{ "type": "genome", "identifier": "GCA_001508095.1", "organism": "Thermodesulfobacterium commune", "title": "Thermodesulfobacterium commune", "description": "derived from metagenome; incomplete metagenome", "data type": "Genome sequencing and assembly", "organization": "Lawrence Berkeley National Lab", "publication": [ {} ], "properties": { "assembly_accession": "GCA_001508095.1", "bioproject": "PRJNA278302", "biosample": "SAMN03445130", "wgs_master": "LGFE00000000.1", "refseq_category": "na", "taxid": "1741", "species_taxid": "1741", "organism_name": "Thermodesulfobacterium commune", "infraspecific_name": "", "isolate": "37_1485", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/01/08", "asm_name": "ASM150809v1", "submitter": "Lawrence Berkeley National Lab", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/508/095/GCA_001508095.1_ASM150809v1", "excluded_from_refseq": "derived from metagenome; incomplete metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-01-08", "dateModified": "2016-01-08", "datePublished": "2016-01-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Thermodesulfobacterium commune" ], "sample_taxid": [ "1741" ], "sample_host_organism": [ "NA" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Alaska, North Slope, Kuparuk formation" ], "sample_host_location_id": [], "data_size": "0.318 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1134876", "Number of Sequences": "157", "Longest Sequences (bp)": "40987", "N50 (bp)": "9749", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "36.9", "Number of CDSs": "978", "Average Protein Length": "305.9", "Coding Ratio (%)": "79.1", "Number of rRNAs": "3", "Number of tRNAs": "31", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thermodesulfobacterium commune", "strain": "strain=DSM 2178", "accession": "GCA_000746435.1", "taxid": 1741, "species_taxid": 1741, "relation_to_type": "type", "validated": true, "ani": 99.2572, "matched_fragments": 291, "total_fragments": 295, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Thermodesulfobacterium commune", "strain": "strain=DSM 2178", "accession": "GCA_000734015.1", "taxid": 1741, "species_taxid": 1741, "relation_to_type": "type", "validated": true, "ani": 99.1745, "matched_fragments": 293, "total_fragments": 295, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Thermodesulfobacterium thermophilum", "strain": "strain=DSM 1276", "accession": "GCA_000421605.1", "taxid": 886, "species_taxid": 886, "relation_to_type": "type", "validated": true, "ani": 96.0823, "matched_fragments": 289, "total_fragments": 295, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Thermodesulfobacterium hveragerdense", "strain": "strain=DSM 12571", "accession": "GCA_000423845.1", "taxid": 53424, "species_taxid": 53424, "relation_to_type": "type", "validated": true, "ani": 93.4891, "matched_fragments": 278, "total_fragments": 295, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermodesulfobacterium geofontis", "strain": "strain=OPF15", "accession": "GCA_000215975.1", "taxid": 1295609, "species_taxid": 1295609, "relation_to_type": "type", "validated": true, "ani": 77.0592, "matched_fragments": 55, "total_fragments": 295, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000734015.1", "gtdb_species": "s__Thermodesulfobacterium commune", "ani": 99.1745, "matched_fragments": 293, "total_fragments": 295, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium", "ani_circumscription_radius": 95.9677, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 10, "status": "inconclusive" }, { "accession": "GCF_000421605.1", "gtdb_species": "s__Thermodesulfobacterium thermophilum", "ani": 96.0823, "matched_fragments": 289, "total_fragments": 295, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium", "ani_circumscription_radius": 95.9677, "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": "inconclusive" }, { "accession": "GCF_000423845.1", "gtdb_species": "s__Thermodesulfobacterium hveragerdense", "ani": 93.4891, "matched_fragments": 278, "total_fragments": 295, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium", "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_008630935.1", "gtdb_species": "s__Thermodesulfobacterium sp008630935", "ani": 80.4945, "matched_fragments": 230, "total_fragments": 295, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium", "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_000215975.1", "gtdb_species": "s__Thermodesulfobacterium geofontis", "ani": 77.0592, "matched_fragments": 55, "total_fragments": 295, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.03", "min_intra_species_ani": "96.03", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.046, "doubling_h": 0.363, "growth_tmp": 69.8, "optimum_tmp": 70.0, "optimum_ph": null, "genome_size": 1764046.0, "gc_content": 37.0, "coding_genes": 1612.333, "rRNA16S_genes": 1.0, "tRNA_genes": 46.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 1.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Thermodesulfobacteria", "o__Thermodesulfobacteriales", "f__Thermodesulfobacteriaceae", "g__Thermodesulfobacterium", "s__Thermodesulfobacterium commune" ], "_genome_taxon": [ "Thermodesulfobacterium", "commune", "d__Bacteria", "p__Desulfobacterota", "c__Thermodesulfobacteria", "o__Thermodesulfobacteriales", "f__Thermodesulfobacteriaceae", "g__Thermodesulfobacterium", "s__Thermodesulfobacterium commune", "Bacteria", "Desulfobacterota", "Thermodesulfobacteria", "Thermodesulfobacteriales", "Thermodesulfobacteriaceae", "Thermodesulfobacterium", "Thermodesulfobacterium", "commune" ], "_meo": [ { "id": "MEO_0001474", "label": "oil associated feature" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }