{ "type": "genome", "identifier": "GCF_000337635.1", "organism": "Natrinema pellirubrum DSM 15624", "title": "Natrinema pellirubrum DSM 15624", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of California, Davis", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000337635.1", "bioproject": "PRJNA224116", "biosample": "SAMN02471626", "wgs_master": "AOIE00000000.1", "refseq_category": "na", "taxid": "797303", "species_taxid": "69525", "organism_name": "Natrinema pellirubrum DSM 15624", "infraspecific_name": "strain=DSM 15624", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/02/04", "asm_name": "ASM33763v1", "asm_submitter": "University of California, Davis", "gbrs_paired_asm": "GCA_000337635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/635/GCF_000337635.1_ASM33763v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "4264455", "genome_size_ungapped": "4264455", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "134", "contig_count": "134", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000337635.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "4334", "protein_coding_gene_count": "4079", "non_coding_gene_count": "58", "pubmed_id": "25393412" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-02-04", "dateModified": "2013-02-04", "datePublished": "2013-02-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Natrinema pellirubrum DSM 15624" ], "sample_taxid": [ "797303" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.178 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4264455", "Number of Sequences": "134", "Longest Sequences (bp)": "253823", "N50 (bp)": "83437", "Gap Ratio (%)": "0.004268", "GCcontent (%)": "64.1", "Number of CDSs": "4186", "Average Protein Length": "281.1", "Coding Ratio (%)": "82.8", "Number of rRNAs": "5", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Natrinema pellirubrum", "strain": "strain=DSM 15624", "accession": "GCA_000337635.1", "taxid": 69525, "species_taxid": 69525, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1361, "total_fragments": 1368, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Natrinema pellirubrum", "strain": "strain=DSM 15624", "accession": "GCA_000230735.3", "taxid": 69525, "species_taxid": 69525, "relation_to_type": "type", "validated": true, "ani": 99.98, "matched_fragments": 1364, "total_fragments": 1368, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Natrinema versiforme", "strain": "strain=JCM 10478", "accession": "GCA_000337195.1", "taxid": 88724, "species_taxid": 88724, "relation_to_type": "type", "validated": true, "ani": 84.8333, "matched_fragments": 902, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natrinema amylolyticum", "strain": "strain=LT61", "accession": "GCA_020515625.1", "taxid": 2878679, "species_taxid": 2878679, "relation_to_type": "type", "validated": true, "ani": 84.7565, "matched_fragments": 934, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natrinema altunense", "strain": "strain=JCM 12890", "accession": "GCA_000337155.1", "taxid": 222984, "species_taxid": 222984, "relation_to_type": "type", "validated": true, "ani": 84.7066, "matched_fragments": 863, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natrinema gari", "strain": "strain=JCM 14663", "accession": "GCA_000337175.1", "taxid": 419186, "species_taxid": 419186, "relation_to_type": "type", "validated": true, "ani": 84.461, "matched_fragments": 882, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopiger salifodinae", "strain": "strain=CGMCC 1.12284", "accession": "GCA_900110455.1", "taxid": 1202768, "species_taxid": 1202768, "relation_to_type": "type", "validated": true, "ani": 83.4293, "matched_fragments": 817, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloterrigena limicola", "strain": "strain=JCM 13563", "accession": "GCA_000337475.1", "taxid": 370323, "species_taxid": 370323, "relation_to_type": "type", "validated": true, "ani": 82.9614, "matched_fragments": 763, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloterrigena salina", "strain": "strain=JCM 13891", "accession": "GCA_000337495.1", "taxid": 504937, "species_taxid": 504937, "relation_to_type": "type", "validated": true, "ani": 82.7453, "matched_fragments": 829, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloterrigena salifodinae", "strain": "strain=ZY19", "accession": "GCA_003977755.1", "taxid": 2675099, "species_taxid": 2675099, "relation_to_type": "type", "validated": true, "ani": 82.3591, "matched_fragments": 824, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000230735.2", "gtdb_species": "s__Natrinema pellirubrum", "ani": 99.98, "matched_fragments": 1364, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "ani_circumscription_radius": 95.7501, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000337115.1", "gtdb_species": "s__Natrinema thermotolerans", "ani": 95.5811, "matched_fragments": 1073, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "ani_circumscription_radius": 95.7501, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000690595.2", "gtdb_species": "s__Natrinema mahii", "ani": 92.3154, "matched_fragments": 1031, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "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_001953745.1", "gtdb_species": "s__Natrinema saccharevitans", "ani": 91.1881, "matched_fragments": 995, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "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_002572525.1", "gtdb_species": "s__Natrinema sp002572525", "ani": 83.6818, "matched_fragments": 948, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "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_000337475.1", "gtdb_species": "s__Natrinema limicola", "ani": 82.9669, "matched_fragments": 763, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "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_900111485.1", "gtdb_species": "s__Natrinema hispanicum_A", "ani": 82.7724, "matched_fragments": 782, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.65", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000337495.1", "gtdb_species": "s__Haloterrigena salina", "ani": 82.7488, "matched_fragments": 831, "total_fragments": 1368, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena", "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": -0.155, "cell_length": 0.176, "doubling_h": 0.271, "growth_tmp": 44.0, "optimum_tmp": 32.5, "optimum_ph": 7.5, "genome_size": 4354100.0, "gc_content": 63.96, "coding_genes": 4112.0, "rRNA16S_genes": 3.0, "tRNA_genes": 48.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.6, "range_salinity": null, "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": 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": [ "Natrinema", "pellirubrum", "DSM", "15624" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }