{ "type": "genome", "identifier": "GCF_016807805.1", "organism": "Xanthobacter dioxanivorans", "title": "Xanthobacter dioxanivorans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Harbin Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016807805.1", "bioproject": "PRJNA224116", "biosample": "SAMN10992855", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2528964", "species_taxid": "2528964", "organism_name": "Xanthobacter dioxanivorans", "infraspecific_name": "strain=YN2", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/04", "asm_name": "ASM1680780v1", "asm_submitter": "Harbin Institute of Technology", "gbrs_paired_asm": "GCA_016807805.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/807/805/GCF_016807805.1_ASM1680780v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6650762", "genome_size_ungapped": "6650762", "gc_percent": "68.000000", "replicon_count": "5", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016807805.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "6379", "protein_coding_gene_count": "6013", "non_coding_gene_count": "59", "pubmed_id": "33547937" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-04", "dateModified": "2021-02-04", "datePublished": "2021-02-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthobacter dioxanivorans" ], "sample_taxid": [ "2528964" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Harbin" ], "sample_host_location_id": [], "data_size": "1.810 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)": "6650762", "Number of Sequences": "5", "Longest Sequences (bp)": "6277310", "N50 (bp)": "6277310", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.9", "Number of CDSs": "6521", "Average Protein Length": "299.4", "Coding Ratio (%)": "88.1", "Number of rRNAs": "6", "Number of tRNAs": "58", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xanthobacter dioxanivorans", "strain": "strain=YN2", "accession": "GCA_016807805.1", "taxid": 2528964, "species_taxid": 2528964, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2212, "total_fragments": 2215, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xanthobacter oligotrophicus", "strain": "strain=29k", "accession": "GCA_008364685.1", "taxid": 2607286, "species_taxid": 2607286, "relation_to_type": "type", "validated": true, "ani": 85.5385, "matched_fragments": 1205, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter autotrophicus", "strain": "strain=DSM 432", "accession": "GCA_005871085.1", "taxid": 280, "species_taxid": 280, "relation_to_type": "type", "validated": true, "ani": 85.2221, "matched_fragments": 1148, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter aminoxidans", "strain": "strain=ATCC BAA-299", "accession": "GCA_023571765.1", "taxid": 186280, "species_taxid": 186280, "relation_to_type": "type", "validated": true, "ani": 85.0672, "matched_fragments": 1218, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=ATCC 700314", "accession": "GCA_003667445.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 83.5204, "matched_fragments": 953, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=DSM 11105", "accession": "GCA_014206845.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 83.4207, "matched_fragments": 959, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter agilis", "strain": "strain=LMG 16336", "accession": "GCA_021730435.1", "taxid": 47492, "species_taxid": 47492, "relation_to_type": "type", "validated": true, "ani": 82.4321, "matched_fragments": 916, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Starkeya novella", "strain": "strain=DSM 506", "accession": "GCA_000092925.1", "taxid": 921, "species_taxid": 921, "relation_to_type": "type", "validated": true, "ani": 79.5938, "matched_fragments": 613, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016807805.1", "gtdb_species": "s__Xanthobacter sp016807805", "ani": 100.0, "matched_fragments": 2211, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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_000017645.1", "gtdb_species": "s__Xanthobacter autotrophicus", "ani": 85.6603, "matched_fragments": 1196, 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"d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.09", "min_intra_species_ani": "96.09", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012275355.1", "gtdb_species": "s__Xanthobacter sp012275355", "ani": 84.6911, "matched_fragments": 1216, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017875275.1", "gtdb_species": "s__Xanthobacter flavus", "ani": 84.6632, "matched_fragments": 1229, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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_017849325.1", "gtdb_species": "s__Xanthobacter autotrophicus_B", "ani": 83.2456, "matched_fragments": 567, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter", "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": 0.0, "doubling_h": null, "growth_tmp": 29.5, "optimum_tmp": null, "optimum_ph": null, "genome_size": 5525748.167, "gc_content": 66.672, "coding_genes": 5009.667, "rRNA16S_genes": 2.0, "tRNA_genes": 51.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.2, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.8, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Xanthobacter", "dioxanivorans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }