{ "type": "genome", "identifier": "GCF_000422825.1", "organism": "Nocardioides insulae DSM 17944", "title": "Nocardioides insulae DSM 17944", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000422825.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441164", "wgs_master": "AUGU00000000.1", "refseq_category": "reference genome", "taxid": "1122610", "species_taxid": "394734", "organism_name": "Nocardioides insulae DSM 17944", "infraspecific_name": "strain=DSM 17944", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/11", "asm_name": "ASM42282v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000422825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/825/GCF_000422825.1_ASM42282v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4060447", "genome_size_ungapped": "4060022", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000422825.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "3700", "protein_coding_gene_count": "3623", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-11", "dateModified": "2013-07-11", "datePublished": "2013-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardioides insulae DSM 17944" ], "sample_taxid": [ "1122610" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.087 MB", "sample_ph_range": { "min": 8.0, "max": 8.0 }, "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)": "4060447", "Number of Sequences": "17", "Longest Sequences (bp)": "945781", "N50 (bp)": "769778", "Gap Ratio (%)": "0.010467", "GCcontent (%)": "70.8", "Number of CDSs": "3679", "Average Protein Length": "334.6", "Coding Ratio (%)": "91.0", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardioides insulae", "strain": "strain=DSM 17944", "accession": "GCA_000422825.1", "taxid": 394734, "species_taxid": 394734, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1346, 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"below_threshold" }, { "organism_name": "Nocardioides deserti", "strain": "strain=CGMCC 4.7183", "accession": "GCA_014646035.1", "taxid": 1588644, "species_taxid": 1588644, "relation_to_type": "type", "validated": true, "ani": 79.7867, "matched_fragments": 558, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides ferulae", "strain": "strain=SZ4R5S7", "accession": "GCA_003660455.1", "taxid": 2340821, "species_taxid": 2340821, "relation_to_type": "type", "validated": true, "ani": 79.7589, "matched_fragments": 572, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides deserti", "strain": "strain=SC8A-24", "accession": "GCA_014266025.1", "taxid": 1588644, "species_taxid": 1588644, "relation_to_type": "type", "validated": true, "ani": 79.7447, "matched_fragments": 553, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides 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105498", "accession": "GCA_014191495.1", "taxid": 1036020, "species_taxid": 1036020, "relation_to_type": "type", "validated": true, "ani": 79.5677, "matched_fragments": 617, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides luteus", "strain": "strain=JCM 3358", "accession": "GCA_014648595.1", "taxid": 1844, "species_taxid": 1844, "relation_to_type": "type", "validated": true, "ani": 79.5675, "matched_fragments": 583, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides nematodiphilus", "strain": "strain=R-N-C8", "accession": "GCA_020216525.1", "taxid": 2849669, "species_taxid": 2849669, "relation_to_type": "type", "validated": true, "ani": 79.5532, "matched_fragments": 515, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides szechwanensis", "strain": "strain=NBRC 108562", "accession": "GCA_007992395.1", "taxid": 1005944, "species_taxid": 1005944, "relation_to_type": "type", "validated": true, "ani": 79.4997, "matched_fragments": 533, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides euryhalodurans", "strain": "strain=MMS17-SY117", "accession": "GCA_004564375.1", "taxid": 2518370, "species_taxid": 2518370, "relation_to_type": "type", "validated": true, "ani": 79.4547, "matched_fragments": 501, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides nitrophenolicus", "strain": "strain=DSM 15529", "accession": "GCA_016907515.1", "taxid": 60489, "species_taxid": 60489, "relation_to_type": "type", "validated": true, "ani": 79.4026, "matched_fragments": 611, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lianchengensis", "strain": "strain=CGMCC 4.6858", "accession": "GCA_900101465.1", "taxid": 1045774, "species_taxid": 1045774, "relation_to_type": "type", "validated": true, "ani": 79.3569, "matched_fragments": 639, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lacusdianchii", "strain": "strain=JXJ CY 38", "accession": "GCA_020102855.1", "taxid": 2783664, "species_taxid": 2783664, "relation_to_type": "type", "validated": true, "ani": 79.3408, "matched_fragments": 502, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides albus", "strain": "strain=JCM 3185", "accession": "GCA_014648255.1", "taxid": 1841, "species_taxid": 1841, "relation_to_type": "type", "validated": true, "ani": 79.3066, "matched_fragments": 589, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lianchengensis", "strain": "strain=CGMCC 4.6858", "accession": "GCA_013409225.1", "taxid": 1045774, "species_taxid": 1045774, "relation_to_type": "type", 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"matched_fragments": 600, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides coralli", "strain": "strain=SCSIO 67246", "accession": "GCA_019880385.1", "taxid": 2872154, "species_taxid": 2872154, "relation_to_type": "type", "validated": true, "ani": 78.9876, "matched_fragments": 483, "total_fragments": 1346, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000422825.1", "gtdb_species": "s__Nocardioides insulae", "ani": 100.0, "matched_fragments": 1346, "total_fragments": 1346, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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, 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79.6528, "matched_fragments": 529, "total_fragments": 1346, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_900103935.1", "gtdb_species": "s__Nocardioides szechwanensis", "ani": 79.5952, "matched_fragments": 529, "total_fragments": 1346, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014191495.1", "gtdb_species": "s__Nocardioides soli", "ani": 79.5947, "matched_fragments": 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