{ "type": "genome", "identifier": "GCF_900188065.1", "organism": "Halorubrum vacuolatum", "title": "Halorubrum vacuolatum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900188065.1", "bioproject": "PRJNA224116", "biosample": "SAMN06264855", "wgs_master": "FZNQ00000000.1", "refseq_category": "reference genome", "taxid": "63740", "species_taxid": "63740", "organism_name": "Halorubrum vacuolatum", "infraspecific_name": "strain=DSM 8800", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/07/16", "asm_name": "IMG-taxon 2724679803 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900188065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/188/065/GCF_900188065.1_IMG-taxon_2724679803_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": "3477860", "genome_size_ungapped": "3477860", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900188065.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "3421", "protein_coding_gene_count": "3253", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-07-16", "dateModified": "2017-07-16", "datePublished": "2017-07-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Halorubrum vacuolatum" ], "sample_taxid": [ "63740" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Kenya:Lake Magadi, Kenya" ], "sample_host_location_id": [], "data_size": "0.965 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 5.56, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3477860", "Number of Sequences": "72", "Longest Sequences (bp)": "488433", "N50 (bp)": "153076", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.9", "Number of CDSs": "3335", "Average Protein Length": "299.2", "Coding Ratio (%)": "86.1", "Number of rRNAs": "2", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halorubrum halodurans", "strain": "strain=Cb34", "accession": "GCA_002252985.1", "taxid": 1383851, 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true, "ani": 80.096, "matched_fragments": 509, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum depositum", "strain": "strain=Y78", "accession": "GCA_007671725.1", "taxid": 2583992, "species_taxid": 2583992, "relation_to_type": "type", "validated": true, "ani": 80.0791, "matched_fragments": 498, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum saccharovorum", "strain": "strain=DSM 1137", "accession": "GCA_000337915.1", "taxid": 2248, "species_taxid": 2248, "relation_to_type": "type", "validated": true, "ani": 80.0034, "matched_fragments": 477, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum lipolyticum", "strain": "strain=DSM 21995", "accession": "GCA_000337375.1", "taxid": 368624, "species_taxid": 368624, "relation_to_type": "type", "validated": true, "ani": 79.871, "matched_fragments": 476, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum salipaludis", "strain": "strain=WN019", "accession": "GCA_002286985.1", "taxid": 2032630, "species_taxid": 2032630, "relation_to_type": "type", "validated": true, "ani": 79.8688, "matched_fragments": 498, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum rutilum", "strain": "strain=YJ-18-S1", "accession": "GCA_024494565.1", "taxid": 1364933, "species_taxid": 1364933, "relation_to_type": "type", "validated": true, "ani": 79.8667, "matched_fragments": 503, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum arcis", "strain": "strain=JCM 13916", "accession": "GCA_000337015.1", "taxid": 368454, "species_taxid": 368454, "relation_to_type": "type", "validated": true, "ani": 79.8225, "matched_fragments": 494, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum aidingense", "strain": "strain=JCM 13560", "accession": "GCA_000336995.1", "taxid": 368623, "species_taxid": 368623, "relation_to_type": "type", "validated": true, "ani": 79.7857, "matched_fragments": 496, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum persicum", "strain": "strain=C49", "accession": "GCA_002727125.1", "taxid": 1383844, "species_taxid": 1383844, "relation_to_type": "type", "validated": true, "ani": 79.694, "matched_fragments": 482, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum salinum", "strain": "strain=GX71", "accession": "GCA_024494575.1", "taxid": 767517, "species_taxid": 767517, "relation_to_type": "type", "validated": true, "ani": 79.5471, "matched_fragments": 429, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 5.56, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900188065.1", "gtdb_species": "s__Halorubrum vacuolatum", "ani": 100.0, "matched_fragments": 1117, "total_fragments": 1123, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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": "GCA_003554605.1", "gtdb_species": "s__Halorubrum sp003554605", "ani": 87.7194, "matched_fragments": 579, "total_fragments": 1123, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.64", "min_intra_species_ani": "99.64", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009806985.1", "gtdb_species": "s__Halorubrum sp009806985", "ani": 80.964, "matched_fragments": 561, "total_fragments": 1123, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_002252985.1", "gtdb_species": "s__Halorubrum halodurans", "ani": 80.2653, "matched_fragments": 466, "total_fragments": 1123, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_007671725.1", "gtdb_species": 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"gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000336995.1", "gtdb_species": "s__Halorubrum aidingense", "ani": 79.7889, "matched_fragments": 495, "total_fragments": 1123, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_002727125.1", "gtdb_species": "s__Halorubrum persicum", "ani": 79.737, "matched_fragments": 478, "total_fragments": 1123, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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": -0.302, "cell_length": 0.176, "doubling_h": 0.945, "growth_tmp": 37.0, "optimum_tmp": 37.5, "optimum_ph": 7.755, "genome_size": 3477860.0, "gc_content": 66.134, "coding_genes": 3172.833, "rRNA16S_genes": 2.5, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Halorubrum", "vacuolatum" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }