{ "type": "genome", "identifier": "GCF_028607105.1", "organism": "Novosphingobium humi", "title": "Novosphingobium humi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Agricultural Sciences, Rural Development Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_028607105.1", "bioproject": "PRJNA224116", "biosample": "SAMN33039045", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2282397", "species_taxid": "2282397", "organism_name": "Novosphingobium humi", "infraspecific_name": "strain=KACC 19094", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/02/13", "asm_name": "ASM2860710v1", "asm_submitter": "National Institute of Agricultural Sciences, Rural Development Administration", "gbrs_paired_asm": "GCA_028607105.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/028/607/105/GCF_028607105.1_ASM2860710v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4890578", "genome_size_ungapped": "4890578", "gc_percent": "63.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_028607105.1-RS_2024_03_24", "annotation_date": "2024-03-24", "total_gene_count": "4438", "protein_coding_gene_count": "4349", "non_coding_gene_count": "67", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-02-13", "dateModified": "2023-02-13", "datePublished": "2023-02-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium humi" ], "sample_taxid": [ "2282397" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jeollanam-do, Jangseong-gun" ], "sample_host_location_id": [], "data_size": "1.340 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)": "4890578", "Number of Sequences": "4", "Longest Sequences (bp)": "3439207", "N50 (bp)": "3439207", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.6", "Number of CDSs": "4382", "Average Protein Length": "338.6", "Coding Ratio (%)": "91.0", "Number of rRNAs": "6", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium sediminicola", "strain": "strain=DSM 27057", "accession": "GCA_014196525.1", "taxid": 563162, "species_taxid": 563162, "relation_to_type": "type", "validated": true, "ani": 90.9674, "matched_fragments": 1299, "total_fragments": 1628, "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": 82.0945, "matched_fragments": 815, "total_fragments": 1628, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium ovatum", "strain": "strain=FSY-8", "accession": "GCA_009909235.1", "taxid": 1908523, "species_taxid": 1908523, "relation_to_type": "type", "validated": true, "ani": 81.3919, "matched_fragments": 724, "total_fragments": 1628, "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": 79.9833, "matched_fragments": 733, "total_fragments": 1628, "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": 78.8916, "matched_fragments": 423, "total_fragments": 1628, "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": 78.6715, "matched_fragments": 466, "total_fragments": 1628, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium kunmingense", "strain": "strain=CGMCC 1.12274", "accession": "GCA_002813245.1", "taxid": 1211806, "species_taxid": 1211806, "relation_to_type": "type", "validated": true, "ani": 78.5497, "matched_fragments": 354, "total_fragments": 1628, "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": 78.5441, "matched_fragments": 389, "total_fragments": 1628, "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": 78.5361, "matched_fragments": 404, "total_fragments": 1628, "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": 78.433, "matched_fragments": 411, "total_fragments": 1628, "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": 78.3267, "matched_fragments": 413, "total_fragments": 1628, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium barchaimii", "strain": "strain=LL02", "accession": "GCA_001046635.1", "taxid": 1420591, "species_taxid": 1420591, "relation_to_type": "type", "validated": true, "ani": 78.1327, "matched_fragments": 388, "total_fragments": 1628, "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": 78.1302, "matched_fragments": 331, "total_fragments": 1628, "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": 77.8787, "matched_fragments": 287, "total_fragments": 1628, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania gelatinilytica", "strain": "strain=1NDH1", "accession": "GCA_019711315.1", "taxid": 2867231, "species_taxid": 2867231, "relation_to_type": "type", "validated": true, "ani": 77.5341, "matched_fragments": 224, "total_fragments": 1628, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012275515.1", "gtdb_species": "s__Novosphingobium sp001898925", "ani": 93.0969, "matched_fragments": 1374, "total_fragments": 1628, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "97.63", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014196525.1", "gtdb_species": "s__Novosphingobium sediminicola", "ani": 90.996, "matched_fragments": 1296, "total_fragments": 1628, "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_013149295.1", "gtdb_species": "s__Novosphingobium sp013149295", "ani": 90.8928, "matched_fragments": 1314, "total_fragments": 1628, "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_004005905.1", "gtdb_species": "s__Novosphingobium umbonatum", "ani": 82.0604, "matched_fragments": 817, "total_fragments": 1628, "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_002336765.1", "gtdb_species": "s__Novosphingobium sp002336765", "ani": 81.4465, "matched_fragments": 499, "total_fragments": 1628, "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_009909235.1", "gtdb_species": "s__Novosphingobium sp009909235", "ani": 81.3721, "matched_fragments": 726, "total_fragments": 1628, "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_017163935.1", "gtdb_species": "s__Novosphingobium sp017163935", "ani": 80.1054, "matched_fragments": 730, "total_fragments": 1628, "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", "humi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }