{ "type": "genome", "identifier": "GCF_000337735.1", "organism": "Natronorubrum sulfidifaciens JCM 14089", "title": "Natronorubrum sulfidifaciens JCM 14089", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of California, Davis", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000337735.1", "bioproject": "PRJNA224116", "biosample": "SAMN02471621", "wgs_master": "AOHX00000000.1", "refseq_category": "reference genome", "taxid": "1230460", "species_taxid": "388259", "organism_name": "Natronorubrum sulfidifaciens JCM 14089", "infraspecific_name": "strain=JCM 14089", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/02/04", "asm_name": "ASM33773v1", "asm_submitter": "University of California, Davis", "gbrs_paired_asm": "GCA_000337735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/735/GCF_000337735.1_ASM33773v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3460288", "genome_size_ungapped": "3460288", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "63", "contig_count": "63", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000337735.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "3498", "protein_coding_gene_count": "3375", "non_coding_gene_count": "55", "pubmed_id": "25393412" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-02-04", "dateModified": "2013-02-04", "datePublished": "2013-02-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Natronorubrum sulfidifaciens JCM 14089" ], "sample_taxid": [ "1230460" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.960 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3460288", "Number of Sequences": "63", "Longest Sequences (bp)": "461211", "N50 (bp)": "186182", "Gap Ratio (%)": "0.002774", "GCcontent (%)": "61.8", "Number of CDSs": "3391", "Average Protein Length": "286.6", "Coding Ratio (%)": "84.3", "Number of rRNAs": "2", "Number of tRNAs": "44", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Natronorubrum sulfidifaciens", "strain": "strain=JCM 14089", "accession": "GCA_000337735.1", "taxid": 388259, "species_taxid": 388259, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1125, "total_fragments": 1128, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Natronorubrum bangense", "strain": "strain=JCM 10635", "accession": "GCA_000337715.1", "taxid": 61858, "species_taxid": 61858, "relation_to_type": "type", "validated": true, "ani": 88.7652, "matched_fragments": 894, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronorubrum bangense", "strain": "strain=JCM 10635", "accession": "GCA_004799645.1", "taxid": 61858, "species_taxid": 61858, "relation_to_type": "type", "validated": true, "ani": 88.7417, "matched_fragments": 927, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronorubrum aibiense", "strain": "strain=7-3", "accession": "GCA_009392895.1", "taxid": 348826, "species_taxid": 348826, "relation_to_type": "type", "validated": true, "ani": 88.2881, "matched_fragments": 916, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronorubrum halalkaliphilum", "strain": "strain=JWXQ-INN-674", "accession": "GCA_009834785.1", "taxid": 2691917, "species_taxid": 2691917, "relation_to_type": "type", "validated": true, "ani": 81.814, "matched_fragments": 756, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natrinema altunense", "strain": "strain=AJ2", "accession": "GCA_000731985.1", "taxid": 222984, "species_taxid": 222984, "relation_to_type": "type", "validated": true, "ani": 80.6437, "matched_fragments": 610, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natrinema altunense", "strain": "strain=JCM 12890", "accession": "GCA_000337155.1", "taxid": 222984, "species_taxid": 222984, "relation_to_type": "type", "validated": true, "ani": 80.6207, "matched_fragments": 610, "total_fragments": 1128, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000337735.1", "gtdb_species": "s__Natronorubrum sulfidifaciens", "ani": 100.0, "matched_fragments": 1125, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum", "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_004799645.1", "gtdb_species": "s__Natronorubrum bangense", "ani": 88.7377, "matched_fragments": 923, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "95.84", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009392895.1", "gtdb_species": "s__Natronorubrum aibiense", "ani": 88.2961, "matched_fragments": 915, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum", "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_900156475.1", "gtdb_species": "s__Natronorubrum thiooxidans", "ani": 87.3978, "matched_fragments": 923, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum", "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_009834785.1", "gtdb_species": "s__Natronorubrum halalkaliphilum", "ani": 81.8415, "matched_fragments": 753, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum", "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_013342135.1", "gtdb_species": "s__Haloterrigena sp013342135", "ani": 81.5144, "matched_fragments": 738, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001953745.1", "gtdb_species": "s__Natrinema saccharevitans", "ani": 80.9963, "matched_fragments": 664, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "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_000731985.1", "gtdb_species": "s__Natrinema altunense", "ani": 80.6563, "matched_fragments": 610, "total_fragments": 1128, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.071, "cell_length": 0.267, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 45.5, "optimum_ph": 8.95, "genome_size": 3460288.0, "gc_content": null, "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": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Natronorubrum", "sulfidifaciens", "JCM", "14089" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }