{ "type": "genome", "identifier": "GCF_014672695.1", "organism": "Defluviicoccus vanus", "title": "Defluviicoccus vanus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Singapore Centre for Environmental Life Sciences Engineering", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014672695.1", "bioproject": "PRJNA224116", "biosample": "SAMN15030566", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "111831", "species_taxid": "111831", "organism_name": "Defluviicoccus vanus", "infraspecific_name": "strain=Ben 114", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/21", "asm_name": "ASM1467269v1", "asm_submitter": "Singapore Centre for Environmental Life Sciences Engineering", "gbrs_paired_asm": "GCA_014672695.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/672/695/GCF_014672695.1_ASM1467269v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4226795", "genome_size_ungapped": "4226795", "gc_percent": "63.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014672695.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3860", "protein_coding_gene_count": "3481", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-21", "dateModified": "2020-09-21", "datePublished": "2020-09-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Defluviicoccus vanus" ], "sample_taxid": [ "111831" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Singapore: Jurong West" ], "sample_host_location_id": [], "data_size": "1.174 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4226795", "Number of Sequences": "2", "Longest Sequences (bp)": "4156012", "N50 (bp)": "4156012", "Gap Ratio (%)": "0.052735", "GCcontent (%)": "63.6", "Number of CDSs": "3816", "Average Protein Length": "314.6", "Coding Ratio (%)": "85.2", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Defluviicoccus vanus", "strain": "strain=Ben 114", "accession": "GCA_014672695.1", "taxid": 111831, "species_taxid": 111831, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1408, "total_fragments": 1408, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhizobium subbaraonis", "strain": "strain=JC85", "accession": "GCA_900220975.1", "taxid": 908946, "species_taxid": 908946, "relation_to_type": "type", "validated": true, "ani": 76.9615, "matched_fragments": 111, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nisaea acidiphila", "strain": "strain=MEBiC11861", "accession": "GCA_024662015.1", "taxid": 1862145, "species_taxid": 1862145, "relation_to_type": "type", "validated": true, "ani": 76.9177, "matched_fragments": 104, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas vitisensis", "strain": "strain=GR-TSA-9", "accession": "GCA_016656965.1", "taxid": 2800818, "species_taxid": 2800818, "relation_to_type": "type", "validated": true, "ani": 76.6706, "matched_fragments": 50, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella pratensis", "strain": "strain=W17", "accession": "GCA_008843145.1", "taxid": 2233999, "species_taxid": 2233999, "relation_to_type": "type", "validated": true, "ani": 76.665, "matched_fragments": 160, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hypericibacter adhaerens", "strain": "strain=R5959", "accession": "GCA_008728835.1", "taxid": 2602016, "species_taxid": 2602016, "relation_to_type": "type", "validated": true, "ani": 76.6058, "matched_fragments": 159, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pseudosanguinis", "strain": "strain=DSM 19512", "accession": "GCA_014196255.1", "taxid": 413712, "species_taxid": 413712, "relation_to_type": "type", "validated": true, "ani": 76.5515, "matched_fragments": 92, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum aberrantis", "strain": "strain=SpK", "accession": "GCA_011022235.1", "taxid": 1105283, "species_taxid": 1105283, "relation_to_type": "type", "validated": true, "ani": 76.4003, "matched_fragments": 102, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanibaculum nanhaiense", "strain": "strain=L54-1-50", "accession": "GCA_002148795.1", "taxid": 1909734, "species_taxid": 1909734, "relation_to_type": "type", "validated": true, "ani": 76.3859, "matched_fragments": 122, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Inquilinus limosus", "strain": "strain=DSM 16000", "accession": "GCA_000423185.1", "taxid": 171674, "species_taxid": 171674, "relation_to_type": "type", "validated": true, "ani": 76.3528, "matched_fragments": 198, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanibaculum indicum", "strain": "strain=P24", "accession": "GCA_000299935.1", "taxid": 526216, "species_taxid": 526216, "relation_to_type": "type", "validated": true, "ani": 76.3093, "matched_fragments": 123, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum caucaseum", "strain": "strain=SO-1", "accession": "GCA_000342045.1", "taxid": 1244869, "species_taxid": 1244869, "relation_to_type": "type", "validated": true, "ani": 76.2961, "matched_fragments": 143, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella mucosa", "strain": "strain=KEMB 2255-438", "accession": "GCA_016765655.2", "taxid": 1789672, "species_taxid": 1789672, "relation_to_type": "type", "validated": true, "ani": 76.2941, "matched_fragments": 164, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum thiophilum", "strain": "strain=DSM 21654", "accession": "GCA_000960825.1", "taxid": 528244, "species_taxid": 528244, "relation_to_type": "type", "validated": true, "ani": 76.2732, "matched_fragments": 172, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aureimonas phyllosphaerae", "strain": "strain=DSM 25024", "accession": "GCA_014196405.1", "taxid": 1166078, "species_taxid": 1166078, "relation_to_type": "type", "validated": true, "ani": 76.2694, "matched_fragments": 74, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tistlia consotensis", "strain": "strain=USBA 355", "accession": "GCA_900177295.1", "taxid": 1321365, "species_taxid": 1321365, "relation_to_type": "type", "validated": true, "ani": 76.2351, "matched_fragments": 205, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum