{ "type": "genome", "identifier": "GCF_014652855.1", "organism": "Novosphingobium pokkalii", "title": "Novosphingobium pokkalii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014652855.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245644", "wgs_master": "BMZP00000000.1", "refseq_category": "reference genome", "taxid": "1770194", "species_taxid": "1770194", "organism_name": "Novosphingobium pokkalii", "infraspecific_name": "strain=KCTC 42224", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1465285v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014652855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/652/855/GCF_014652855.1_ASM1465285v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4674965", "genome_size_ungapped": "4674347", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "61", "contig_count": "61", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014652855.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "4207", "protein_coding_gene_count": "4108", "non_coding_gene_count": "60", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium pokkalii" ], "sample_taxid": [ "1770194" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.277 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)": "4674965", "Number of Sequences": "61", "Longest Sequences (bp)": "453808", "N50 (bp)": "222935", "Gap Ratio (%)": "0.013326", "GCcontent (%)": "66.5", "Number of CDSs": "4140", "Average Protein Length": "340.3", "Coding Ratio (%)": "90.4", "Number of rRNAs": "2", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium pokkalii", "strain": "strain=KCTC 42224", "accession": "GCA_014652855.1", "taxid": 1770194, "species_taxid": 1770194, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1529, "total_fragments": 1529, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Novosphingobium capsulatum", "strain": "strain=NBRC 12533", "accession": "GCA_001598375.1", "taxid": 13688, "species_taxid": 13688, "relation_to_type": "type", "validated": true, "ani": 87.8831, "matched_fragments": 1183, "total_fragments": 1529, "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": 81.1513, "matched_fragments": 642, "total_fragments": 1529, "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": 80.8494, "matched_fragments": 623, "total_fragments": 1529, "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": 80.7095, "matched_fragments": 648, "total_fragments": 1529, "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": 80.3223, "matched_fragments": 619, "total_fragments": 1529, "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": 80.2469, "matched_fragments": 582, "total_fragments": 1529, "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": 80.0432, "matched_fragments": 569, "total_fragments": 1529, "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": 80.021, "matched_fragments": 568, "total_fragments": 1529, "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": 79.9436, "matched_fragments": 583, "total_fragments": 1529, "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": 79.9046, "matched_fragments": 591, "total_fragments": 1529, "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": 79.8835, "matched_fragments": 574, "total_fragments": 1529, "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": 79.762, "matched_fragments": 515, "total_fragments": 1529, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium acidiphilum", "strain": "strain=DSM 19966", "accession": "GCA_000429005.1", "taxid": 505248, "species_taxid": 505248, "relation_to_type": "type", "validated": true, "ani": 79.3615, "matched_fragments": 577, "total_fragments": 1529, "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": 78.7294, "matched_fragments": 435, "total_fragments": 1529, "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": 78.4499, "matched_fragments": 435, "total_fragments": 1529, "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": 78.3765, "matched_fragments": 468, "total_fragments": 1529, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014652855.1", "gtdb_species": "s__Novosphingobium pokkalii", "ani": 100.0, "matched_fragments": 1529, "total_fragments": 1529, "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_014200275.1", "gtdb_species": "s__Novosphingobium sp014200275", "ani": 88.0309, "matched_fragments": 1056, "total_fragments": 1529, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001598375.1", "gtdb_species": "s__Novosphingobium capsulatum", "ani": 87.8906, "matched_fragments": 1182, "total_fragments": 1529, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.40", "min_intra_species_ani": "97.25", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.83", "num_clustered_genomes": 50, "status": "-" }, { "accession": "GCF_003208305.1", "gtdb_species": "s__Novosphingobium sp003208305", "ani": 86.3622, "matched_fragments": 901, "total_fragments": 1529, "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_015661825.1", "gtdb_species": "s__Novosphingobium capsulatum_A", "ani": 83.8925, "matched_fragments": 687, "total_fragments": 1529, "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", "pokkalii" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }