{ "type": "genome", "identifier": "GCF_000745855.1", "organism": "Xenophilus azovorans DSM 13620", "title": "Xenophilus azovorans DSM 13620", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000745855.1", "bioproject": "PRJNA224116", "biosample": "SAMN02745804", "wgs_master": "JQKD00000000.1", "refseq_category": "reference genome", "taxid": "1123504", "species_taxid": "151755", "organism_name": "Xenophilus azovorans DSM 13620", "infraspecific_name": "strain=DSM 13620", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/08/28", "asm_name": "ASM74585v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000745855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/745/855/GCF_000745855.1_ASM74585v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6535173", "genome_size_ungapped": "6529317", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "132", "contig_count": "137", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000745855.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "6417", "protein_coding_gene_count": "6280", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-08-28", "dateModified": "2014-08-28", "datePublished": "2014-08-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Xenophilus azovorans DSM 13620" ], "sample_taxid": [ "1123504" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.757 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)": "6535173", "Number of Sequences": "132", "Longest Sequences (bp)": "554567", "N50 (bp)": "123864", "Gap Ratio (%)": "0.089607", "GCcontent (%)": "69.8", "Number of CDSs": "6225", "Average Protein Length": "318.4", "Coding Ratio (%)": "91.0", "Number of rRNAs": "2", "Number of tRNAs": "64", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Variovorax soli", "strain": "strain=NBRC 106424", "accession": "GCA_001591385.1", "taxid": 376815, "species_taxid": 376815, "relation_to_type": "type", "validated": true, "ani": 83.5215, "matched_fragments": 1012, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax boronicumulans", "strain": "strain=NBRC 103145", "accession": "GCA_001591345.1", "taxid": 436515, "species_taxid": 436515, "relation_to_type": "type", "validated": true, "ani": 83.2218, "matched_fragments": 1107, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax guangxiensis", "strain": "strain=DSM 27352", "accession": "GCA_003952165.1", "taxid": 1775474, "species_taxid": 1775474, "relation_to_type": "type", "validated": true, "ani": 83.1705, "matched_fragments": 1167, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax paradoxus", "strain": "strain=NBRC 15149", "accession": "GCA_001591365.1", "taxid": 34073, "species_taxid": 34073, "relation_to_type": "suspected-type", "validated": true, "ani": 82.9855, "matched_fragments": 1115, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax beijingensis", "strain": "strain=502", "accession": "GCA_003951285.1", "taxid": 2496117, "species_taxid": 2496117, "relation_to_type": "type", "validated": true, "ani": 82.898, "matched_fragments": 1096, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax gossypii", "strain": "strain=DSM 100435", "accession": "GCA_003965815.1", "taxid": 1679495, "species_taxid": 1679495, "relation_to_type": "type", "validated": true, "ani": 82.6257, "matched_fragments": 963, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter tataouinensis", "strain": "strain=TTB310", "accession": "GCA_000215705.1", "taxid": 94132, "species_taxid": 94132, "relation_to_type": "type", "validated": true, "ani": 82.2655, "matched_fragments": 797, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodoferax aquiterrae", "strain": "strain=KCTC 23314", "accession": "GCA_014652235.1", "taxid": 747304, "species_taxid": 747304, "relation_to_type": "type", "validated": true, "ani": 82.0262, "matched_fragments": 1044, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter humi", "strain": "strain=18x22-1", "accession": "GCA_004681975.1", "taxid": 2530451, "species_taxid": 2530451, "relation_to_type": "type", "validated": true, "ani": 81.9, "matched_fragments": 798, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter aquaticus", "strain": "strain=LMG 30558", "accession": "GCA_015159745.1", "taxid": 2780094, "species_taxid": 2780094, "relation_to_type": "type", "validated": true, "ani": 81.896, "matched_fragments": 734, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ottowia beijingensis", "strain": "strain=GCS-AN-3", "accession": "GCA_013423955.1", "taxid": 1207057, "species_taxid": 1207057, "relation_to_type": "type", "validated": true, "ani": 81.7229, "matched_fragments": 810, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter pinisoli", "strain": "strain=MAH-25", "accession": "GCA_009758015.1", "taxid": 2682844, "species_taxid": 2682844, "relation_to_type": "type", "validated": true, "ani": 81.2571, "matched_fragments": 888, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylophilus ampelinus", "strain": "strain=CFBP 1192", "accession": "GCA_024832295.1", "taxid": 54067, "species_taxid": 54067, "relation_to_type": "type", "validated": true, "ani": 81.1607, "matched_fragments": 711, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax anthurii", "strain": "strain=CFPB 3232", "accession": "GCA_003269065.1", "taxid": 78229, "species_taxid": 78229, "relation_to_type": "type", "validated": true, "ani": 81.1, "matched_fragments": 809, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter rhizophilus", "strain": "strain=CCTCC AB2015357", "accession": "GCA_004681965.1", "taxid": 1781167, "species_taxid": 1781167, "relation_to_type": "type", "validated": true, "ani": 81.0063, "matched_fragments": 790, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga crocea", "strain": "strain=BA0156", "accession": "GCA_011388215.1", "taxid": 2716225, "species_taxid": 2716225, "relation_to_type": "type", "validated": true, "ani": 80.906, "matched_fragments": 809, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax oryzae", "strain": "strain=ATCC 19882", "accession": "GCA_000687165.1", "taxid": 862720, "species_taxid": 862720, "relation_to_type": "type", "validated": true, "ani": 80.7487, "matched_fragments": 837, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter agri", "strain": "strain=G-1-2-2", "accession": "GCA_012927085.1", "taxid": 2728837, "species_taxid": 2728837, "relation_to_type": "type", "validated": true, "ani": 80.7465, "matched_fragments": 954, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidimonas sediminis", "strain": "strain=YIM 72259", "accession": "GCA_007556605.1", "taxid": 2588941, "species_taxid": 2588941, "relation_to_type": "type", "validated": true, "ani": 80.1656, "matched_fragments": 552, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ideonella dechloratans", "strain": "strain=CCUG 30977", "accession": "GCA_021049305.1", "taxid": 36863, "species_taxid": 36863, "relation_to_type": "type", "validated": true, "ani": 79.4907, "matched_fragments": 641, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelomonas saccharophila", "strain": "strain=DSM 654", "accession": "GCA_004342485.1", "taxid": 304, "species_taxid": 304, "relation_to_type": "type", "validated": true, "ani": 78.9605, "matched_fragments": 739, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paucibacter toxinivorans", "strain": "strain=DSM 16998", "accession": "GCA_004362525.1", "taxid": 270368, "species_taxid": 270368, "relation_to_type": "type", "validated": true, "ani": 78.3696, "matched_fragments": 683, "total_fragments": 2110, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000745855.1", "gtdb_species": "s__Xenophilus azovorans", "ani": 100.0, "matched_fragments": 2094, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus", "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": "GCF_901875635.1", "gtdb_species": "s__ALPHA2B sp901875635", "ani": 86.7609, "matched_fragments": 1204, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "99.68", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_005503065.1", "gtdb_species": "s__ALPHA2B sp005503065", "ani": 86.4181, "matched_fragments": 1226, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B", "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_003671765.1", "gtdb_species": "s__ALPHA2B sp003671765", "ani": 85.8918, "matched_fragments": 1205, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B", "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_018241185.1", "gtdb_species": "s__ALPHA2B sp018241185", "ani": 85.2694, "matched_fragments": 1093, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B", "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_001476815.1", "gtdb_species": "s__Pseudacidovorax intermedius_A", "ani": 84.7232, "matched_fragments": 1012, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax", "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_903864295.1", "gtdb_species": "s__Pseudacidovorax sp903864295", "ani": 84.3488, "matched_fragments": 1157, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "95.11", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003350475.1", "gtdb_species": "s__Pseudacidovorax intermedius", "ani": 84.104, "matched_fragments": 1122, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax", "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_004217005.1", "gtdb_species": "s__Variovorax sp004217005", "ani": 83.7405, "matched_fragments": 1085, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "99.70", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900114785.1", "gtdb_species": "s__Variovorax sp900114785", "ani": 83.4594, "matched_fragments": 1098, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "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_015159745.1", "gtdb_species": "s__Ramlibacter aquaticus", "ani": 81.8889, "matched_fragments": 735, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009914555.1", "gtdb_species": "s__WNDY01 sp009914555", "ani": 81.0041, "matched_fragments": 770, "total_fragments": 2110, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WNDY01", "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": -0.188, "cell_length": 0.041, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 27.5, "optimum_ph": 7.0, "genome_size": 6535173.0, "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": [ "Xenophilus", "azovorans", "DSM", "13620" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }