{ "type": "genome", "identifier": "GCA_004193555.1", "organism": "Desulfobacteraceae bacterium Eth-SRB1", "title": "Desulfobacteraceae bacterium Eth-SRB1", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Helmholtz Centre for Environmental Research GmbH - UFZ", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004193555.1", "bioproject": "PRJNA495932", "biosample": "SAMN10235261", "wgs_master": "RPGP00000000.1", "refseq_category": "na", "taxid": "2528437", "species_taxid": "2528437", "organism_name": "Desulfobacteraceae bacterium Eth-SRB1", "infraspecific_name": "", "isolate": "Eth-SRB1", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/12", "asm_name": "ASM419355v1", "submitter": "Helmholtz Centre for Environmental Research GmbH - UFZ", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/193/555/GCA_004193555.1_ASM419355v1", "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": "2019-02-12", "dateModified": "2019-02-12", "datePublished": "2019-02-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfobacteraceae bacterium Eth-SRB1" ], "sample_taxid": [ "2528437" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Atlantic Ocean: Gulf of Mexico" ], "sample_host_location_id": [], "data_size": "0.943 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3338582", "Number of Sequences": "52", "Longest Sequences (bp)": "1330458", "N50 (bp)": "1248101", "Gap Ratio (%)": "0.000300", "GCcontent (%)": "42.3", "Number of CDSs": "3012", "Average Protein Length": "299.7", "Coding Ratio (%)": "81.1", "Number of rRNAs": "5", "Number of tRNAs": "53", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfonema magnum", "strain": "strain=4be13", "accession": "GCA_017377395.1", "taxid": 45655, "species_taxid": 45655, "relation_to_type": "type", "validated": true, "ani": 76.3607, "matched_fragments": 75, "total_fragments": 1089, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004193555.1", "gtdb_species": "s__ETH-SRB1 sp004193555", "ani": 100.0, "matched_fragments": 1088, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__ETH-SRB1", "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_014381545.1", "gtdb_species": "s__Desulfaltia bathyphila", "ani": 82.606, "matched_fragments": 383, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__Desulfaltia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.82", "min_intra_species_ani": "99.78", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_013202725.1", "gtdb_species": "s__Desulfaltia sp013202725", "ani": 82.0677, "matched_fragments": 241, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__Desulfaltia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.32", "min_intra_species_ani": "96.29", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_004193595.1", "gtdb_species": "s__S5133MH16 sp004193595", "ani": 80.3834, "matched_fragments": 145, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16", "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_013792055.1", "gtdb_species": "s__B13-G4 sp013792055", "ani": 78.0645, "matched_fragments": 192, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "97.50", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_018897415.1", "gtdb_species": "s__B13-G4 sp018897415", "ani": 77.9851, "matched_fragments": 125, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "99.07", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001751005.1", "gtdb_species": "s__S5133MH16 sp001751005", "ani": 76.4516, "matched_fragments": 87, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16", "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_017377395.1", "gtdb_species": "s__Desulfonema_C magnum", "ani": 76.4291, "matched_fragments": 71, "total_fragments": 1089, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__4be13;g__Desulfonema_C", "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": -0.042, "cell_length": 0.364, "doubling_h": 1.305, "growth_tmp": 28.037, "optimum_tmp": 30.588, "optimum_ph": 7.267, "genome_size": 5675869.625, "gc_content": 51.573, "coding_genes": 4621.583, "rRNA16S_genes": 3.75, "tRNA_genes": 52.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.619, "range_salinity": 1.0, "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": 0.695, "coccus_cell_shape": 0.043, "filament_cell_shape": 0.043, "coccobacillus_cell_shape": 0.086, "vibrio_cell_shape": 0.13, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfobacteria", "o__Desulfobacterales", "f__ETH-SRB1", "g__ETH-SRB1", "s__ETH-SRB1 sp004193555" ], "_genome_taxon": [ "Desulfobacteraceae", "bacterium", "Eth-SRB1", "d__Bacteria", "p__Desulfobacterota", "c__Desulfobacteria", "o__Desulfobacterales", "f__ETH-SRB1", "g__ETH-SRB1", "s__ETH-SRB1 sp004193555", "Bacteria", "Desulfobacterota", "Desulfobacteria", "Desulfobacterales", "ETH-SRB1", "ETH-SRB1", "ETH-SRB1", "sp004193555" ], "_meo": [ { "id": "MEO_0000040", "label": "marine sediment" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }