{ "type": "genome", "identifier": "GCF_000685635.1", "organism": "Haloferax mediterranei ATCC 33500", "title": "Haloferax mediterranei ATCC 33500", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Alicante", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000685635.1", "bioproject": "PRJNA224116", "biosample": "SAMN02724739", "wgs_master": "na", "refseq_category": "na", "taxid": "523841", "species_taxid": "2252", "organism_name": "Haloferax mediterranei ATCC 33500", "infraspecific_name": "strain=ATCC 33500", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/05/08", "asm_name": "ASM68563v1", "asm_submitter": "University of Alicante", "gbrs_paired_asm": "GCA_000685635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/685/635/GCF_000685635.1_ASM68563v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3906699", "genome_size_ungapped": "3896000", "gc_percent": "60.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000685635.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "3957", "protein_coding_gene_count": "3718", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-05-08", "dateModified": "2014-05-08", "datePublished": "2014-05-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Haloferax mediterranei ATCC 33500" ], "sample_taxid": [ "523841" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Alicante" ], "sample_host_location_id": [], "data_size": "1.088 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)": "3906699", "Number of Sequences": "4", "Longest Sequences (bp)": "2946877", "N50 (bp)": "2946877", "Gap Ratio (%)": "0.288300", "GCcontent (%)": "60.3", "Number of CDSs": "3897", "Average Protein Length": "280.6", "Coding Ratio (%)": "84.0", "Number of rRNAs": "4", "Number of tRNAs": "51", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Haloferax mediterranei", "strain": "strain=ATCC 33500", "accession": "GCA_000685635.1", "taxid": 2252, "species_taxid": 2252, "relation_to_type": "type", "validated": true, "ani": 99.9971, "matched_fragments": 1297, "total_fragments": 1300, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Haloferax mediterranei", "strain": "strain=ATCC 33500", "accession": "GCA_000337295.1", "taxid": 2252, "species_taxid": 2252, "relation_to_type": "type", "validated": true, "ani": 99.9753, "matched_fragments": 1287, "total_fragments": 1300, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Haloferax mediterranei", "strain": "strain=CGMCC 1.2087", "accession": "GCA_000306765.2", "taxid": 2252, "species_taxid": 2252, "relation_to_type": "type", "validated": true, "ani": 99.965, "matched_fragments": 1291, "total_fragments": 1300, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Haloferax mediterranei", "strain": "strain=ATCC 33500", "accession": "GCA_005406325.1", "taxid": 2252, "species_taxid": 2252, "relation_to_type": "type", "validated": true, "ani": 99.9637, "matched_fragments": 1293, "total_fragments": 1300, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Haloferax mucosum", "strain": "strain=ATCC BAA-1512", "accession": "GCA_000337815.1", "taxid": 403181, "species_taxid": 403181, "relation_to_type": "type", "validated": true, "ani": 86.0277, "matched_fragments": 914, "total_fragments": 1300, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloferax massiliensis", "strain": "strain=Arc-Hr", "accession": "GCA_001368915.1", "taxid": 1476858, "species_taxid": 1476858, "relation_to_type": "type", "validated": true, "ani": 84.3437, "matched_fragments": 828, "total_fragments": 1300, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloferax elongans", "strain": "strain=ATCC BAA-1513", "accession": "GCA_000336755.1", "taxid": 403191, "species_taxid": 403191, "relation_to_type": "type", "validated": true, "ani": 83.3191, "matched_fragments": 789, "total_fragments": 1300, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, 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"s__Haloferax sp001482285", "ani": 84.4001, "matched_fragments": 832, "total_fragments": 1300, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax", "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_001368915.1", "gtdb_species": "s__Haloferax massiliensis", "ani": 84.3724, "matched_fragments": 825, "total_fragments": 1300, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax", "ani_circumscription_radius": 95.2845, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "96.94", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000336815.1", "gtdb_species": "s__Haloferax prahovense", "ani": 84.3467, 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"d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000336755.1", "gtdb_species": "s__Haloferax elongans", "ani": 83.3155, "matched_fragments": 790, "total_fragments": 1300, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax", "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": -0.302, "cell_length": 0.301, "doubling_h": 0.264, "growth_tmp": 36.0, "optimum_tmp": 35.0, "optimum_ph": 7.1, "genome_size": 3905106.0, "gc_content": 58.696, 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