{ "type": "genome", "identifier": "GCF_900142595.1", "organism": "Streptomyces yunnanensis", "title": "Streptomyces yunnanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900142595.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216268", "wgs_master": "FRBK00000000.1", "refseq_category": "na", "taxid": "156453", "species_taxid": "156453", "organism_name": "Streptomyces yunnanensis", "infraspecific_name": "strain=CGMCC 4.3555", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2667527450 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900142595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/142/595/GCF_900142595.1_IMG-taxon_2667527450_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9356146", "genome_size_ungapped": "9356076", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "94", "contig_count": "94", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900142595.1-RS_2024_06_22", "annotation_date": "2024-06-22", "total_gene_count": "8462", "protein_coding_gene_count": "8089", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-03", "dateModified": "2016-12-03", "datePublished": "2016-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces yunnanensis" ], "sample_taxid": [ "156453" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.523 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 13.54, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9356146", "Number of Sequences": "94", "Longest Sequences (bp)": "698257", "N50 (bp)": "328307", "Gap Ratio (%)": "0.000748", "GCcontent (%)": "71.4", "Number of CDSs": "8529", "Average Protein Length": "310.7", "Coding Ratio (%)": "85.0", "Number of rRNAs": "6", "Number of tRNAs": "91", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces albulus", "strain": "strain=JCM 4718", "accession": "GCA_014650635.1", "taxid": 68570, "species_taxid": 68570, "relation_to_type": "suspected-type", "validated": true, "ani": 96.1199, "matched_fragments": 2534, "total_fragments": 3071, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces albospinus", "strain": "strain=JCM 3399", "accession": "GCA_014648695.1", "taxid": 285515, "species_taxid": 285515, "relation_to_type": "type", "validated": true, "ani": 87.8852, "matched_fragments": 2029, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lydicus", "strain": "strain=ATCC 25470", "accession": "GCA_004125245.1", "taxid": 47763, "species_taxid": 47763, "relation_to_type": "suspected-type", "validated": true, "ani": 85.8835, "matched_fragments": 1809, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lydicus", "strain": "strain=NRRL ISP-5461", "accession": "GCA_000717345.1", "taxid": 47763, "species_taxid": 47763, "relation_to_type": "suspected-type", "validated": true, "ani": 85.818, "matched_fragments": 1801, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces kronopolitis", "strain": "strain=CGMCC 4.7323", "accession": "GCA_014646275.1", "taxid": 1612435, "species_taxid": 1612435, "relation_to_type": "type", "validated": true, "ani": 85.6054, "matched_fragments": 1687, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces decoyicus", "strain": "strain=NRRL 2666", "accession": "GCA_019880305.1", "taxid": 249567, "species_taxid": 249567, "relation_to_type": "type", "validated": true, "ani": 85.5385, "matched_fragments": 1781, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces lydicamycinicus", "strain": "strain=NBRC 110027", "accession": "GCA_000829715.2", "taxid": 1546107, "species_taxid": 1546107, "relation_to_type": "type", "validated": true, "ani": 85.5329, "matched_fragments": 1764, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces decoyicus", "strain": "strain=NRRL 2666", "accession": "GCA_001270575.1", "taxid": 249567, "species_taxid": 249567, "relation_to_type": "type", "validated": true, "ani": 85.5324, "matched_fragments": 1711, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces platensis", "strain": "strain=ATCC 23948", "accession": "GCA_008704855.1", "taxid": 58346, "species_taxid": 58346, "relation_to_type": "type", "validated": true, "ani": 85.4638, "matched_fragments": 1750, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces platensis", "strain": "strain=DSM 40041", "accession": "GCA_002119195.1", "taxid": 58346, "species_taxid": 58346, "relation_to_type": "type", "validated": true, "ani": 85.4546, "matched_fragments": 1718, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces caniferus", "strain": "strain=NBRC 15389", "accession": "GCA_009811555.1", "taxid": 285557, "species_taxid": 285557, "relation_to_type": "type", "validated": true, "ani": 85.4485, "matched_fragments": 1816, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces pinistramenti", "strain": "strain=SF28", "accession": "GCA_020564935.1", "taxid": 2884812, "species_taxid": 2884812, "relation_to_type": "type", "validated": true, "ani": 84.6904, "matched_fragments": 1608, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces benahoarensis", "strain": "strain=MZ03-37", "accession": "GCA_007280575.1", "taxid": 2595054, "species_taxid": 2595054, "relation_to_type": "type", "validated": true, "ani": 84.2516, "matched_fragments": 1260, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rimosus subsp. rimosus", "strain": "strain=R7", "accession": "GCA_022760195.1", "taxid": 132474, "species_taxid": 1927, "relation_to_type": "type", "validated": true, "ani": 83.4199, "matched_fragments": 1676, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces monomycini", "strain": "strain=NRRL B-24309", "accession": "GCA_022271435.1", "taxid": 371720, "species_taxid": 371720, "relation_to_type": "type", "validated": true, "ani": 83.3027, "matched_fragments": 1599, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces violens", "strain": "strain=NRRL ISP-5597", "accession": "GCA_000717745.1", "taxid": 66377, "species_taxid": 66377, "relation_to_type": "type", "validated": true, "ani": 83.2985, "matched_fragments": 1446, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces paromomycinus", "strain": "strain=NBRC 15454", "accession": "GCA_003865155.1", "taxid": 92743, "species_taxid": 92743, "relation_to_type": "type", "validated": true, "ani": 83.2771, "matched_fragments": 1633, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces purpurogeneiscleroticus", "strain": "strain=DSM 43156", "accession": "GCA_020024005.1", "taxid": 68259, "species_taxid": 68259, "relation_to_type": "type", "validated": true, "ani": 83.2302, "matched_fragments": 1327, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces ochraceiscleroticus", "strain": "strain=NRRL ISP-5594", "accession": "GCA_000720485.1", "taxid": 47761, "species_taxid": 47761, "relation_to_type": "type", "validated": true, "ani": 83.1016, "matched_fragments": 1492, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces netropsis", "strain": "strain=CECT 3265", "accession": "GCA_014203545.1", "taxid": 55404, "species_taxid": 55404, "relation_to_type": "type", "validated": true, "ani": 81.8209, "matched_fragments": 1338, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces netropsis", "strain": "strain=JCM 4063", "accession": "GCA_014648835.1", "taxid": 55404, "species_taxid": 55404, "relation_to_type": "type", "validated": true, "ani": 81.7907, "matched_fragments": 1329, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces bungoensis", "strain": "strain=DSM 41781", "accession": "GCA_001514215.1", "taxid": 285568, "species_taxid": 285568, "relation_to_type": "type", "validated": true, "ani": 80.8111, "matched_fragments": 1306, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces malachitofuscus", "strain": "strain=JCM 4493", "accession": "GCA_014650055.1", "taxid": 67322, "species_taxid": 67322, "relation_to_type": "type", "validated": true, "ani": 80.7983, "matched_fragments": 1230, "total_fragments": 3071, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 13.54, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016917755.1", "gtdb_species": "s__Streptomyces yunnanensis", "ani": 97.4386, "matched_fragments": 2603, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.5028, "mean_intra_species_ani": "97.38", "min_intra_species_ani": "97.21", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_001704275.1", "gtdb_species": "s__Streptomyces noursei", "ani": 96.2429, "matched_fragments": 2512, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.5028, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002803155.1", "gtdb_species": "s__Streptomyces sp002803155", "ani": 90.7775, "matched_fragments": 2261, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_000373585.1", "gtdb_species": "s__Streptomyces sp000373585", "ani": 90.6951, "matched_fragments": 2066, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_000963515.1", "gtdb_species": "s__Streptomyces albulus_C", "ani": 89.9553, "matched_fragments": 2171, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.39", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_009176265.1", "gtdb_species": "s__Streptomyces angustmyceticus", "ani": 85.8035, "matched_fragments": 1732, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014203555.1", "gtdb_species": "s__Streptomyces olivoverticillatus", "ani": 82.0477, "matched_fragments": 1191, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_000717595.1", "gtdb_species": "s__Streptomyces flavochromogenes", "ani": 80.7901, "matched_fragments": 1318, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.5951, "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_008705135.1", "gtdb_species": "s__Streptomyces coeruleorubidus", "ani": 80.6196, "matched_fragments": 1317, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014646115.1", "gtdb_species": "s__Streptomyces camponoticapitis", "ani": 80.285, "matched_fragments": 1174, "total_fragments": 3071, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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": -0.201, "cell_length": -0.05, "doubling_h": 0.103, "growth_tmp": 29.0, "optimum_tmp": 29.036, "optimum_ph": 7.341, "genome_size": 9356146.0, "gc_content": 71.543, "coding_genes": 7141.289, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 1.0, "sporulation": 0.958, "motility": 0.049, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.98, "thermophilic_range_tmp": 0.019, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.208, "coccus_cell_shape": 0.032, "filament_cell_shape": 0.582, "coccobacillus_cell_shape": 0.098, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.076 }, "_genome_taxon": [ "Streptomyces", "yunnanensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }