{ "type": "genome", "identifier": "GCF_000400975.1", "organism": "Halarchaeum acidiphilum MH1-52-1", "title": "Halarchaeum acidiphilum MH1-52-1", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Japan Agency for Marine-Earth Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000400975.1", "bioproject": "PRJNA224116", "biosample": "SAMD00036650", "wgs_master": "BANO00000000.1", "refseq_category": "na", "taxid": "1261545", "species_taxid": "489138", "organism_name": "Halarchaeum acidiphilum MH1-52-1", "infraspecific_name": "strain=MH1-52-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/05/16", "asm_name": "ASM40097v1", "asm_submitter": "Japan Agency for Marine-Earth Science and Technology", "gbrs_paired_asm": "GCA_000400975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/400/975/GCF_000400975.1_ASM40097v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "2431759", "genome_size_ungapped": "2431759", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "537", "contig_count": "537", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000400975.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "2887", "protein_coding_gene_count": "2363", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-05-16", "dateModified": "2013-05-16", "datePublished": "2013-05-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Halarchaeum acidiphilum MH1-52-1" ], "sample_taxid": [ "1261545" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.660 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.15, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2431759", "Number of Sequences": "537", "Longest Sequences (bp)": "41867", "N50 (bp)": "7386", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "2224", "Average Protein Length": "250.7", "Coding Ratio (%)": "68.8", "Number of rRNAs": "3", "Number of tRNAs": "36", "Number of CRISPRs": "11" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halarchaeum acidiphilum", "strain": "strain=MH1-52-1", "accession": "GCA_000400975.1", "taxid": 489138, "species_taxid": 489138, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 546, "total_fragments": 558, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halarchaeum acidiphilum", "strain": "strain=JCM 16109", "accession": "GCA_000474235.1", "taxid": 489138, "species_taxid": 489138, "relation_to_type": "type", "validated": true, "ani": 99.6905, "matched_fragments": 533, "total_fragments": 558, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halarchaeum rubridurum", "strain": "strain=DSM 22443", "accession": "GCA_017873775.1", "taxid": 489911, "species_taxid": 489911, "relation_to_type": "type", "validated": true, "ani": 87.2676, "matched_fragments": 419, "total_fragments": 558, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halarchaeum rubridurum", "strain": "strain=JCM 16108", "accession": "GCA_014647115.1", "taxid": 489911, "species_taxid": 489911, "relation_to_type": "type", "validated": true, "ani": 87.1991, "matched_fragments": 418, "total_fragments": 558, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halarchaeum grantii", "strain": "strain=JCM 19585", "accession": "GCA_014647455.2", "taxid": 1193105, "species_taxid": 1193105, "relation_to_type": "type", "validated": true, "ani": 85.0002, "matched_fragments": 406, "total_fragments": 558, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacterium bonnevillei", "strain": "strain=PCN9", "accession": "GCA_009831555.1", "taxid": 2692200, "species_taxid": 2692200, "relation_to_type": "type", "validated": true, "ani": 78.828, "matched_fragments": 228, "total_fragments": 558, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.15, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000474235.1", "gtdb_species": "s__Halarchaeum acidiphilum", "ani": 99.6905, "matched_fragments": 533, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014647115.1", "gtdb_species": "s__Halarchaeum rubridurum", "ani": 87.1991, "matched_fragments": 418, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum", "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_017874335.1", "gtdb_species": "s__Halarchaeum salinum", "ani": 86.8487, "matched_fragments": 420, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum", "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_014647155.1", "gtdb_species": "s__Halarchaeum nitratireducens", "ani": 86.545, "matched_fragments": 404, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014647455.2", "gtdb_species": "s__Halarchaeum grantii", "ani": 85.0127, "matched_fragments": 405, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.76", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000230955.2", "gtdb_species": "s__Halobacterium sp000230955", "ani": 79.1601, "matched_fragments": 243, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium", "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_009831555.1", "gtdb_species": "s__Halobacterium sp009831555", "ani": 78.8672, "matched_fragments": 226, "total_fragments": 558, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium", "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": 0.301, "cell_length": 0.085, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 4.45, "genome_size": 2617647.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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": [ "Halarchaeum", "acidiphilum", "MH1-52-1" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }