{ "type": "genome", "identifier": "GCF_009604385.1", "organism": "Streptomyces smaragdinus", "title": "Streptomyces smaragdinus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Karlsruhe Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009604385.1", "bioproject": "PRJNA224116", "biosample": "SAMN11898449", "wgs_master": "WEGJ00000000.1", "refseq_category": "reference genome", "taxid": "2585196", "species_taxid": "2585196", "organism_name": "Streptomyces smaragdinus", "infraspecific_name": "strain=RB5", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/11/06", "asm_name": "ASM960438v1", "asm_submitter": "Karlsruhe Institute of Technology", "gbrs_paired_asm": "GCA_009604385.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/604/385/GCF_009604385.1_ASM960438v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7857212", "genome_size_ungapped": "7857212", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "106", "contig_count": "106", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009604385.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "7214", "protein_coding_gene_count": "7011", "non_coding_gene_count": "81", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-11-06", "dateModified": "2019-11-06", "datePublished": "2019-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces smaragdinus" ], "sample_taxid": [ "2585196" ], "sample_host_organism": [ "Macrotermes natalensis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Africa:Pretoria" ], "sample_host_location_id": [], "data_size": "2.104 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)": "7857212", "Number of Sequences": "106", "Longest Sequences (bp)": "733946", "N50 (bp)": "161565", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.0", "Number of CDSs": "7155", "Average Protein Length": "328.1", "Coding Ratio (%)": "89.6", "Number of rRNAs": "5", "Number of tRNAs": "94", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces smaragdinus", "strain": "strain=RB5", "accession": "GCA_009604385.1", "taxid": 2585196, "species_taxid": 2585196, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2561, "total_fragments": 2564, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces coryli", "strain": "strain=A7024", "accession": "GCA_011044975.1", "taxid": 1128680, "species_taxid": 1128680, "relation_to_type": "type", "validated": true, "ani": 80.8475, "matched_fragments": 1225, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces pathocidini", "strain": "strain=NRRL B-24287", "accession": "GCA_001418495.1", "taxid": 1650571, "species_taxid": 1650571, "relation_to_type": "type", "validated": true, "ani": 80.8089, "matched_fragments": 769, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces galbus", "strain": "strain=DSM 40089", "accession": "GCA_005280195.1", "taxid": 33898, "species_taxid": 33898, "relation_to_type": "type", "validated": true, "ani": 80.146, "matched_fragments": 1182, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces minutiscleroticus", "strain": "strain=JCM 4790", "accession": "GCA_014650875.1", "taxid": 68238, "species_taxid": 68238, "relation_to_type": "type", "validated": true, "ani": 80.1386, "matched_fragments": 1195, "total_fragments": 2564, "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": 80.0845, "matched_fragments": 1190, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces melanogenes", "strain": "strain=JCM 4398", "accession": "GCA_014649795.1", "taxid": 67326, "species_taxid": 67326, "relation_to_type": "type", "validated": true, "ani": 80.0791, "matched_fragments": 1145, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces sudanensis", "strain": "strain=SD 504", "accession": "GCA_023614315.1", "taxid": 436397, "species_taxid": 436397, "relation_to_type": "type", "validated": true, "ani": 80.077, "matched_fragments": 927, "total_fragments": 2564, "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": 80.0708, "matched_fragments": 1052, "total_fragments": 2564, "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": 80.0413, "matched_fragments": 1201, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces hiroshimensis", "strain": "strain=JCM 4586", "accession": "GCA_014650335.1", "taxid": 66424, "species_taxid": 66424, "relation_to_type": "type", "validated": true, "ani": 80.0278, "matched_fragments": 1064, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces panaciradicis", "strain": "strain=NBRC 109811", "accession": "GCA_023516615.1", "taxid": 1470261, "species_taxid": 1470261, "relation_to_type": "type", "validated": true, "ani": 80.0224, "matched_fragments": 1157, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rubradiris", "strain": "strain=NBRC 14000", "accession": "GCA_016860525.1", "taxid": 285531, "species_taxid": 285531, "relation_to_type": "type", "validated": true, "ani": 79.9459, "matched_fragments": 1156, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces alfalfae", "strain": "strain=XY25", "accession": "GCA_004127445.1", 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79.706, "matched_fragments": 1038, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces flavofungini", "strain": "strain=JCM 4753", "accession": "GCA_014650815.1", "taxid": 68200, "species_taxid": 68200, "relation_to_type": "type", "validated": true, "ani": 79.6897, "matched_fragments": 1160, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces flavofungini", "strain": "strain=JCM 4753", "accession": "GCA_016411765.1", "taxid": 68200, "species_taxid": 68200, "relation_to_type": "type", "validated": true, "ani": 79.6799, "matched_fragments": 1179, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces alboflavus", "strain": "strain=NRRL B-2373", "accession": "GCA_000716675.1", "taxid": 67267, "species_taxid": 67267, "relation_to_type": "type", "validated": true, "ani": 79.6648, "matched_fragments": 1180, 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"below_threshold" }, { "organism_name": "Streptomyces bathyalis", "strain": "strain=ASO4wet", "accession": "GCA_015910445.1", "taxid": 2710756, "species_taxid": 2710756, "relation_to_type": "type", "validated": true, "ani": 79.1581, "matched_fragments": 903, "total_fragments": 2564, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009604385.1", "gtdb_species": "s__Streptomyces sp009604385", "ani": 100.0, "matched_fragments": 2561, "total_fragments": 2564, "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_011044975.1", "gtdb_species": 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80.4202, "matched_fragments": 1173, "total_fragments": 2564, "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_005280195.1", "gtdb_species": "s__Streptomyces galbus", "ani": 80.1792, "matched_fragments": 1175, "total_fragments": 2564, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_006782915.1", "gtdb_species": "s__Streptomyces calvus", "ani": 80.1573, "matched_fragments": 1176, 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