{ "type": "genome", "identifier": "GCF_900104065.1", "organism": "Natronobacterium texcoconense", "title": "Natronobacterium texcoconense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900104065.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489842", "wgs_master": "FNLC00000000.1", "refseq_category": "reference genome", "taxid": "1095778", "species_taxid": "1095778", "organism_name": "Natronobacterium texcoconense", "infraspecific_name": "strain=DSM 24767", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/21", "asm_name": "IMG-taxon 2636416047 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900104065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/104/065/GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "4009868", "genome_size_ungapped": "4009788", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900104065.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "4112", "protein_coding_gene_count": "4023", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-21", "dateModified": "2016-10-21", "datePublished": "2016-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Natronobacterium texcoconense" ], "sample_taxid": [ "1095778" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.100 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4009868", "Number of Sequences": "9", "Longest Sequences (bp)": "1458395", "N50 (bp)": "1245734", "Gap Ratio (%)": "0.001995", "GCcontent (%)": "62.9", "Number of CDSs": "4022", "Average Protein Length": "289.2", "Coding Ratio (%)": "87.0", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Natronobacterium texcoconense", "strain": "strain=DSM 24767", "accession": "GCA_900104065.1", "taxid": 1095778, "species_taxid": 1095778, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1332, "total_fragments": 1332, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Natronobacterium gregoryi", "strain": "strain=SP2", "accession": "GCA_002855455.1", "taxid": 44930, "species_taxid": 44930, "relation_to_type": "type", "validated": true, "ani": 85.2903, "matched_fragments": 866, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronobacterium gregoryi", "strain": "strain=SP2", "accession": "GCA_900114025.1", "taxid": 44930, "species_taxid": 44930, "relation_to_type": "type", "validated": true, "ani": 85.2262, "matched_fragments": 902, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronobacterium gregoryi", "strain": "strain=SP2", "accession": "GCA_000337655.1", "taxid": 44930, "species_taxid": 44930, "relation_to_type": "type", "validated": true, "ani": 85.1471, "matched_fragments": 874, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronobacterium gregoryi", "strain": "strain=SP2", "accession": "GCA_000230715.3", "taxid": 44930, "species_taxid": 44930, "relation_to_type": "type", "validated": true, "ani": 85.1231, "matched_fragments": 925, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobiforma haloterrestris", "strain": "strain=DSM 13078", "accession": "GCA_900112205.1", "taxid": 148448, "species_taxid": 148448, "relation_to_type": "type", "validated": true, "ani": 83.1434, "matched_fragments": 900, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobiforma lacisalsi", "strain": "strain=AJ5", "accession": "GCA_000226975.3", "taxid": 229731, "species_taxid": 229731, "relation_to_type": "type", "validated": true, "ani": 83.1303, "matched_fragments": 890, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopiger xanaduensis", "strain": "strain=SH-6", "accession": "GCA_000217715.1", "taxid": 387343, "species_taxid": 387343, "relation_to_type": "type", "validated": true, "ani": 81.4464, "matched_fragments": 760, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopiger goleimassiliensis", "strain": "strain=IIH3", "accession": "GCA_000455345.1", "taxid": 1293048, "species_taxid": 1293048, "relation_to_type": "type", "validated": true, "ani": 81.4258, "matched_fragments": 768, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopiger aswanensis", "strain": "strain=DSM 13151", "accession": "GCA_003610195.1", "taxid": 148449, "species_taxid": 148449, "relation_to_type": "type", "validated": true, "ani": 81.4036, "matched_fragments": 796, "total_fragments": 1332, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900104065.1", "gtdb_species": "s__Natronobacterium texcoconense", "ani": 100.0, "matched_fragments": 1332, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium", "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_000230715.2", "gtdb_species": "s__Natronobacterium gregoryi", "ani": 85.1461, "matched_fragments": 923, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900112205.1", "gtdb_species": "s__Halobiforma haloterrestris", "ani": 83.1434, "matched_fragments": 901, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma", "ani_circumscription_radius": 95.4693, "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_000226975.2", "gtdb_species": "s__Halobiforma lacisalsi", "ani": 83.1433, "matched_fragments": 889, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma", "ani_circumscription_radius": 95.4693, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000337895.1", "gtdb_species": "s__Halobiforma nitratireducens", "ani": 82.5422, "matched_fragments": 750, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma", "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_000217715.1", "gtdb_species": "s__Halopiger xanaduensis", "ani": 81.4987, "matched_fragments": 754, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger", "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_000455345.1", "gtdb_species": "s__Halopiger_A goleimassiliensis", "ani": 81.4389, "matched_fragments": 765, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_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": "-" }, { "accession": "GCF_003610195.1", "gtdb_species": "s__Halopiger aswanensis", "ani": 81.4303, "matched_fragments": 792, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger", "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_017352155.1", "gtdb_species": "s__Haloterrigena sp017352155", "ani": 81.313, "matched_fragments": 686, "total_fragments": 1332, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena", "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": -0.046, "cell_length": 0.929, "doubling_h": 0.301, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 8.0, "genome_size": 4009868.0, "gc_content": 62.2, "coding_genes": 3615.333, "rRNA16S_genes": 3.0, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Natronobacterium", "texcoconense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }