{ "type": "genome", "identifier": "GCA_004296945.1", "organism": "Variovorax sp.", "title": "Variovorax sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Oklahoma", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004296945.1", "bioproject": "PRJNA514088", "biosample": "SAMN10720237", "wgs_master": "SCVF00000000.1", "refseq_category": "na", "taxid": "1871043", "species_taxid": "1871043", "organism_name": "Variovorax sp.", "infraspecific_name": "", "isolate": "GW715_bin.44", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/25", "asm_name": "ASM429694v1", "submitter": "University of Oklahoma", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/296/945/GCA_004296945.1_ASM429694v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-25", "dateModified": "2019-02-25", "datePublished": "2019-02-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Variovorax sp." ], "sample_taxid": [ "1871043" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Tennessee" ], "sample_host_location_id": [], "data_size": "2.399 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 93.56, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "8976933", "Number of Sequences": "91", "Longest Sequences (bp)": "634046", "N50 (bp)": "178790", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.6", "Number of CDSs": "8171", "Average Protein Length": "336.2", "Coding Ratio (%)": "91.8", "Number of rRNAs": "0", "Number of tRNAs": "75", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Variovorax boronicumulans", "strain": "strain=NBRC 103145", "accession": "GCA_001591345.1", "taxid": 436515, "species_taxid": 436515, "relation_to_type": "type", "validated": true, "ani": 87.4603, "matched_fragments": 1589, "total_fragments": 2951, "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": 87.2321, "matched_fragments": 1712, "total_fragments": 2951, "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": 86.8582, "matched_fragments": 1450, "total_fragments": 2951, "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": 86.7027, "matched_fragments": 1555, "total_fragments": 2951, "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": 86.456, "matched_fragments": 1533, "total_fragments": 2951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax soli", "strain": "strain=NBRC 106424", "accession": "GCA_001591385.1", "taxid": 376815, "species_taxid": 376815, "relation_to_type": "type", "validated": true, "ani": 83.1179, "matched_fragments": 1169, "total_fragments": 2951, "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": 81.061, "matched_fragments": 791, "total_fragments": 2951, "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": 80.5925, "matched_fragments": 919, "total_fragments": 2951, "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": 80.0031, "matched_fragments": 1143, "total_fragments": 2951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax facilis", "strain": "strain=DSM 649", "accession": "GCA_023913775.1", "taxid": 12917, "species_taxid": 12917, "relation_to_type": "type", "validated": true, "ani": 79.4466, "matched_fragments": 793, "total_fragments": 2951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphaerotilus sulfidivorans", "strain": "strain=D-501", "accession": "GCA_013426975.1", "taxid": 639200, "species_taxid": 639200, "relation_to_type": "type", "validated": true, "ani": 78.9728, "matched_fragments": 803, "total_fragments": 2951, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 93.56, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016806145.1", "gtdb_species": "s__Variovorax sp900115375", "ani": 96.2619, "matched_fragments": 2492, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.08", "min_intra_species_ani": "95.68", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.79", "num_clustered_genomes": 13, "status": "conclusive" }, { "accession": "GCF_003053685.1", "gtdb_species": "s__Variovorax sp003053685", "ani": 87.5556, "matched_fragments": 1758, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "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": 5, "status": "-" }, { "accession": "GCF_001591345.1", "gtdb_species": "s__Variovorax boronicumulans", "ani": 87.4248, "matched_fragments": 1594, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.07", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003952165.1", "gtdb_species": "s__Variovorax guangxiensis", "ani": 87.2365, "matched_fragments": 1711, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013376045.1", "gtdb_species": "s__Variovorax sp013376045", "ani": 87.1431, "matched_fragments": 1700, "total_fragments": 2951, "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_004216615.1", "gtdb_species": "s__Variovorax sp004216615", "ani": 87.1139, "matched_fragments": 1600, "total_fragments": 2951, "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": "GCA_016082275.1", "gtdb_species": "s__Variovorax sp016082275", "ani": 87.0418, "matched_fragments": 1709, "total_fragments": 2951, "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_000382045.1", "gtdb_species": "s__Variovorax paradoxus_A", "ani": 87.0333, "matched_fragments": 1729, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003952185.1", "gtdb_species": "s__Variovorax sp003952185", "ani": 86.9877, "matched_fragments": 1739, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_001899795.1", "gtdb_species": "s__Variovorax sp001899795", "ani": 86.9475, "matched_fragments": 1824, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003019815.1", "gtdb_species": "s__Variovorax sp003019815", "ani": 86.9181, "matched_fragments": 1694, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017161115.1", "gtdb_species": "s__Variovorax sp017161115", "ani": 86.8673, "matched_fragments": 1792, "total_fragments": 2951, "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_003965815.1", "gtdb_species": "s__Variovorax gossypii", "ani": 86.8239, "matched_fragments": 1455, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900106655.1", "gtdb_species": "s__Variovorax sp900106655", "ani": 86.7127, "matched_fragments": 1697, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.15", "min_intra_species_ani": "98.06", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001591365.1", "gtdb_species": "s__Variovorax paradoxus", "ani": 86.6602, "matched_fragments": 1560, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000184745.1", "gtdb_species": "s__Variovorax paradoxus_C", "ani": 86.6058, "matched_fragments": 1647, "total_fragments": 2951, "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_000834655.1", "gtdb_species": "s__Variovorax paradoxus_F", "ani": 86.5668, "matched_fragments": 1688, "total_fragments": 2951, "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_007828835.1", "gtdb_species": "s__Variovorax beijingensis_A", "ani": 86.5365, "matched_fragments": 1558, "total_fragments": 2951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.397, "cell_length": 0.09, "doubling_h": null, "growth_tmp": 28.25, "optimum_tmp": 29.583, "optimum_ph": 7.0, "genome_size": 6677628.603, "gc_content": 67.783, "coding_genes": 6232.321, "rRNA16S_genes": 2.0, "tRNA_genes": 54.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.8, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.2, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Variovorax", "s__Variovorax sp900115375" ], "_genome_taxon": [ "Variovorax", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Variovorax", "s__Variovorax sp900115375", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Burkholderiaceae", "Variovorax", "Variovorax", "sp900115375" ], "_meo": [ { "id": "MEO_0000366", "label": "ground water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }