{ "type": "genome", "identifier": "GCF_003112515.1", "organism": "Streptomyces fragilis", "title": "Streptomyces fragilis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation Biological Resource Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003112515.1", "bioproject": "PRJNA224116", "biosample": "SAMD00090286", "wgs_master": "BEVZ00000000.1", "refseq_category": "reference genome", "taxid": "67301", "species_taxid": "67301", "organism_name": "Streptomyces fragilis", "infraspecific_name": "strain=NBRC 12862", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/30", "asm_name": "ASM311251v1", "asm_submitter": "National Institute of Technology and Evaluation Biological Resource Center", "gbrs_paired_asm": "GCA_003112515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/112/515/GCF_003112515.1_ASM311251v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6847990", "genome_size_ungapped": "6847990", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003112515.1-RS_2024_08_12", "annotation_date": "2024-08-12", "total_gene_count": "5993", "protein_coding_gene_count": "5803", "non_coding_gene_count": "82", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-30", "dateModified": "2018-03-30", "datePublished": "2018-03-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces fragilis" ], "sample_taxid": [ "67301" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.812 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6847990", "Number of Sequences": "19", "Longest Sequences (bp)": "2004156", "N50 (bp)": "607197", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.2", "Number of CDSs": "6007", "Average Protein Length": "333.2", "Coding Ratio (%)": "87.7", "Number of rRNAs": "5", "Number of tRNAs": "89", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces fragilis", "strain": "strain=NBRC 12862", "accession": "GCA_003112515.1", "taxid": 67301, "species_taxid": 67301, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2273, "total_fragments": 2274, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces chilikensis", "strain": "strain=RC 1830", "accession": "GCA_001642695.2", "taxid": 1194079, "species_taxid": 1194079, "relation_to_type": "type", "validated": true, "ani": 89.511, "matched_fragments": 1720, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces abyssomicinicus", "strain": "strain=CHI39", "accession": "GCA_008974245.1", "taxid": 574929, "species_taxid": 574929, "relation_to_type": "type", "validated": true, "ani": 89.1158, "matched_fragments": 1771, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces harenosi", "strain": "strain=PRKS01-65", "accession": "GCA_011008945.1", "taxid": 2697029, "species_taxid": 2697029, "relation_to_type": "type", "validated": true, "ani": 82.7582, "matched_fragments": 1203, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces sennicomposti", "strain": "strain=RCPT1-4", "accession": "GCA_019890635.1", "taxid": 2873384, "species_taxid": 2873384, "relation_to_type": "type", "validated": true, "ani": 82.5402, "matched_fragments": 1247, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces longwoodensis", "strain": "strain=DSM 41677", "accession": "GCA_001514125.1", "taxid": 68231, "species_taxid": 68231, "relation_to_type": "type", "validated": true, "ani": 82.5389, "matched_fragments": 1357, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces calvus", "strain": "strain=JCM 4326", "accession": "GCA_014649315.1", "taxid": 67282, "species_taxid": 67282, "relation_to_type": "type", "validated": true, "ani": 82.5253, "matched_fragments": 1344, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces calvus", "strain": "strain=CECT 3271", "accession": "GCA_014138735.1", "taxid": 67282, "species_taxid": 67282, "relation_to_type": "type", "validated": true, "ani": 82.5065, "matched_fragments": 1368, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces galbus", "strain": "strain=JCM 4639", "accession": "GCA_014650535.1", "taxid": 33898, "species_taxid": 33898, "relation_to_type": "type", "validated": true, "ani": 82.4988, "matched_fragments": 1370, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces griseosporeus", "strain": "strain=JCM 4766", "accession": "GCA_014656055.1", "taxid": 1910, "species_taxid": 1910, "relation_to_type": "type", "validated": true, "ani": 82.4961, "matched_fragments": 1362, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces viridosporus", "strain": "strain=NRRL 2414", "accession": "GCA_002078235.1", "taxid": 67581, "species_taxid": 67581, "relation_to_type": "type", "validated": true, "ani": 82.4616, "matched_fragments": 1135, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces bauhiniae", "strain": "strain=Bv016", "accession": "GCA_004784475.1", "taxid": 2340725, "species_taxid": 2340725, "relation_to_type": "type", "validated": true, "ani": 82.4259, "matched_fragments": 1193, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces griseoluteus", "strain": "strain=JCM 4765", "accession": "GCA_004784465.1", "taxid": 29306, "species_taxid": 29306, "relation_to_type": "type", "validated": true, "ani": 82.3083, "matched_fragments": 1200, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces indiaensis", "strain": "strain=DSM 43803", "accession": "GCA_021474405.1", "taxid": 284033, "species_taxid": 284033, "relation_to_type": "type", "validated": true, "ani": 82.1985, "matched_fragments": 1201, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces barringtoniae", "strain": "strain=JA03", "accession": "GCA_020819595.1", "taxid": 2892029, "species_taxid": 2892029, "relation_to_type": "type", "validated": true, "ani": 82.0078, "matched_fragments": 1253, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces monashensis", "strain": "strain=MUSC 1", "accession": "GCA_001866665.1", "taxid": 1678012, "species_taxid": 1678012, "relation_to_type": "type", "validated": true, "ani": 81.866, "matched_fragments": 1295, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces avermitilis", "strain": "strain=DSM 46492", "accession": "GCA_001514135.1", "taxid": 33903, "species_taxid": 33903, "relation_to_type": "type", "validated": true, "ani": 81.7181, "matched_fragments": 1244, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces deccanensis", "strain": "strain=KCTC 19241", "accession": "GCA_022385335.1", "taxid": 424188, "species_taxid": 424188, "relation_to_type": "type", "validated": true, "ani": 81.6998, "matched_fragments": 1275, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces avermitilis", "strain": "strain=MA-4680", "accession": "GCA_000009765.2", "taxid": 33903, "species_taxid": 33903, "relation_to_type": "type", "validated": true, "ani": 81.6652, "matched_fragments": 1274, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces avermitilis", "strain": "strain=NBRC 14893", "accession": "GCA_005405965.1", "taxid": 33903, "species_taxid": 33903, "relation_to_type": "type", "validated": true, "ani": 81.5641, "matched_fragments": 1307, "total_fragments": 2274, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003112515.1", "gtdb_species": "s__Streptomyces fragilis", "ani": 100.0, "matched_fragments": 2273, "total_fragments": 2274, "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": "conclusive" }, { "accession": "GCF_001642695.1", "gtdb_species": "s__Streptomyces chilikensis", "ani": 89.5105, "matched_fragments": 1720, "total_fragments": 2274, "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_008974245.1", "gtdb_species": "s__Streptomyces abyssomicinicus", "ani": 89.1094, "matched_fragments": 1772, "total_fragments": 2274, "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_000761215.1", "gtdb_species": "s__Streptomyces glaucescens", "ani": 82.6876, "matched_fragments": 1356, "total_fragments": 2274, "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": "GCA_003248315.1", "gtdb_species": "s__Streptomyces sp003248315", "ani": 82.6595, "matched_fragments": 1309, "total_fragments": 2274, "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_001514125.1", "gtdb_species": "s__Streptomyces longwoodensis", "ani": 82.546, "matched_fragments": 1357, "total_fragments": 2274, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.95", "min_intra_species_ani": "95.95", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014656055.1", "gtdb_species": "s__Streptomyces griseosporeus", "ani": 82.5039, "matched_fragments": 1361, "total_fragments": 2274, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.69", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000383935.1", "gtdb_species": "s__Streptomyces sp000383935", "ani": 82.4992, "matched_fragments": 1325, "total_fragments": 2274, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013364255.1", "gtdb_species": "s__Streptomyces seoulensis_A", "ani": 82.4319, "matched_fragments": 1353, "total_fragments": 2274, "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_004784475.1", "gtdb_species": "s__Streptomyces bauhiniae", "ani": 82.4222, "matched_fragments": 1194, "total_fragments": 2274, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.3953, "mean_intra_species_ani": "95.70", "min_intra_species_ani": "95.47", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000373625.1", "gtdb_species": "s__Streptomyces sp000373625", "ani": 82.2998, "matched_fragments": 1189, "total_fragments": 2274, "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_000720185.1", "gtdb_species": "s__Streptomyces sp000720185", "ani": 82.1489, "matched_fragments": 1307, "total_fragments": 2274, "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_900236475.1", "gtdb_species": "s__Streptomyces chartreusis_D", "ani": 82.0064, "matched_fragments": 1280, "total_fragments": 2274, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004346005.1", "gtdb_species": "s__Streptomyces sp004346005", "ani": 81.9472, "matched_fragments": 1289, "total_fragments": 2274, "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_001280015.1", "gtdb_species": "s__Streptomyces sp001280015", "ani": 81.9219, "matched_fragments": 1255, "total_fragments": 2274, "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_000009765.2", "gtdb_species": "s__Streptomyces avermitilis", "ani": 81.6994, "matched_fragments": 1268, "total_fragments": 2274, "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": "99.91", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000317595.1", "gtdb_species": "s__Streptomyces ipomoeae", "ani": 81.1991, "matched_fragments": 1154, "total_fragments": 2274, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_016598615.1", "gtdb_species": "s__Streptomyces sp016598615", "ani": 81.1421, "matched_fragments": 1276, "total_fragments": 2274, "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": 27.0, "optimum_tmp": 28.0, "optimum_ph": 7.341, "genome_size": 6847990.0, "gc_content": 73.2, "coding_genes": 7141.289, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 1.0, "sporulation": 0.958, "motility": 0.0, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Streptomyces", "fragilis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }