{ "type": "genome", "identifier": "GCF_013377855.1", "organism": "Undibacterium oligocarboniphilum", "title": "Undibacterium oligocarboniphilum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013377855.1", "bioproject": "PRJNA224116", "biosample": "SAMN15324618", "wgs_master": "JABXYJ000000000.1", "refseq_category": "reference genome", "taxid": "666702", "species_taxid": "666702", "organism_name": "Undibacterium oligocarboniphilum", "infraspecific_name": "strain=EM 1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/30", "asm_name": "ASM1337785v1", "asm_submitter": "Institute of Microbiology", "gbrs_paired_asm": "GCA_013377855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/377/855/GCF_013377855.1_ASM1337785v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3674452", "genome_size_ungapped": "3674440", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "34", "contig_count": "34", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013377855.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3443", "protein_coding_gene_count": "3343", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-30", "dateModified": "2020-06-30", "datePublished": "2020-06-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Undibacterium oligocarboniphilum" ], "sample_taxid": [ "666702" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany:Penzberg" ], "sample_host_location_id": [], "data_size": "1.040 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)": "3674452", "Number of Sequences": "34", "Longest Sequences (bp)": "647486", "N50 (bp)": "436939", "Gap Ratio (%)": "0.000844", "GCcontent (%)": "52.2", "Number of CDSs": "3339", "Average Protein Length": "322.6", "Coding Ratio (%)": "88.0", "Number of rRNAs": "2", "Number of tRNAs": "62", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Undibacterium oligocarboniphilum", "strain": "strain=EM 1", "accession": "GCA_013377855.1", "taxid": 666702, "species_taxid": 666702, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1207, "total_fragments": 1208, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Undibacterium griseum", "strain": "strain=FT31W", "accession": "GCA_014284195.1", "taxid": 2762295, "species_taxid": 2762295, "relation_to_type": "type", "validated": true, "ani": 92.511, "matched_fragments": 1059, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium crateris", "strain": "strain=B2R-29", "accession": "GCA_010078235.1", "taxid": 2528175, "species_taxid": 2528175, "relation_to_type": "type", "validated": true, "ani": 79.2482, "matched_fragments": 456, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium curvum", "strain": "strain=CY22W", "accession": "GCA_014284235.1", "taxid": 2762294, "species_taxid": 2762294, "relation_to_type": "type", "validated": true, "ani": 79.2456, "matched_fragments": 451, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium rugosum", "strain": "strain=CY7W", "accession": "GCA_014284365.1", "taxid": 2762291, "species_taxid": 2762291, "relation_to_type": "type", "validated": true, "ani": 79.1302, "matched_fragments": 446, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium jejuense", "strain": "strain=KACC 12607", "accession": "GCA_014284255.1", "taxid": 1344949, "species_taxid": 1344949, "relation_to_type": "type", "validated": true, "ani": 78.7576, "matched_fragments": 332, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium hunanense", "strain": "strain=CY18W", "accession": "GCA_014284335.1", "taxid": 2762292, "species_taxid": 2762292, "relation_to_type": "type", "validated": true, "ani": 78.4295, "matched_fragments": 412, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium pigrum", "strain": "strain=DSM 19792", "accession": "GCA_003201815.1", "taxid": 401470, "species_taxid": 401470, "relation_to_type": "type", "validated": true, "ani": 78.3549, "matched_fragments": 369, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum saxi", "strain": "strain=K1R23-30", "accession": "GCA_003591035.1", "taxid": 2320863, "species_taxid": 2320863, "relation_to_type": "type", "validated": true, "ani": 77.2761, "matched_fragments": 151, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella phyllosphaerae", "strain": "strain=T54", "accession": "GCA_001758785.1", "taxid": 762836, "species_taxid": 762836, "relation_to_type": "type", "validated": true, "ani": 76.8579, "matched_fragments": 130, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella aceris", "strain": "strain=SAP-35", "accession": "GCA_011090165.1", "taxid": 2703883, "species_taxid": 2703883, "relation_to_type": "type", "validated": true, "ani": 76.7144, "matched_fragments": 157, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia soli", "strain": "strain=R798", "accession": "GCA_016809835.2", "taxid": 2792854, "species_taxid": 2792854, "relation_to_type": "type", "validated": true, "ani": 76.466, "matched_fragments": 139, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia arenosa", "strain": "strain=MC02", "accession": "GCA_004614185.1", "taxid": 2561931, "species_taxid": 2561931, "relation_to_type": "type", "validated": true, "ani": 76.0568, "matched_fragments": 108, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium aquaticum", "strain": "strain=DSM 19852", "accession": "GCA_021129195.1", "taxid": 467180, "species_taxid": 467180, "relation_to_type": "type", "validated": true, "ani": 75.6949, "matched_fragments": 52, "total_fragments": 1208, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013377855.1", "gtdb_species": "s__Undibacterium oligocarboniphilum", "ani": 100.0, "matched_fragments": 1207, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014284195.1", "gtdb_species": "s__Undibacterium sp014284195", "ani": 92.511, "matched_fragments": 1059, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_014284235.1", "gtdb_species": "s__Undibacterium sp014284235", "ani": 79.2621, "matched_fragments": 450, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_010078235.1", "gtdb_species": "s__Undibacterium crateris", "ani": 79.2584, "matched_fragments": 454, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_014284365.1", "gtdb_species": "s__Undibacterium sp014284365", "ani": 79.1461, "matched_fragments": 444, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "99.07", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014284255.1", "gtdb_species": "s__Undibacterium jejuense", "ani": 78.7448, "matched_fragments": 333, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_014284335.1", "gtdb_species": "s__Undibacterium sp014284335", "ani": 78.4603, "matched_fragments": 410, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_003201815.1", "gtdb_species": "s__Undibacterium pigrum", "ani": 78.3629, "matched_fragments": 367, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_012927585.1", "gtdb_species": "s__AVCC01 sp012927585", "ani": 76.5637, "matched_fragments": 132, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01", "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_004614185.1", "gtdb_species": "s__Massilia arenosa", "ani": 76.0717, "matched_fragments": 107, "total_fragments": 1208, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia", "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": -0.302, "cell_length": 0.243, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": 6.5, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Undibacterium", "oligocarboniphilum" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }