{ "type": "genome", "identifier": "GCF_030814935.1", "organism": "Xanthobacter agilis", "title": "Xanthobacter agilis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030814935.1", "bioproject": "PRJNA224116", "biosample": "SAMN35367915", "wgs_master": "JAUSVY000000000.1", "refseq_category": "reference genome", "taxid": "47492", "species_taxid": "47492", "organism_name": "Xanthobacter agilis", "infraspecific_name": "strain=DSM 3770", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/08/18", "asm_name": "ASM3081493v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_030814935.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/814/935/GCF_030814935.1_ASM3081493v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4827619", "genome_size_ungapped": "4827619", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "30", "contig_count": "30", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030814935.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "4343", "protein_coding_gene_count": "4204", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-08-18", "dateModified": "2023-08-18", "datePublished": "2023-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthobacter agilis" ], "sample_taxid": [ "47492" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.322 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)": "4827619", "Number of Sequences": "30", "Longest Sequences (bp)": "801907", "N50 (bp)": "494220", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.4", "Number of CDSs": "4370", "Average Protein Length": "319.2", "Coding Ratio (%)": "86.7", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xanthobacter agilis", "strain": "strain=LMG 16336", "accession": "GCA_021730435.1", "taxid": 47492, "species_taxid": 47492, "relation_to_type": "type", "validated": true, "ani": 99.9781, "matched_fragments": 1564, "total_fragments": 1593, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xanthobacter dioxanivorans", "strain": "strain=YN2", "accession": "GCA_016807805.1", "taxid": 2528964, "species_taxid": 2528964, "relation_to_type": "type", "validated": true, "ani": 82.4947, "matched_fragments": 915, "total_fragments": 1593, "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": 82.2237, "matched_fragments": 892, "total_fragments": 1593, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter oligotrophicus", "strain": "strain=29k", "accession": "GCA_008364685.1", "taxid": 2607286, "species_taxid": 2607286, "relation_to_type": "type", "validated": true, "ani": 82.1924, "matched_fragments": 912, "total_fragments": 1593, "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": 81.9793, "matched_fragments": 892, "total_fragments": 1593, "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": 81.4621, "matched_fragments": 775, "total_fragments": 1593, "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": 81.458, "matched_fragments": 769, "total_fragments": 1593, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azorhizobium caulinodans", "strain": "strain=ORS 571", 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2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 28.0, "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", "agilis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }