{ "type": "genome", "identifier": "GCF_900113145.1", "organism": "Actinopolymorpha cephalotaxi", "title": "Actinopolymorpha cephalotaxi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900113145.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421678", "wgs_master": "FOOI00000000.1", "refseq_category": "na", "taxid": "504797", "species_taxid": "504797", "organism_name": "Actinopolymorpha cephalotaxi", "infraspecific_name": "strain=CPCC 202808", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/05", "asm_name": "IMG-taxon 2675903058 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900113145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/113/145/GCF_900113145.1_IMG-taxon_2675903058_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": "6822861", "genome_size_ungapped": "6819989", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "40", "contig_count": "40", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900113145.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "6179", "protein_coding_gene_count": "6075", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-05", "dateModified": "2016-11-05", "datePublished": "2016-11-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinopolymorpha cephalotaxi" ], "sample_taxid": [ "504797" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Yunnan Province" ], "sample_host_location_id": [], "data_size": "1.829 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6822861", "Number of Sequences": "40", "Longest Sequences (bp)": "635070", "N50 (bp)": "325160", "Gap Ratio (%)": "0.042094", "GCcontent (%)": "70.9", "Number of CDSs": "6199", "Average Protein Length": "328.1", "Coding Ratio (%)": "89.4", "Number of rRNAs": "3", "Number of tRNAs": "62", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinopolymorpha cephalotaxi", "strain": "strain=DSM 45117", "accession": "GCA_013408535.1", "taxid": 504797, "species_taxid": 504797, "relation_to_type": "type", "validated": true, "ani": 99.9897, "matched_fragments": 2252, "total_fragments": 2254, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinopolymorpha rutila", "strain": "strain=DSM 18448", "accession": "GCA_013407855.1", "taxid": 446787, "species_taxid": 446787, "relation_to_type": "type", "validated": true, "ani": 91.1078, "matched_fragments": 1905, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolymorpha singaporensis", "strain": "strain=DSM 22024", "accession": "GCA_900104745.1", "taxid": 117157, "species_taxid": 117157, "relation_to_type": "type", "validated": true, "ani": 90.3703, "matched_fragments": 1837, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolymorpha pittospori", "strain": "strain=DSM 45354", "accession": "GCA_014873875.1", "taxid": 648752, "species_taxid": 648752, "relation_to_type": "type", "validated": true, "ani": 81.2762, "matched_fragments": 1358, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolymorpha alba", "strain": "strain=DSM 45243", "accession": "GCA_000373925.1", "taxid": 533267, "species_taxid": 533267, "relation_to_type": "type", "validated": true, "ani": 79.7452, "matched_fragments": 1050, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermasporomyces composti", "strain": "strain=DSM 22891", "accession": "GCA_003386795.1", "taxid": 696763, "species_taxid": 696763, "relation_to_type": "type", "validated": true, "ani": 78.9406, "matched_fragments": 686, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides panacis", "strain": "strain=G188", "accession": "GCA_019039255.1", "taxid": 2849501, "species_taxid": 2849501, "relation_to_type": "type", "validated": true, "ani": 77.4499, "matched_fragments": 510, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kribbella turkmenica", "strain": "strain=16K104", "accession": "GCA_004348725.1", "taxid": 2530375, "species_taxid": 2530375, "relation_to_type": "type", "validated": true, "ani": 77.2117, "matched_fragments": 563, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kribbella capetownensis", "strain": "strain=YM53", "accession": "GCA_004331485.1", "taxid": 1572659, "species_taxid": 1572659, "relation_to_type": "type", "validated": true, "ani": 77.1905, "matched_fragments": 562, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kribbella jiaozuonensis", "strain": "strain=NEAU-THZ27", "accession": "GCA_005233875.1", "taxid": 2575441, "species_taxid": 2575441, "relation_to_type": "type", "validated": true, "ani": 77.0263, "matched_fragments": 541, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides okcheonensis", "strain": "strain=MMS20-HV4-12", "accession": "GCA_020991065.1", "taxid": 2894081, "species_taxid": 2894081, "relation_to_type": "type", "validated": true, "ani": 76.8828, "matched_fragments": 461, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces gossypiisoli", "strain": "strain=TRM 44567", "accession": "GCA_013433285.1", "taxid": 2748864, "species_taxid": 2748864, "relation_to_type": "type", "validated": true, "ani": 76.3878, "matched_fragments": 529, "total_fragments": 2254, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013408535.1", "gtdb_species": "s__Actinopolymorpha cephalotaxi", "ani": 99.9897, "matched_fragments": 2252, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha", "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": "conclusive" }, { "accession": "GCF_013407855.1", "gtdb_species": "s__Actinopolymorpha rutila", "ani": 91.0973, "matched_fragments": 1905, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha", "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_900104745.1", "gtdb_species": "s__Actinopolymorpha singaporensis", "ani": 90.3887, "matched_fragments": 1833, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha", "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_014873875.1", "gtdb_species": "s__Actinopolymorpha pittospori", "ani": 81.2438, "matched_fragments": 1364, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha", "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_000373925.1", "gtdb_species": "s__Actinopolymorpha alba", "ani": 79.7771, "matched_fragments": 1044, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha", "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_003386795.1", "gtdb_species": "s__Thermasporomyces composti", "ani": 78.9285, "matched_fragments": 688, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Thermasporomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.77", "min_intra_species_ani": "99.77", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013177455.1", "gtdb_species": "s__Nocardioides sp013177455", "ani": 76.9343, "matched_fragments": 481, "total_fragments": 2254, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 27.916, "optimum_ph": 6.5, "genome_size": 6822861.0, "gc_content": 68.0, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Actinopolymorpha", "cephalotaxi" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }