{ "type": "genome", "identifier": "GCF_002911015.1", "organism": "Streptomyces populi", "title": "Streptomyces populi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SiChuan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002911015.1", "bioproject": "PRJNA224116", "biosample": "SAMN08166457", "wgs_master": "PJOS00000000.1", "refseq_category": "reference genome", "taxid": "2058924", "species_taxid": "2058924", "organism_name": "Streptomyces populi", "infraspecific_name": "strain=A249", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/20", "asm_name": "ASM291101v1", "asm_submitter": "SiChuan University", "gbrs_paired_asm": "GCA_002911015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/911/015/GCF_002911015.1_ASM291101v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9587301", "genome_size_ungapped": "9587281", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "277", "contig_count": "279", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002911015.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "8510", "protein_coding_gene_count": "8147", "non_coding_gene_count": "86", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-12-20", "dateModified": "2017-12-20", "datePublished": "2017-12-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces populi" ], "sample_taxid": [ "2058924" ], "sample_host_organism": [ "Populus adenopoda Maxim" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Sichuan" ], "sample_host_location_id": [], "data_size": "2.585 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)": "9587301", "Number of Sequences": "277", "Longest Sequences (bp)": "259593", "N50 (bp)": "75083", "Gap Ratio (%)": "0.000209", "GCcontent (%)": "71.7", "Number of CDSs": "8360", "Average Protein Length": "320.6", "Coding Ratio (%)": "83.9", "Number of rRNAs": "1", "Number of tRNAs": "101", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces populi", "strain": "strain=A249", "accession": "GCA_002911015.1", "taxid": 2058924, "species_taxid": 2058924, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3049, "total_fragments": 3063, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces triticiradicis", "strain": "strain=NEAU-H2", "accession": "GCA_008868685.1", "taxid": 2651189, "species_taxid": 2651189, "relation_to_type": "type", "validated": true, "ani": 95.1705, "matched_fragments": 2516, "total_fragments": 3063, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Streptomyces albiflavescens", "strain": "strain=CGMCC 4.7111", "accession": "GCA_014645835.1", "taxid": 1623582, "species_taxid": 1623582, "relation_to_type": "type", "validated": true, "ani": 86.5083, "matched_fragments": 2027, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces dengpaensis", "strain": "strain=XZHG99", "accession": "GCA_002946835.1", "taxid": 2049881, "species_taxid": 2049881, "relation_to_type": "type", "validated": true, "ani": 86.4234, "matched_fragments": 1720, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces mirabilis", "strain": "strain=JCM 4551", "accession": "GCA_014650275.1", "taxid": 68239, "species_taxid": 68239, "relation_to_type": "suspected-type", "validated": true, "ani": 86.0258, "matched_fragments": 1975, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces olivochromogenes", "strain": "strain=DSM 40451", "accession": "GCA_001514115.1", "taxid": 1963, "species_taxid": 1963, "relation_to_type": "type", "validated": true, "ani": 85.8547, "matched_fragments": 2012, "total_fragments": 3063, "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": 85.2367, "matched_fragments": 1819, "total_fragments": 3063, "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": 85.2357, "matched_fragments": 1830, "total_fragments": 3063, "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": 85.0902, "matched_fragments": 1898, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces umbrinus", "strain": "strain=JCM 4521", "accession": "GCA_014650195.1", "taxid": 67370, "species_taxid": 67370, "relation_to_type": "type", "validated": true, "ani": 83.961, "matched_fragments": 1891, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces fructofermentans", "strain": "strain=JCM 4956", "accession": "GCA_014651055.1", "taxid": 152141, "species_taxid": 152141, "relation_to_type": "type", "validated": true, "ani": 83.9357, "matched_fragments": 1831, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces hokutonensis", "strain": "strain=R1-NS-10", "accession": "GCA_000376565.1", "taxid": 1306990, "species_taxid": 1306990, "relation_to_type": "type", "validated": true, "ani": 83.8558, "matched_fragments": 1846, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces glomeratus", "strain": "strain=DSM 41457", "accession": "GCA_021462825.1", "taxid": 284452, "species_taxid": 284452, "relation_to_type": "type", "validated": true, "ani": 83.774, "matched_fragments": 1620, "total_fragments": 3063, "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": 83.6119, "matched_fragments": 1629, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces blattellae", "strain": "strain=TRM63209", "accession": "GCA_009709555.1", "taxid": 2569855, "species_taxid": 2569855, "relation_to_type": "type", "validated": true, "ani": 83.5967, "matched_fragments": 1565, "total_fragments": 3063, "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": 83.5402, "matched_fragments": 1761, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces neyagawaensis", "strain": "strain=JCM 4796", "accession": "GCA_023516595.1", "taxid": 42238, "species_taxid": 42238, "relation_to_type": "type", "validated": true, "ani": 83.4473, "matched_fragments": 1726, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces caniscabiei", "strain": "strain=NE06-02D", "accession": "GCA_014930365.1", "taxid": 2746961, "species_taxid": 2746961, "relation_to_type": "type", "validated": true, "ani": 83.441, "matched_fragments": 1799, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces geranii", "strain": "strain=A301", "accession": "GCA_002954775.1", "taxid": 2058923, "species_taxid": 2058923, "relation_to_type": "type", "validated": true, "ani": 83.3336, "matched_fragments": 1588, "total_fragments": 3063, "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": 81.8611, "matched_fragments": 1486, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces nymphaeiformis", "strain": "strain=SFB5A", "accession": "GCA_014203895.1", "taxid": 2663842, "species_taxid": 2663842, "relation_to_type": "type", "validated": true, "ani": 81.6856, "matched_fragments": 1497, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces wuyuanensis", "strain": "strain=CGMCC 4.7042", "accession": "GCA_900103455.1", "taxid": 1196353, "species_taxid": 1196353, "relation_to_type": "type", "validated": true, "ani": 81.3104, "matched_fragments": 1383, "total_fragments": 3063, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002911015.1", "gtdb_species": "s__Streptomyces populi", "ani": 100.0, "matched_fragments": 3049, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.17", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000725495.1", "gtdb_species": "s__Streptomyces aureus_B", "ani": 91.5994, "matched_fragments": 2415, "total_fragments": 3063, "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_002078175.1", "gtdb_species": "s__Streptomyces sp002078175", "ani": 87.5432, "matched_fragments": 2019, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "97.16", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002300165.1", "gtdb_species": "s__Streptomyces sp002300165", "ani": 86.6595, "matched_fragments": 1905, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.35", "min_intra_species_ani": "96.35", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014645835.1", "gtdb_species": "s__Streptomyces albiflavescens", "ani": 86.514, "matched_fragments": 2026, "total_fragments": 3063, "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_002946835.1", "gtdb_species": "s__Streptomyces dengpaensis", "ani": 86.4203, "matched_fragments": 1721, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014650275.1", "gtdb_species": "s__Streptomyces mirabilis", "ani": 86.0466, "matched_fragments": 1972, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.2382, "mean_intra_species_ani": "96.82", "min_intra_species_ani": "96.27", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_012273535.1", "gtdb_species": "s__Streptomyces sp002846625", "ani": 85.84, "matched_fragments": 2001, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.4492, "mean_intra_species_ani": "97.43", "min_intra_species_ani": "96.23", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001514115.1", "gtdb_species": "s__Streptomyces olivochromogenes", "ani": 85.8366, "matched_fragments": 2016, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 96.2382, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_008042115.1", "gtdb_species": "s__Streptomyces sp008042115", "ani": 85.509, "matched_fragments": 1900, "total_fragments": 3063, "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": 85.2328, "matched_fragments": 1830, "total_fragments": 3063, "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_008369065.1", "gtdb_species": "s__Streptomyces sp008369065", "ani": 84.0838, "matched_fragments": 1699, "total_fragments": 3063, "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_014651055.1", "gtdb_species": "s__Streptomyces fructofermentans", "ani": 83.934, "matched_fragments": 1832, "total_fragments": 3063, "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_002954775.1", "gtdb_species": "s__Streptomyces geranii", "ani": 83.29, "matched_fragments": 1597, "total_fragments": 3063, "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_900105415.1", "gtdb_species": "s__Streptomyces sp900105415", "ani": 81.7525, "matched_fragments": 1474, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.65", "min_intra_species_ani": "95.65", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014649755.1", "gtdb_species": "s__Streptomyces litmocidini", "ani": 81.6462, "matched_fragments": 1439, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.07", "min_intra_species_ani": "95.07", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014649855.1", "gtdb_species": "s__Streptomyces roseolus", "ani": 81.5627, "matched_fragments": 1370, "total_fragments": 3063, "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_000716445.1", "gtdb_species": "s__Streptomyces wedmorensis", "ani": 81.5568, "matched_fragments": 1483, "total_fragments": 3063, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "97.63", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.201, "cell_length": -0.05, "doubling_h": 0.103, "growth_tmp": 27.757, "optimum_tmp": 29.036, "optimum_ph": 7.341, "genome_size": 8292419.302, "gc_content": 71.543, "coding_genes": 7141.289, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 0.998, "sporulation": 0.958, "motility": 0.049, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.005, "aerobic_respiration": 0.994, "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", "populi" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }