{ "type": "genome", "identifier": "GCF_000934745.1", "organism": "Desulfonatronum thioautotrophicum", "title": "Desulfonatronum thioautotrophicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000934745.1", "bioproject": "PRJNA224116", "biosample": "SAMN03351823", "wgs_master": "JYNO00000000.1", "refseq_category": "reference genome", "taxid": "617001", "species_taxid": "617001", "organism_name": "Desulfonatronum thioautotrophicum", "infraspecific_name": "strain=ASO4-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/02/26", "asm_name": "ASM93474v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000934745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/934/745/GCF_000934745.1_ASM93474v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4634603", "genome_size_ungapped": "4628390", "gc_percent": "57.000000", "replicon_count": "0", "scaffold_count": "53", "contig_count": "63", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000934745.1-RS_2024_07_03", "annotation_date": "2024-07-03", "total_gene_count": "4303", "protein_coding_gene_count": "4185", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-02-26", "dateModified": "2015-02-26", "datePublished": "2015-02-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfonatronum thioautotrophicum" ], "sample_taxid": [ "617001" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: South West Siberia" ], "sample_host_location_id": [], "data_size": "1.309 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4634603", "Number of Sequences": "53", "Longest Sequences (bp)": "1103534", "N50 (bp)": "457370", "Gap Ratio (%)": "0.134057", "GCcontent (%)": "57.0", "Number of CDSs": "4193", "Average Protein Length": "314.4", "Coding Ratio (%)": "85.3", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfonatronum thioautotrophicum", "strain": "strain=ASO4-1", "accession": "GCA_000934745.1", "taxid": 617001, "species_taxid": 617001, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1519, "total_fragments": 1520, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfonatronum lacustre", "strain": "strain=DSM 10312", "accession": "GCA_000519265.1", "taxid": 66849, "species_taxid": 66849, "relation_to_type": "type", "validated": true, "ani": 81.7872, "matched_fragments": 756, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonatronum thiodismutans", "strain": "strain=MLF-1", "accession": "GCA_000717475.2", "taxid": 159290, "species_taxid": 159290, "relation_to_type": "type", "validated": true, "ani": 81.7436, "matched_fragments": 766, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonatronum thiosulfatophilum", "strain": "strain=ASO4-2", "accession": "GCA_900104215.1", "taxid": 617002, "species_taxid": 617002, "relation_to_type": "type", "validated": true, "ani": 78.9245, "matched_fragments": 473, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio sulfodismutans", "strain": "strain=DSM 3696", "accession": "GCA_010499425.1", "taxid": 63561, "species_taxid": 63561, "relation_to_type": "type", "validated": true, "ani": 76.13, "matched_fragments": 118, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio sulfodismutans", "strain": "strain=DSM 3696", "accession": "GCA_013376455.1", "taxid": 63561, "species_taxid": 63561, "relation_to_type": "type", "validated": true, "ani": 76.1054, "matched_fragments": 121, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfohalovibrio reitneri", "strain": "strain=L21-Syr-AB", "accession": "GCA_000711295.1", "taxid": 1307759, "species_taxid": 1307759, "relation_to_type": "type", "validated": true, "ani": 76.0979, "matched_fragments": 105, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paucidesulfovibrio gracilis", "strain": "strain=DSM 16080", "accession": "GCA_900167125.1", "taxid": 47158, "species_taxid": 47158, "relation_to_type": "type", "validated": true, "ani": 75.8222, "matched_fragments": 64, "total_fragments": 1520, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000934745.1", "gtdb_species": "s__Desulfonatronum thioautotrophicum", "ani": 100.0, "matched_fragments": 1519, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_007693505.1", "gtdb_species": "s__Desulfonatronum sp007693505", "ani": 90.8267, "matched_fragments": 1047, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_000519265.1", "gtdb_species": "s__Desulfonatronum lacustre", "ani": 81.7944, "matched_fragments": 756, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_000717475.1", "gtdb_species": "s__Desulfonatronum thiodismutans", "ani": 81.707, "matched_fragments": 770, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_003046795.1", "gtdb_species": "s__Desulfonatronum sp003046795", "ani": 81.6537, "matched_fragments": 752, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_007127655.1", "gtdb_species": "s__Desulfonatronum sp007127655", "ani": 81.5287, "matched_fragments": 478, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_900104215.1", "gtdb_species": "s__Desulfonatronum thiosulfatophilum", "ani": 78.9247, "matched_fragments": 473, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum", "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_013376475.1", "gtdb_species": "s__Desulfolutivibrio sulfoxidireducens", "ani": 76.1839, "matched_fragments": 120, "total_fragments": 1520, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.285, "cell_length": 0.161, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 36.833, "optimum_ph": 8.5, "genome_size": 4634603.0, "gc_content": 59.3, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.5, "spiral_cell_shape": 0.5 }, "_genome_taxon": [ "Desulfonatronum", "thioautotrophicum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }