{ "type": "genome", "identifier": "GCF_900108505.1", "organism": "Halopenitus malekzadehii", "title": "Halopenitus malekzadehii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900108505.1", "bioproject": "PRJNA224116", "biosample": "SAMN05192561", "wgs_master": "FNWU00000000.1", "refseq_category": "reference genome", "taxid": "1267564", "species_taxid": "1267564", "organism_name": "Halopenitus malekzadehii", "infraspecific_name": "strain=IBRC-M10418", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/27", "asm_name": "IMG-taxon 2651870118 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900108505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/108/505/GCF_900108505.1_IMG-taxon_2651870118_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": "3136824", "genome_size_ungapped": "3136583", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "41", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900108505.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "3195", "protein_coding_gene_count": "3050", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-27", "dateModified": "2016-10-27", "datePublished": "2016-10-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Halopenitus malekzadehii" ], "sample_taxid": [ "1267564" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.860 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3136824", "Number of Sequences": "41", "Longest Sequences (bp)": "1105460", "N50 (bp)": "308520", "Gap Ratio (%)": "0.007683", "GCcontent (%)": "64.5", "Number of CDSs": "3079", "Average Protein Length": "290.3", "Coding Ratio (%)": "85.5", "Number of rRNAs": "5", "Number of tRNAs": "46", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halorubrum halodurans", "strain": "strain=Cb34", "accession": "GCA_002252985.1", "taxid": 1383851, "species_taxid": 1383851, "relation_to_type": "type", "validated": true, "ani": 79.8962, "matched_fragments": 411, "total_fragments": 1022, "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": 79.8669, "matched_fragments": 440, "total_fragments": 1022, "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": 79.8175, "matched_fragments": 437, "total_fragments": 1022, "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": 79.7506, "matched_fragments": 428, "total_fragments": 1022, "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": 79.728, "matched_fragments": 424, "total_fragments": 1022, "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": 79.3821, "matched_fragments": 435, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum ezzemoulense", "strain": "strain=DSM 17463", "accession": "GCA_002114285.1", "taxid": 337243, "species_taxid": 337243, "relation_to_type": "type", "validated": true, "ani": 79.3116, "matched_fragments": 409, "total_fragments": 1022, "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": 79.1384, "matched_fragments": 422, "total_fragments": 1022, "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": 79.0772, "matched_fragments": 391, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronomonas salina", "strain": "strain=YPL13", "accession": "GCA_013391105.1", "taxid": 1710540, "species_taxid": 1710540, "relation_to_type": "type", "validated": true, "ani": 77.9286, "matched_fragments": 321, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloferax volcanii", "strain": "strain=DS2", "accession": "GCA_000337315.1", "taxid": 2246, "species_taxid": 2246, "relation_to_type": "type", "validated": true, "ani": 77.5714, "matched_fragments": 290, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinigranum halophilum", "strain": "strain=YJ-53", "accession": "GCA_007004735.1", "taxid": 2565931, "species_taxid": 2565931, "relation_to_type": "type", "validated": true, "ani": 77.462, "matched_fragments": 302, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloferax prahovense", "strain": "strain=DSM 18310", "accession": "GCA_000336815.1", "taxid": 381852, "species_taxid": 381852, "relation_to_type": "type", "validated": true, "ani": 77.444, "matched_fragments": 309, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinirubellus salinus", "strain": "strain=ZS-35-S2", "accession": "GCA_025231485.1", "taxid": 1364945, "species_taxid": 1364945, "relation_to_type": "type", "validated": true, "ani": 77.3187, "matched_fragments": 259, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900108505.1", "gtdb_species": "s__Halopenitus malekzadehii", "ani": 100.0, "matched_fragments": 1022, "total_fragments": 1022, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopenitus", "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_900107205.1", "gtdb_species": "s__Halopenitus persicus", "ani": 88.5254, "matched_fragments": 791, "total_fragments": 1022, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopenitus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002355635.1", "gtdb_species": "s__Halopenitus persicus_A", "ani": 87.9486, "matched_fragments": 728, "total_fragments": 1022, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopenitus", "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_017873555.1", "gtdb_species": "s__Halorubrum trapanicum", "ani": 79.7562, "matched_fragments": 422, "total_fragments": 1022, "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_000337915.1", "gtdb_species": "s__Halorubrum saccharovorum", "ani": 79.7456, "matched_fragments": 430, "total_fragments": 1022, "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": 79.2305, "matched_fragments": 420, "total_fragments": 1022, "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_000336995.1", "gtdb_species": "s__Halorubrum aidingense", "ani": 78.9986, "matched_fragments": 398, "total_fragments": 1022, "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_013391105.1", "gtdb_species": "s__Natronomonas salina", "ani": 77.9401, "matched_fragments": 320, "total_fragments": 1022, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas", "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": "GCA_018609665.1", "gtdb_species": "s__Natronomonas sp018609665", "ani": 77.2093, "matched_fragments": 243, "total_fragments": 1022, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas", "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": -0.188, "cell_length": 0.176, "doubling_h": null, "growth_tmp": null, "optimum_tmp": 40.0, "optimum_ph": 7.5, "genome_size": 3136824.0, "gc_content": 66.004, "coding_genes": 2855.0, "rRNA16S_genes": 2.0, "tRNA_genes": 63.0, "gram_stain": null, "sporulation": null, "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": 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": [ "Halopenitus", "malekzadehii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }