{ "type": "genome", "identifier": "GCF_900113615.1", "organism": "Halorubrum aquaticum", "title": "Halorubrum aquaticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900113615.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488066", "wgs_master": "FOPZ00000000.1", "refseq_category": "reference genome", "taxid": "387340", "species_taxid": "387340", "organism_name": "Halorubrum aquaticum", "infraspecific_name": "strain=CGMCC 1.6377", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/11", "asm_name": "IMG-taxon 2617270873 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900113615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/113/615/GCF_900113615.1_IMG-taxon_2617270873_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": "3184102", "genome_size_ungapped": "3184102", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "40", "contig_count": "40", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900113615.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3199", "protein_coding_gene_count": "3079", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-11", "dateModified": "2019-09-11", "datePublished": "2019-09-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Halorubrum aquaticum" ], "sample_taxid": [ "387340" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.858 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3184102", "Number of Sequences": "40", "Longest Sequences (bp)": "391303", "N50 (bp)": "151981", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.4", "Number of CDSs": "3126", "Average Protein Length": "293.6", "Coding Ratio (%)": "86.5", "Number of rRNAs": "5", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halorubrum aquaticum", "strain": "strain=CGMCC 1.6377", "accession": "GCA_900113615.1", "taxid": 387340, "species_taxid": 387340, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1043, "total_fragments": 1045, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halorubrum cibi", "strain": "strain=DSM 19504", "accession": "GCA_900182635.1", "taxid": 413815, "species_taxid": 413815, "relation_to_type": "type", "validated": true, "ani": 92.0526, "matched_fragments": 818, "total_fragments": 1045, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum aethiopicum", "strain": "strain=SAH-A6", "accession": "GCA_001542905.1", "taxid": 1758255, "species_taxid": 1758255, "relation_to_type": "type", "validated": true, "ani": 90.6596, "matched_fragments": 809, "total_fragments": 1045, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum rubrum", "strain": "strain=YC87", "accession": "GCA_024494685.1", "taxid": 1126240, "species_taxid": 1126240, "relation_to_type": "type", "validated": true, "ani": 90.2656, "matched_fragments": 804, "total_fragments": 1045, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum halodurans", "strain": "strain=Cb34", "accession": "GCA_002252985.1", "taxid": 1383851, "species_taxid": 1383851, "relation_to_type": "type", "validated": true, "ani": 90.0093, "matched_fragments": 739, "total_fragments": 1045, "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": 83.7254, "matched_fragments": 650, "total_fragments": 1045, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900113615.1", "gtdb_species": "s__Halorubrum aquaticum", "ani": 100.0, "matched_fragments": 1043, "total_fragments": 1045, "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": "GCF_900182635.1", "gtdb_species": "s__Halorubrum cibi", "ani": 92.0526, "matched_fragments": 818, "total_fragments": 1045, "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_001542905.1", "gtdb_species": "s__Halorubrum aethiopicum", "ani": 90.6596, "matched_fragments": 809, "total_fragments": 1045, "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": 90.0383, "matched_fragments": 737, "total_fragments": 1045, "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_003697845.1", "gtdb_species": "s__Halorubrum sp003697845", "ani": 89.6701, "matched_fragments": 816, "total_fragments": 1045, "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_003287355.1", "gtdb_species": "s__Halorubrum sp003287355", "ani": 88.8163, "matched_fragments": 787, "total_fragments": 1045, "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": -0.207, "cell_length": 0.287, "doubling_h": 0.945, "growth_tmp": 37.0, "optimum_tmp": 38.687, "optimum_ph": 7.755, "genome_size": 3184102.0, "gc_content": 66.134, "coding_genes": 3172.833, "rRNA16S_genes": 2.5, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.857, "range_salinity": 1.0, "facultative_respiration": 0.13, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.869, "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", "aquaticum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }