{ "type": "genome", "identifier": "GCA_018435705.1", "organism": "Deltaproteobacteria bacterium", "title": "Deltaproteobacteria bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018435705.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056061", "wgs_master": "JAHDNB000000000.1", "refseq_category": "na", "taxid": "2026735", "species_taxid": "2026735", "organism_name": "Deltaproteobacteria bacterium", "infraspecific_name": "", "isolate": "R3-B35.2", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/21", "asm_name": "R3", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/435/705/GCA_018435705.1_R3", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-21", "dateModified": "2021-05-21", "datePublished": "2021-05-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Deltaproteobacteria bacterium" ], "sample_taxid": [ "2026735" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Richmond, CA" ], "sample_host_location_id": [], "data_size": "1.160 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 93.75, "contamination": 4.63, "strain_heterogeneity": 50.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4083962", "Number of Sequences": "160", "Longest Sequences (bp)": "135370", "N50 (bp)": "47853", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.4", "Number of CDSs": "3499", "Average Protein Length": "322.5", "Coding Ratio (%)": "82.9", "Number of rRNAs": "1", "Number of tRNAs": "44", "Number of CRISPRs": "7" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nonomuraea basaltis", "strain": "strain=160415", "accession": "GCA_005893125.1", "taxid": 2495887, "species_taxid": 2495887, "relation_to_type": "type", "validated": true, "ani": 74.592, "matched_fragments": 56, "total_fragments": 1278, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 93.75, "contamination": 4.63, "strain_heterogeneity": 50.0 }, "gtdb_result": [ { "accession": "GCA_018436855.1", "gtdb_species": "s__UBA1062 sp018436855", "ani": 99.3351, "matched_fragments": 1159, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "99.34", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_018433775.1", "gtdb_species": "s__UBA1062 sp018433775", "ani": 94.7229, "matched_fragments": 1105, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062", "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_018433085.1", "gtdb_species": "s__UBA1062 sp018433085", "ani": 90.7865, "matched_fragments": 1002, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062", "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_001896555.1", "gtdb_species": "s__UBA1062 sp001896555", "ani": 88.7663, "matched_fragments": 911, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.48", "min_intra_species_ani": "99.38", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_002316295.1", "gtdb_species": "s__UBA1062 sp002316295", "ani": 81.0098, "matched_fragments": 532, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.10", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.79", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002448235.1", "gtdb_species": "s__UBA1062 sp002448235", "ani": 77.7331, "matched_fragments": 304, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062", "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_011372875.1", "gtdb_species": "s__DSAD01 sp011372875", "ani": 76.2882, "matched_fragments": 75, "total_fragments": 1278, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__DSAD01", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfomonilia", "o__UBA1062", "f__UBA1062", "g__UBA1062", "s__UBA1062 sp018436855" ], "_genome_taxon": [ "Deltaproteobacteria", "bacterium", "d__Bacteria", "p__Desulfobacterota", "c__Desulfomonilia", "o__UBA1062", "f__UBA1062", "g__UBA1062", "s__UBA1062 sp018436855", "Bacteria", "Desulfobacterota", "Desulfomonilia", "UBA1062", "UBA1062", "UBA1062", "UBA1062", "sp018436855" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }