{ "type": "genome", "identifier": "GCF_001485435.1", "organism": "Deinococcus grandis", "title": "Deinococcus grandis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Japan Atomic Energy Agency", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001485435.1", "bioproject": "PRJNA224116", "biosample": "SAMD00043215", "wgs_master": "BCMS00000000.1", "refseq_category": "reference genome", "taxid": "57498", "species_taxid": "57498", "organism_name": "Deinococcus grandis", "infraspecific_name": "strain=ATCC 43672", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/12/08", "asm_name": "ASM148543v1", "asm_submitter": "Japan Atomic Energy Agency", "gbrs_paired_asm": "GCA_001485435.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/485/435/GCF_001485435.1_ASM148543v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4092497", "genome_size_ungapped": "4092497", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001485435.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4041", "protein_coding_gene_count": "3942", "non_coding_gene_count": "67", "pubmed_id": "26868384" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-12-08", "dateModified": "2015-12-08", "datePublished": "2015-12-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Deinococcus grandis" ], "sample_taxid": [ "57498" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Tokyo" ], "sample_host_location_id": [], "data_size": "1.101 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4092497", "Number of Sequences": "7", "Longest Sequences (bp)": "3250361", "N50 (bp)": "3250361", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.9", "Number of CDSs": "4031", "Average Protein Length": "302.9", "Coding Ratio (%)": "89.5", "Number of rRNAs": "7", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Deinococcus grandis", "strain": "strain=ATCC 43672", "accession": "GCA_001485435.1", "taxid": 57498, "species_taxid": 57498, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1359, "total_fragments": 1360, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Deinococcus xianganensis", "strain": "strain=Y35", "accession": "GCA_009834985.1", "taxid": 1507289, "species_taxid": 1507289, "relation_to_type": "type", "validated": true, "ani": 95.5887, "matched_fragments": 1081, "total_fragments": 1360, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Deinococcus daejeonensis", "strain": "strain=JCM 16918", "accession": "GCA_014647175.1", "taxid": 1007098, "species_taxid": 1007098, "relation_to_type": "type", "validated": true, "ani": 95.4681, "matched_fragments": 1115, "total_fragments": 1360, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Deinococcus soli (ex Cha et al. 2016)", "strain": "strain=N5", "accession": "GCA_001007995.1", "taxid": 1309411, "species_taxid": 1309411, "relation_to_type": "type", "validated": true, "ani": 94.2775, "matched_fragments": 981, "total_fragments": 1360, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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"strain=SJW1-2", "accession": "GCA_002901445.1", "taxid": 2054903, "species_taxid": 2054903, "relation_to_type": "type", "validated": true, "ani": 80.4905, "matched_fragments": 765, "total_fragments": 1360, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus budaensis", "strain": "strain=DSM 101791", "accession": "GCA_014201885.1", "taxid": 1665626, "species_taxid": 1665626, "relation_to_type": "type", "validated": true, "ani": 79.523, "matched_fragments": 637, "total_fragments": 1360, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus metallilatus", "strain": "strain=DSM 105434", "accession": "GCA_014202095.1", "taxid": 1211322, "species_taxid": 1211322, "relation_to_type": "type", "validated": true, "ani": 79.4283, "matched_fragments": 656, "total_fragments": 1360, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001485435.1", "gtdb_species": "s__Deinococcus grandis", "ani": 100.0, "matched_fragments": 1359, "total_fragments": 1360, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "95.40", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_001007995.1", "gtdb_species": "s__Deinococcus soli", "ani": 94.2775, "matched_fragments": 981, "total_fragments": 1360, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013337115.1", 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91.8946, "matched_fragments": 1113, "total_fragments": 1360, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_014647435.1", "gtdb_species": "s__Deinococcus radiotolerans", "ani": 90.1685, "matched_fragments": 1030, "total_fragments": 1360, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_002017875.1", "gtdb_species": "s__Deinococcus sp002017875", "ani": 86.5907, "matched_fragments": 993, "total_fragments": 1360, 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