{ "type": "genome", "identifier": "GCF_900129895.1", "organism": "Desulforamulus hydrothermalis Lam5 = DSM 18033", "title": "Desulforamulus hydrothermalis Lam5 = DSM 18033", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900129895.1", "bioproject": "PRJNA224116", "biosample": "SAMN02745177", "wgs_master": "FQXF00000000.1", "refseq_category": "na", "taxid": "1121428", "species_taxid": "412895", "organism_name": "Desulforamulus hydrothermalis Lam5 = DSM 18033", "infraspecific_name": "strain=DSM 18033", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2585428063 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900129895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/129/895/GCF_900129895.1_IMG-taxon_2585428063_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2628775", "genome_size_ungapped": "2628765", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "59", "contig_count": "59", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900129895.1-RS_2024_03_27", "annotation_date": "2024-03-27", "total_gene_count": "2744", "protein_coding_gene_count": "2643", "non_coding_gene_count": "81", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-03", "dateModified": "2016-12-03", "datePublished": "2016-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulforamulus hydrothermalis Lam5 = DSM 18033" ], "sample_taxid": [ "1121428" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tunisia:North East Tunisia" ], "sample_host_location_id": [], "data_size": "0.744 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2628775", "Number of Sequences": "59", "Longest Sequences (bp)": "391248", "N50 (bp)": "115768", "Gap Ratio (%)": "0.000380", "GCcontent (%)": "49.5", "Number of CDSs": "2587", "Average Protein Length": "294.3", "Coding Ratio (%)": "86.9", "Number of rRNAs": "4", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulforamulus hydrothermalis", "strain": "strain=DSM 18033", "accession": "GCA_900129895.1", "taxid": 412895, "species_taxid": 412895, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 842, "total_fragments": 846, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulforamulus hydrothermalis", "strain": "strain=Lam5", "accession": "GCA_000315365.1", "taxid": 412895, "species_taxid": 412895, "relation_to_type": "type", "validated": true, "ani": 99.952, "matched_fragments": 843, "total_fragments": 846, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulforamulus putei", "strain": "strain=DSM 12395", "accession": "GCA_900129195.1", "taxid": 74701, "species_taxid": 74701, "relation_to_type": "type", "validated": true, "ani": 81.035, "matched_fragments": 537, "total_fragments": 846, "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": 79.3358, "matched_fragments": 415, "total_fragments": 846, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfotomaculum nigrificans", "strain": "strain=DSM 574", "accession": "GCA_000189755.3", "taxid": 1565, "species_taxid": 1565, "relation_to_type": "type", "validated": true, "ani": 79.1148, "matched_fragments": 238, "total_fragments": 846, "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": 78.9126, "matched_fragments": 222, "total_fragments": 846, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulforamulus reducens", "strain": "strain=MI-1", "accession": "GCA_000016165.1", "taxid": 59610, "species_taxid": 59610, "relation_to_type": "type", "validated": true, "ani": 77.9392, "matched_fragments": 194, "total_fragments": 846, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_000315365.1", "gtdb_species": "s__Desulfotomaculum hydrothermale", "ani": 99.952, "matched_fragments": 843, "total_fragments": 846, "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": "conclusive" }, { "accession": "GCF_900129195.1", "gtdb_species": "s__Desulfotomaculum putei", "ani": 81.0305, "matched_fragments": 537, "total_fragments": 846, "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": 79.3358, "matched_fragments": 415, "total_fragments": 846, "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_000189755.2", "gtdb_species": "s__Desulfotomaculum nigrificans", "ani": 79.1348, "matched_fragments": 237, "total_fragments": 846, "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": 78.9135, "matched_fragments": 221, "total_fragments": 846, "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_900142375.1", "gtdb_species": "s__Desulfotomaculum aeronauticum", "ani": 77.9791, "matched_fragments": 177, "total_fragments": 846, "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_000016165.1", "gtdb_species": "s__Desulfotomaculum reducens", "ani": 77.9392, "matched_fragments": 194, "total_fragments": 846, "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": "-" } ] }, "_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", "hydrothermalis", "Lam5", "=", "DSM", "18033" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }