{ "type": "genome", "identifier": "GCF_000016165.1", "organism": "Desulforamulus reducens MI-1", "title": "Desulforamulus reducens MI-1", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000016165.1", "bioproject": "PRJNA224116", "biosample": "SAMN02598304", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "349161", "species_taxid": "59610", "organism_name": "Desulforamulus reducens MI-1", "infraspecific_name": "strain=MI-1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2007/03/24", "asm_name": "ASM1616v1", "asm_submitter": "US DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000016165.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/016/165/GCF_000016165.1_ASM1616v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3608104", "genome_size_ungapped": "3608104", "gc_percent": "42.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000016165.1-RS_2024_03_27", "annotation_date": "2024-03-27", "total_gene_count": "3636", "protein_coding_gene_count": "3489", "non_coding_gene_count": "100", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2007-03-24", "dateModified": "2007-03-24", "datePublished": "2007-03-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulforamulus reducens MI-1" ], "sample_taxid": [ "349161" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.019 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)": "3608104", "Number of Sequences": "1", "Longest Sequences (bp)": "3608104", "N50 (bp)": "3608104", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.3", "Number of CDSs": "3524", "Average Protein Length": "288.5", "Coding Ratio (%)": "84.5", "Number of rRNAs": "26", "Number of tRNAs": "70", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulforamulus reducens", "strain": "strain=MI-1", "accession": "GCA_000016165.1", "taxid": 59610, "species_taxid": 59610, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1199, "total_fragments": 1202, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfotomaculum nigrificans", "strain": "strain=DSM 574", "accession": "GCA_000189755.3", "taxid": 1565, "species_taxid": 1565, "relation_to_type": "type", "validated": true, "ani": 79.062, "matched_fragments": 172, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforamulus ferrireducens", "strain": "strain=GSS09", "accession": "GCA_002005145.1", "taxid": 1833852, "species_taxid": 1833852, "relation_to_type": "type", "validated": true, "ani": 78.8461, "matched_fragments": 221, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforamulus profundi", "strain": "strain=Bs107", "accession": "GCA_002607855.1", "taxid": 1383067, "species_taxid": 1383067, "relation_to_type": "type", "validated": true, "ani": 78.6601, "matched_fragments": 236, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforamulus putei", "strain": "strain=DSM 12395", "accession": "GCA_900129195.1", "taxid": 74701, "species_taxid": 74701, "relation_to_type": "type", "validated": true, "ani": 78.1875, "matched_fragments": 230, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforamulus hydrothermalis", "strain": "strain=Lam5", "accession": "GCA_000315365.1", "taxid": 412895, "species_taxid": 412895, "relation_to_type": "type", "validated": true, "ani": 77.8561, "matched_fragments": 208, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforamulus hydrothermalis", "strain": "strain=DSM 18033", "accession": "GCA_900129895.1", "taxid": 412895, "species_taxid": 412895, "relation_to_type": "type", "validated": true, "ani": 77.569, "matched_fragments": 204, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforadius tongensis", "strain": "strain=DSM 29799", "accession": "GCA_016907915.1", "taxid": 1216062, "species_taxid": 1216062, "relation_to_type": "type", "validated": true, "ani": 76.7423, "matched_fragments": 53, "total_fragments": 1202, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000016165.1", "gtdb_species": "s__Desulfotomaculum reducens", "ani": 100.0, "matched_fragments": 1200, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum", "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": "GCF_000189755.2", "gtdb_species": "s__Desulfotomaculum nigrificans", "ani": 79.1825, "matched_fragments": 174, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002005145.1", "gtdb_species": "s__Desulfotomaculum ferrireducens", "ani": 78.8977, "matched_fragments": 222, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum", "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_002607855.1", "gtdb_species": "s__Desulfotomaculum profundi", "ani": 78.6296, "matched_fragments": 236, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum", "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_900129195.1", "gtdb_species": "s__Desulfotomaculum putei", "ani": 78.1987, "matched_fragments": 230, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum", "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_000315365.1", "gtdb_species": "s__Desulfotomaculum hydrothermale", "ani": 77.8617, "matched_fragments": 209, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016907915.1", "gtdb_species": "s__Desulfohalotomaculum tongense", "ani": 76.7423, "matched_fragments": 53, "total_fragments": 1202, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfohalotomaculaceae;g__Desulfohalotomaculum", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Desulforamulus", "reducens", "MI-1" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }