDSs": "4116", "Average Protein Length": "321.5", "Coding Ratio (%)": "90.1", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium lentum", "strain": "strain=NBRC 107847", "accession": "GCA_001590965.1", "taxid": 145287, "species_taxid": 145287, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1439, "total_fragments": 1442, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Novosphingobium percolationis", "strain": "strain=c1", "accession": "GCA_020179425.1", "taxid": 2871811, "species_taxid": 2871811, "relation_to_type": "type", "validated": true, "ani": 81.1127, "matched_fragments": 646, "total_fragments": 1442, "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": 81.04, "matched_fragments": 632, "total_fragments": 1442, "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": 80.661, "matched_fragments": 608, "total_fragments": 1442, "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": 80.2491, "matched_fragments": 608, "total_fragments": 1442, "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": 80.1797, "matched_fragments": 522, "total_fragments": 1442, "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": 80.1457, "matched_fragments": 597, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium fuchskuhlense", "strain": "strain=FNE08-7", "accession": "GCA_001519075.1", "taxid": 1117702, "species_taxid": 1117702, "relation_to_type": "type", "validated": true, "ani": 79.8633, "matched_fragments": 547, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium sediminis", "strain": "strain=NBRC 106119", "accession": "GCA_007991615.1", "taxid": 707214, "species_taxid": 707214, "relation_to_type": "type", "validated": true, "ani": 79.8596, "matched_fragments": 549, "total_fragments": 1442, "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": 79.704, "matched_fragments": 555, "total_fragments": 1442, "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": 79.6782, "matched_fragments": 565, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium aerophilum", "strain": "strain=4Y4", "accession": "GCA_014230305.1", "taxid": 2839843, "species_taxid": 2839843, "relation_to_type": "type", "validated": true, "ani": 79.6378, "matched_fragments": 522, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium piscinae", "strain": "strain=KCTC 42194", "accession": "GCA_014230355.1", "taxid": 1507448, "species_taxid": 1507448, "relation_to_type": "type", "validated": true, "ani": 79.5357, "matched_fragments": 520, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium meiothermophilum", "strain": "strain=SYSU G00007", "accession": "GCA_003171715.1", "taxid": 2202251, "species_taxid": 2202251, "relation_to_type": "type", "validated": true, "ani": 79.2919, "matched_fragments": 497, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter rhizovicinus", "strain": "strain=AY-3R", "accession": "GCA_004135625.1", "taxid": 2268576, "species_taxid": 2268576, "relation_to_type": "type", "validated": true, "ani": 78.786, "matched_fragments": 384, "total_fragments": 1442, "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": 78.7707, "matched_fragments": 451, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium endophyticum", "strain": "strain=CGMCC 1.15095", "accession": "GCA_014640675.1", "taxid": 1955250, "species_taxid": 1955250, "relation_to_type": "type", "validated": true, "ani": 78.7685, "matched_fragments": 431, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter aerophilus", "strain": "strain=Ery1", "accession": "GCA_003581645.1", "taxid": 2306995, "species_taxid": 2306995, "relation_to_type": "type", "validated": true, "ani": 78.7461, "matched_fragments": 385, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium fluoreni", "strain": "strain=DSM 27568", "accession": "GCA_014196615.1", "taxid": 1391222, "species_taxid": 1391222, "relation_to_type": "type", "validated": true, "ani": 78.5711, "matched_fragments": 389, "total_fragments": 1442, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001590965.1", "gtdb_species": "s__Novosphingobium lentum", "ani": 100.0, "matched_fragments": 1439, "total_fragments": 1442, "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_004364785.1", "gtdb_species": "s__Novosphingobium sp004364785", "ani": 81.2961, "matched_fragments": 655, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_001725355.1", "gtdb_species": "s__Novosphingobium sp001725355", "ani": 80.9741, "matched_fragments": 609, "total_fragments": 1442, "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_015694345.1", "gtdb_species": "s__Novosphingobium jiangmenense", "ani": 80.2542, "matched_fragments": 607, "total_fragments": 1442, "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_014652855.1", "gtdb_species": "s__Novosphingobium pokkalii", "ani": 80.1338, "matched_fragments": 598, "total_fragments": 1442, "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_016719755.1", "gtdb_species": "s__Novosphingobium sp016719755", "ani": 80.0138, "matched_fragments": 505, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.59", "mean_intra_species_af": "0.90", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_007991615.1", "gtdb_species": "s__Novosphingobium sediminis", "ani": 79.8497, "matched_fragments": 550, "total_fragments": 1442, "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_004211435.1", "gtdb_species": "s__Novosphingobium sp004211435", "ani": 79.5284, "matched_fragments": 481, "total_fragments": 1442, "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", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_014763545.1", "gtdb_species": "s__JACXVD01 sp014763545", "ani": 79.0377, "matched_fragments": 453, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.92", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016803135.1", "gtdb_species": "s__Pelagerythrobacter sp016803135", "ani": 78.8837, "matched_fragments": 427, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter", "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_014640675.1", "gtdb_species": "s__Novosphingobium endophyticum", "ani": 78.7833, "matched_fragments": 430, "total_fragments": 1442, "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_001661675.2", "gtdb_species": "s__Croceicoccus marinus", "ani": 78.6702, "matched_fragments": 448, "total_fragments": 1442, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.86", 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