{ "type": "genome", "identifier": "GCF_007671725.1", "organism": "Halorubrum depositum", "title": "Halorubrum depositum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Anhui Normal University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007671725.1", "bioproject": "PRJNA224116", "biosample": "SAMN11869061", "wgs_master": "VCNM00000000.1", "refseq_category": "reference genome", "taxid": "2583992", "species_taxid": "2583992", "organism_name": "Halorubrum depositum", "infraspecific_name": "strain=Y78", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/30", "asm_name": "ASM767172v1", "asm_submitter": "Anhui Normal University", "gbrs_paired_asm": "GCA_007671725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/671/725/GCF_007671725.1_ASM767172v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3182860", "genome_size_ungapped": "3182860", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007671725.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3227", "protein_coding_gene_count": "3142", "non_coding_gene_count": "59", "pubmed_id": "29322241" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-30", "dateModified": "2019-07-30", "datePublished": "2019-07-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Halorubrum depositum" ], "sample_taxid": [ "2583992" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Yunnan" ], "sample_host_location_id": [], "data_size": "0.852 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)": "3182860", "Number of Sequences": "5", "Longest Sequences (bp)": "1474589", "N50 (bp)": "1386341", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.6", "Number of CDSs": "3184", "Average Protein Length": "292.8", "Coding Ratio (%)": "87.9", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halorubrum depositum", "strain": "strain=Y78", "accession": "GCA_007671725.1", "taxid": 2583992, "species_taxid": 2583992, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1058, "total_fragments": 1059, "ani_threshold": 95, "status": "conclusive" }, { "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": 90.9601, "matched_fragments": 766, "total_fragments": 1059, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum salsamenti", "strain": "strain=Y69", "accession": "GCA_007671685.1", "taxid": 2583990, "species_taxid": 2583990, "relation_to_type": "type", "validated": true, "ani": 88.1403, "matched_fragments": 786, "total_fragments": 1059, "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": 87.8794, "matched_fragments": 746, "total_fragments": 1059, "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": 87.6763, "matched_fragments": 778, "total_fragments": 1059, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum halophilum", "strain": "strain=B8", "accession": "GCA_000739595.1", "taxid": 413816, "species_taxid": 413816, "relation_to_type": "type", "validated": true, "ani": 87.5055, "matched_fragments": 728, "total_fragments": 1059, "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": 87.4757, "matched_fragments": 748, "total_fragments": 1059, "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": 87.1636, "matched_fragments": 732, "total_fragments": 1059, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum ezzemoulense", "strain": "strain=DSM 17463", "accession": "GCA_000421805.1", "taxid": 337243, "species_taxid": 337243, "relation_to_type": "type", "validated": true, "ani": 85.3478, "matched_fragments": 702, "total_fragments": 1059, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007671725.1", "gtdb_species": "s__Halorubrum depositum", "ani": 100.0, "matched_fragments": 1058, "total_fragments": 1059, "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_002252755.1", "gtdb_species": "s__Halorubrum sp002252755", "ani": 91.6997, "matched_fragments": 823, "total_fragments": 1059, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003721435.2", "gtdb_species": "s__Halorubrum sp003721435", "ani": 91.1154, "matched_fragments": 844, "total_fragments": 1059, "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_001261915.1", "gtdb_species": "s__Halorubrum sp001261915", "ani": 90.307, "matched_fragments": 699, "total_fragments": 1059, "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_007671685.1", "gtdb_species": "s__Halorubrum salsamenti", "ani": 88.1852, "matched_fragments": 784, "total_fragments": 1059, "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_000337375.1", "gtdb_species": "s__Halorubrum lipolyticum", "ani": 87.9054, "matched_fragments": 744, "total_fragments": 1059, "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_002286985.1", "gtdb_species": "s__Halorubrum sp002286985", "ani": 87.7223, "matched_fragments": 776, "total_fragments": 1059, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004114995.1", "gtdb_species": "s__Halorubrum amylolyticum", "ani": 87.2845, "matched_fragments": 752, "total_fragments": 1059, "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_900102375.1", "gtdb_species": "s__Halorubrum xinjiangense", "ani": 85.6554, "matched_fragments": 743, "total_fragments": 1059, "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": 36.973, "optimum_tmp": 38.687, "optimum_ph": 7.755, "genome_size": 3372661.985, "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", "depositum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }