{ "type": "genome", "identifier": "GCF_000231405.2", "organism": "Desulfitobacterium metallireducens DSM 15288", "title": "Desulfitobacterium metallireducens DSM 15288", "description": "na", "data type": "Genome sequencing and assembly", "organization": "JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000231405.2", "bioproject": "PRJNA224116", "biosample": "SAMN02261393", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "871968", "species_taxid": "142877", "organism_name": "Desulfitobacterium metallireducens DSM 15288", "infraspecific_name": "strain=DSM 15288", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/01/03", "asm_name": "ASM23140v3", "asm_submitter": "JGI", "gbrs_paired_asm": "GCA_000231405.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/231/405/GCF_000231405.2_ASM23140v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3176073", "genome_size_ungapped": "3176073", "gc_percent": "42.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000231405.2-RS_2024_05_13", "annotation_date": "2024-05-13", "total_gene_count": "3122", "protein_coding_gene_count": "2994", "non_coding_gene_count": "101", "pubmed_id": "29040502" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-01-03", "dateModified": "2014-01-03", "datePublished": "2014-01-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfitobacterium metallireducens DSM 15288" ], "sample_taxid": [ "871968" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.902 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": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3176073", "Number of Sequences": "1", "Longest Sequences (bp)": "3176073", "N50 (bp)": "3176073", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "41.9", "Number of CDSs": "3043", "Average Protein Length": "300.1", "Coding Ratio (%)": "86.3", "Number of rRNAs": "24", "Number of tRNAs": "73", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfitobacterium metallireducens", "strain": "strain=853-15A", "accession": "GCA_000231405.3", "taxid": 142877, "species_taxid": 142877, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1057, "total_fragments": 1058, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfosporosinus meridiei", "strain": "strain=DSM 13257", "accession": "GCA_000231385.3", "taxid": 79209, "species_taxid": 79209, "relation_to_type": "type", "validated": true, "ani": 79.1735, "matched_fragments": 73, "total_fragments": 1058, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfosporosinus lacus", "strain": "strain=DSM 15449", "accession": "GCA_900129935.1", "taxid": 329936, "species_taxid": 329936, "relation_to_type": "type", "validated": true, "ani": 77.4598, "matched_fragments": 67, "total_fragments": 1058, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfosporosinus hippei", "strain": "strain=DSM 8344", "accession": "GCA_900100785.1", "taxid": 569859, "species_taxid": 569859, "relation_to_type": "type", "validated": true, "ani": 77.1728, "matched_fragments": 59, "total_fragments": 1058, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfitobacterium chlororespirans", "strain": "strain=DSM 11544", "accession": "GCA_900143285.1", "taxid": 51616, "species_taxid": 51616, "relation_to_type": "type", "validated": true, "ani": 77.1466, "matched_fragments": 72, "total_fragments": 1058, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000231405.2", "gtdb_species": "s__Desulfitobacterium_A metallireducens", "ani": 100.0, "matched_fragments": 1058, "total_fragments": 1058, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium_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": 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1, "status": "-" }, { "accession": "GCA_000961805.1", "gtdb_species": "s__Desulfosporosinus sp000961805", "ani": 76.3308, "matched_fragments": 52, "total_fragments": 1058, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.68", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.369, "doubling_h": 0.522, "growth_tmp": 36.35, "optimum_tmp": 34.968, "optimum_ph": 7.333, "genome_size": 4741950.359, "gc_content": 45.544, "coding_genes": 4081.622, "rRNA16S_genes": 5.777, "tRNA_genes": 70.889, "gram_stain": 0.0, "sporulation": 1.0, "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": 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 }, "_genome_taxon": [ "Desulfitobacterium", "metallireducens", "DSM", "15288" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }