{ "type": "genome", "identifier": "GCF_003574835.2", "organism": "Thermobifida halotolerans", "title": "Thermobifida halotolerans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Seqomics Ltd", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003574835.2", "bioproject": "PRJNA224116", "biosample": "SAMN03105961", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "483545", "species_taxid": "483545", "organism_name": "Thermobifida halotolerans", "infraspecific_name": "strain=DSM 44931", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/04", "asm_name": "ASM357483v2", "asm_submitter": "Seqomics Ltd", "gbrs_paired_asm": "GCA_003574835.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/574/835/GCF_003574835.2_ASM357483v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5506152", "genome_size_ungapped": "5506152", "gc_percent": "71.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003574835.2-RS_2024_04_17", "annotation_date": "2024-04-17", "total_gene_count": "4872", "protein_coding_gene_count": "4750", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-04", "dateModified": "2022-04-04", "datePublished": "2022-04-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Thermobifida halotolerans" ], "sample_taxid": [ "483545" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.475 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)": "5506152", "Number of Sequences": "2", "Longest Sequences (bp)": "5450744", "N50 (bp)": "5450744", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.2", "Number of CDSs": "4947", "Average Protein Length": "316.4", "Coding Ratio (%)": "85.3", "Number of rRNAs": "12", "Number of tRNAs": "66", "Number of CRISPRs": "20" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thermobifida halotolerans", "strain": "strain=DSM 44931", "accession": "GCA_003574835.2", "taxid": 483545, "species_taxid": 483545, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1833, "total_fragments": 1834, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thermobifida halotolerans", "strain": "strain=YIM 90462", "accession": "GCA_001660385.1", "taxid": 483545, "species_taxid": 483545, "relation_to_type": "type", "validated": true, "ani": 99.9317, "matched_fragments": 1774, "total_fragments": 1834, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thermobifida alba", "strain": "strain=DSM 43795", "accession": "GCA_023208015.1", "taxid": 53522, "species_taxid": 53522, "relation_to_type": "type", "validated": true, "ani": 88.7207, "matched_fragments": 1321, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobifida cellulosilytica", "strain": "strain=TB100", "accession": "GCA_001517975.1", "taxid": 144786, "species_taxid": 144786, "relation_to_type": "type", "validated": true, "ani": 88.0585, "matched_fragments": 1201, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobifida fusca", "strain": "strain=NBRC 14071", "accession": "GCA_001592045.1", "taxid": 2021, "species_taxid": 2021, "relation_to_type": "type", "validated": true, "ani": 83.1704, "matched_fragments": 938, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis mwathae", "strain": "strain=DSM 46659", "accession": "GCA_014201195.1", "taxid": 1472723, "species_taxid": 1472723, "relation_to_type": "type", "validated": true, "ani": 80.1271, "matched_fragments": 800, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis sinuspersici", "strain": "strain=UTMC 00102", "accession": "GCA_001998325.1", "taxid": 501010, "species_taxid": 501010, "relation_to_type": "type", "validated": true, "ani": 80.0431, "matched_fragments": 787, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomonospora litoralis", "strain": "strain=M2", "accession": "GCA_004323735.1", "taxid": 2498135, "species_taxid": 2498135, "relation_to_type": "type", "validated": true, "ani": 79.8991, "matched_fragments": 781, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis composta", "strain": "strain=DSM 44551", "accession": "GCA_014200805.1", "taxid": 157465, "species_taxid": 157465, "relation_to_type": "type", "validated": true, "ani": 79.7488, "matched_fragments": 904, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis lucentensis", "strain": "strain=DSM 44048", "accession": "GCA_000341125.1", "taxid": 53441, "species_taxid": 53441, "relation_to_type": "type", "validated": true, "ani": 79.5983, "matched_fragments": 596, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis exhalans", "strain": "strain=JCM11759T", "accession": "GCA_024134545.1", "taxid": 163604, "species_taxid": 163604, "relation_to_type": "type", "validated": true, "ani": 79.4733, "matched_fragments": 741, "total_fragments": 1834, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001660385.1", "gtdb_species": "s__Thermobifida halotolerans", "ani": 99.9317, "matched_fragments": 1774, "total_fragments": 1834, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001517975.1", "gtdb_species": "s__Thermobifida cellulosilytica", "ani": 88.0493, "matched_fragments": 1202, "total_fragments": 1834, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida", "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_004363075.1", "gtdb_species": "s__Actinorugispora endophytica", "ani": 84.4037, "matched_fragments": 1090, "total_fragments": 1834, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora", "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_001592045.1", "gtdb_species": "s__Thermobifida fusca", "ani": 83.1821, "matched_fragments": 937, "total_fragments": 1834, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.61", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_013408795.1", "gtdb_species": "s__Spinactinospora alkalitolerans", "ani": 81.3163, "matched_fragments": 987, "total_fragments": 1834, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora", "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_900167435.1", "gtdb_species": "s__Marinactinospora thermotolerans", "ani": 80.6242, "matched_fragments": 833, "total_fragments": 1834, "gtdb_taxonomy": 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