agricola", "strain": "strain=CC-HIH038", "accession": "GCA_017876095.1", "taxid": 1720247, "species_taxid": 1720247, "relation_to_type": "type", "validated": true, "ani": 76.1734, "matched_fragments": 167, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum gryphiswaldense", "strain": "strain=MSR-1", "accession": "GCA_000513295.1", "taxid": 55518, "species_taxid": 55518, "relation_to_type": "type", "validated": true, "ani": 76.1685, "matched_fragments": 122, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tistlia consotensis", "strain": "strain=DSM 21585", "accession": "GCA_900188055.1", "taxid": 1321365, "species_taxid": 1321365, "relation_to_type": "type", "validated": true, "ani": 76.1649, "matched_fragments": 200, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kaistia adipata", "strain": "strain=DSM 17808", "accession": "GCA_000423225.1", "taxid": 166954, "species_taxid": 166954, "relation_to_type": "type", "validated": true, "ani": 76.1343, "matched_fragments": 132, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassobaculum fulvum", "strain": "strain=KCTC 42651", "accession": "GCA_014652915.1", "taxid": 1633335, "species_taxid": 1633335, "relation_to_type": "type", "validated": true, "ani": 76.1294, "matched_fragments": 163, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum gryphiswaldense", "strain": "strain=MSR-1", "accession": "GCA_002995515.1", "taxid": 55518, "species_taxid": 55518, "relation_to_type": "type", "validated": true, "ani": 76.077, "matched_fragments": 114, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium uaiense", "strain": "strain=UFLA03-164", "accession": "GCA_010811875.1", "taxid": 2594946, "species_taxid": 2594946, "relation_to_type": "type", "validated": true, "ani": 75.6873, "matched_fragments": 131, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Denitrobaculum tricleocarpae", "strain": "strain=R148", "accession": "GCA_007004665.1", "taxid": 2591009, "species_taxid": 2591009, "relation_to_type": "type", "validated": true, "ani": 75.6051, "matched_fragments": 68, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014672695.1", "gtdb_species": "s__Defluviicoccus vanus", "ani": 100.0, "matched_fragments": 1408, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__Defluviicoccus", "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": "GCA_016712375.1", "gtdb_species": "s__SSA4 sp016712375", "ani": 78.2764, "matched_fragments": 274, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4", "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_013414705.1", "gtdb_species": "s__SSA4 sp013414705", "ani": 78.2714, "matched_fragments": 319, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4", "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_016712595.1", "gtdb_species": "s__SSA4 sp016712595", "ani": 78.2257, "matched_fragments": 297, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4", "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_016793875.1", "gtdb_species": "s__SSA4 sp016793875", "ani": 77.9742, "matched_fragments": 289, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4", "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_900609035.2", "gtdb_species": "s__Defluviicoccus_A seviourii", "ani": 77.1396, "matched_fragments": 216, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__Defluviicoccus_A", "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_016793925.1", "gtdb_species": "s__JAEULH01 sp016793925", "ani": 77.0952, "matched_fragments": 213, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JAEULH01", "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_007694935.1", "gtdb_species": "s__REEP01 sp007694935", "ani": 77.0503, "matched_fragments": 162, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01", "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_900220975.1", "gtdb_species": "s__Mycoplana subbaraonis", "ani": 76.943, "matched_fragments": 113, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana", "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_008728835.1", "gtdb_species": "s__Hypericibacter adhaerens", "ani": 76.6513, "matched_fragments": 161, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter", "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_902729435.1", "gtdb_species": "s__Magnetospirillum sp902729435", "ani": 76.6232, "matched_fragments": 167, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum", "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_007695045.1", "gtdb_species": "s__REEP01 sp007695045", "ani": 76.4332, "matched_fragments": 149, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01", "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_902729425.1", "gtdb_species": "s__Phaeospirillum sp902729425", "ani": 76.3462, "matched_fragments": 127, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum", "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_900230255.1", "gtdb_species": "s__Caenispirillum bisanense", "ani": 76.1424, "matched_fragments": 172, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum", "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_018432935.1", "gtdb_species": "s__JAHDSF01 sp018432935", "ani": 76.1194, "matched_fragments": 137, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01", "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_014643375.1", "gtdb_species": "s__Aureimonas_A glaciei", "ani": 76.0858, "matched_fragments": 128, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A", "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_009691105.1", "gtdb_species": "s__SHVU01 sp009691105", "ani": 75.8126, "matched_fragments": 56, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__SHVU01", "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": 0.439, "cell_length": 0.439, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 25.0, "optimum_ph": 7.75, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Defluviicoccus", "vanus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }