{ "type": "genome", "identifier": "GCA_000416005.1", "organism": "Haloquadratum sp. J07HQX50", "title": "Haloquadratum sp. J07HQX50", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, San Diego, Scripps Institution of Oceanography", "publication": [ {} ], "properties": { "assembly_accession": "GCA_000416005.1", "bioproject": "PRJNA176227", "biosample": "SAMN01940911", "wgs_master": "ARPZ00000000.1", "refseq_category": "na", "taxid": "1238426", "species_taxid": "1238426", "organism_name": "Haloquadratum sp. J07HQX50", "infraspecific_name": "", "isolate": "", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/04", "asm_name": "HQX_031812", "submitter": "University of California, San Diego, Scripps Institution of Oceanography", "gbrs_paired_asm": "GCF_000416005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/416/005/GCA_000416005.1_HQX_031812", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-04", "dateModified": "2013-09-04", "datePublished": "2013-09-04", "_annotation": { "sample_count": 1, "sample_organism": [ "hypersaline lake metagenome" ], "sample_taxid": [ "904678" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia: Victoria" ], "sample_host_location_id": [], "data_size": "0.727 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 74.53, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3019909", "Number of Sequences": "2", "Longest Sequences (bp)": "1543888", "N50 (bp)": "1543888", "Gap Ratio (%)": "18.042630", "GCcontent (%)": "50.7", "Number of CDSs": "2263", "Average Protein Length": "247.7", "Coding Ratio (%)": "55.7", "Number of rRNAs": "3", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halosegnis rubeus", "strain": "strain=F17-44", "accession": "GCA_009184545.1", "taxid": 2212850, "species_taxid": 2212850, "relation_to_type": "type", "validated": true, "ani": 77.3347, "matched_fragments": 50, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloquadratum walsbyi", "strain": "strain=DSM 16854 = C23", "accession": "GCA_000237865.1", "taxid": 293091, "species_taxid": 293091, "relation_to_type": "type", "validated": true, "ani": 76.7518, "matched_fragments": 105, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloprofundus marisrubri", "strain": "strain=SB9", "accession": "GCA_001469955.1", "taxid": 1514971, "species_taxid": 1514971, "relation_to_type": "type", "validated": true, "ani": 75.7477, "matched_fragments": 56, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halogranum salarium", "strain": "strain=B-1", "accession": "GCA_000283335.1", "taxid": 693851, "species_taxid": 693851, "relation_to_type": "type", "validated": true, "ani": 75.6913, "matched_fragments": 60, "total_fragments": 1006, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 74.53, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_000416005.1", "gtdb_species": "s__Haloquadratum sp000416005", "ani": 99.9236, "matched_fragments": 909, "total_fragments": 1006, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloquadratum", "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_000237865.1", "gtdb_species": "s__Haloquadratum walsbyi", "ani": 76.7518, "matched_fragments": 105, "total_fragments": 1006, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloquadratum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001469955.1", "gtdb_species": "s__Haloprofundus marisrubri", "ani": 75.7628, "matched_fragments": 55, "total_fragments": 1006, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus", "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": -0.699, "cell_length": 0.301, "doubling_h": 1.38, "growth_tmp": 37.0, "optimum_tmp": 45.0, "optimum_ph": 6.75, "genome_size": 3219918.875, "gc_content": 48.093, "coding_genes": 2687.8, "rRNA16S_genes": 2.0, "tRNA_genes": 44.333, "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": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Archaea", "p__Halobacteriota", "c__Halobacteria", "o__Halobacteriales", "f__Haloferacaceae", "g__Haloquadratum", "s__Haloquadratum sp000416005" ], "_genome_taxon": [ "Haloquadratum", "sp.", "J07HQX50", "d__Archaea", "p__Halobacteriota", "c__Halobacteria", "o__Halobacteriales", "f__Haloferacaceae", "g__Haloquadratum", "s__Haloquadratum sp000416005", "Archaea", "Halobacteriota", "Halobacteria", "Halobacteriales", "Haloferacaceae", "Haloquadratum", "Haloquadratum", "sp000416005" ], "_meo": [ { "id": "MEO_0000024", "label": "lake" }, { "id": "MEO_0000177", "label": "saline lake" } ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }