{ "type": "genome", "identifier": "GCA_001751225.1", "organism": "Desulfuromonadales bacterium C00003107", "title": "Desulfuromonadales bacterium C00003107", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "California Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCA_001751225.1", "bioproject": "PRJNA290197", "biosample": "SAMN05301626", "wgs_master": "MAXT00000000.1", "refseq_category": "na", "taxid": "1869309", "species_taxid": "1869309", "organism_name": "Desulfuromonadales bacterium C00003107", "infraspecific_name": "", "isolate": "C00003107", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/03", "asm_name": "ASM175122v1", "submitter": "California Institute of Technology", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/751/225/GCA_001751225.1_ASM175122v1", "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": "2016-10-03", "dateModified": "2016-10-03", "datePublished": "2016-10-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfuromonadales bacterium C00003107" ], "sample_taxid": [ "1869309" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean: Hydrate Ridge North" ], "sample_host_location_id": [], "data_size": "0.728 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 90.53, "contamination": 18.92, "strain_heterogeneity": 5.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2530867", "Number of Sequences": "423", "Longest Sequences (bp)": "30747", "N50 (bp)": "7116", "Gap Ratio (%)": "0.658035", "GCcontent (%)": "52.7", "Number of CDSs": "2009", "Average Protein Length": "284.8", "Coding Ratio (%)": "67.8", "Number of rRNAs": "0", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Syntrophotalea acetylenivorans", "strain": "strain=SFB93", "accession": "GCA_001887775.1", "taxid": 1842532, "species_taxid": 1842532, "relation_to_type": "type", "validated": true, "ani": 81.1483, "matched_fragments": 373, "total_fragments": 635, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas versatilis", "strain": "strain=NIT-T3", "accession": "GCA_019704135.1", "taxid": 2802975, "species_taxid": 2802975, "relation_to_type": "type", "validated": true, "ani": 76.9294, "matched_fragments": 62, "total_fragments": 635, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Syntrophotalea carbinolica", "strain": "strain=DSM 2380", "accession": "GCA_000012885.1", "taxid": 19, "species_taxid": 19, "relation_to_type": "type", "validated": true, "ani": 76.9251, "matched_fragments": 74, "total_fragments": 635, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas acetexigens", "strain": "strain=2873", "accession": "GCA_007051125.1", "taxid": 38815, "species_taxid": 38815, "relation_to_type": "type", "validated": true, "ani": 76.7029, "matched_fragments": 58, "total_fragments": 635, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas acetexigens", "strain": "", "accession": "GCA_900111775.1", "taxid": 38815, "species_taxid": 38815, "relation_to_type": "type", "validated": true, "ani": 76.7029, "matched_fragments": 58, "total_fragments": 635, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas soudanensis", "strain": "strain=WTL", "accession": "GCA_001278055.1", "taxid": 1603606, "species_taxid": 1603606, "relation_to_type": "type", "validated": true, "ani": 76.52, "matched_fragments": 60, "total_fragments": 635, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 90.53, "contamination": 18.92, "strain_heterogeneity": 5.0 }, "gtdb_result": [ { "accession": "GCA_001751225.1", "gtdb_species": "s__Syntrophotalea_A sp001751225", "ani": 100.0, "matched_fragments": 630, "total_fragments": 635, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea_A", "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": "GCA_013619105.1", "gtdb_species": "s__Syntrophotalea_A sp013619105", "ani": 88.5681, "matched_fragments": 425, "total_fragments": 635, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea_A", "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_001887775.1", "gtdb_species": "s__Syntrophotalea_A acetylenivorans", "ani": 81.1483, "matched_fragments": 373, "total_fragments": 635, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea_A", "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_007134025.1", "gtdb_species": "s__SLLR01 sp007134025", "ani": 77.5433, "matched_fragments": 108, "total_fragments": 635, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__SLLR01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_003561875.1", "gtdb_species": "s__SLLR01 sp003561875", "ani": 77.2489, "matched_fragments": 94, "total_fragments": 635, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__SLLR01", "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_900111775.1", "gtdb_species": "s__Trichloromonas acetexigens", "ani": 76.6958, "matched_fragments": 58, "total_fragments": 635, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas", "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": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.313, "cell_length": 0.202, "doubling_h": 0.943, "growth_tmp": 29.222, "optimum_tmp": 27.813, "optimum_ph": 7.044, "genome_size": 3929744.378, "gc_content": 58.184, "coding_genes": 3362.515, "rRNA16S_genes": 2.727, "tRNA_genes": 51.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.777, "range_salinity": 0.5, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.904, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.047, "vibrio_cell_shape": 0.047, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfuromonadia", "o__Desulfuromonadales", "f__Syntrophotaleaceae", "g__Syntrophotalea_A", "s__Syntrophotalea_A sp001751225" ], "_genome_taxon": [ "Desulfuromonadales", "bacterium", "C00003107", "d__Bacteria", "p__Desulfobacterota", "c__Desulfuromonadia", "o__Desulfuromonadales", "f__Syntrophotaleaceae", "g__Syntrophotalea_A", "s__Syntrophotalea_A sp001751225", "Bacteria", "Desulfobacterota", "Desulfuromonadia", "Desulfuromonadales", "Syntrophotaleaceae", "Syntrophotalea", "A", "Syntrophotalea", "A", "sp001751225" ], "_meo": [ { "id": "MEO_0000040", "label": "marine sediment" }, { "id": "MEO_0001378", "label": "deep" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }