{ "type": "genome", "identifier": "GCF_013408175.1", "organism": "Actinopolyspora biskrensis", "title": "Actinopolyspora biskrensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013408175.1", "bioproject": "PRJNA224116", "biosample": "SAMN12025516", "wgs_master": "JACBYW000000000.1", "refseq_category": "reference genome", "taxid": "1470178", "species_taxid": "1470178", "organism_name": "Actinopolyspora biskrensis", "infraspecific_name": "strain=CECT 8576", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/13", "asm_name": "ASM1340817v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_013408175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/408/175/GCF_013408175.1_ASM1340817v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4949786", "genome_size_ungapped": "4949689", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "15", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013408175.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "4419", "protein_coding_gene_count": "4288", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-13", "dateModified": "2020-07-13", "datePublished": "2020-07-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinopolyspora biskrensis" ], "sample_taxid": [ "1470178" ], "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": "1.349 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4949786", "Number of Sequences": "15", "Longest Sequences (bp)": "1328706", "N50 (bp)": "596905", "Gap Ratio (%)": "0.001960", "GCcontent (%)": "68.7", "Number of CDSs": "4474", "Average Protein Length": "310.4", "Coding Ratio (%)": "84.2", "Number of rRNAs": "2", "Number of tRNAs": "59", "Number of CRISPRs": "11" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinopolyspora biskrensis", "strain": "strain=CECT 8576", "accession": "GCA_013408175.1", "taxid": 1470178, "species_taxid": 1470178, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1638, "total_fragments": 1639, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinopolyspora halophila", "strain": "strain=DSM 43834", "accession": "GCA_000371785.1", "taxid": 1850, "species_taxid": 1850, "relation_to_type": "type", "validated": true, "ani": 93.4682, "matched_fragments": 1411, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolyspora saharensis", "strain": "strain=DSM 45459", "accession": "GCA_900100925.1", "taxid": 995062, "species_taxid": 995062, "relation_to_type": "type", "validated": true, "ani": 91.6514, "matched_fragments": 1329, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolyspora mortivallis", "strain": "strain=HS-1", "accession": "GCA_000384035.1", "taxid": 33906, "species_taxid": 33906, "relation_to_type": "type", "validated": true, "ani": 83.1028, "matched_fragments": 1014, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolyspora erythraea", "strain": "strain=YIM 90600", "accession": "GCA_000763095.1", "taxid": 414996, "species_taxid": 414996, "relation_to_type": "type", "validated": true, "ani": 82.0371, "matched_fragments": 1052, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolyspora xinjiangensis", "strain": "strain=DSM 46732", "accession": "GCA_900104475.1", "taxid": 405564, "species_taxid": 405564, "relation_to_type": "type", "validated": true, "ani": 81.9877, "matched_fragments": 1026, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolyspora alba", "strain": "strain=DSM 45004", "accession": "GCA_900112765.1", "taxid": 673379, "species_taxid": 673379, "relation_to_type": "type", "validated": true, "ani": 81.8992, "matched_fragments": 989, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinopolyspora righensis", "strain": "strain=DSM 45501", "accession": "GCA_900116555.1", "taxid": 995060, "species_taxid": 995060, "relation_to_type": "type", "validated": true, "ani": 81.6447, "matched_fragments": 974, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopolyspora algeriensis", "strain": "strain=CECT 8575", "accession": "GCA_003337235.1", "taxid": 1500506, "species_taxid": 1500506, "relation_to_type": "type", "validated": true, "ani": 79.0861, "matched_fragments": 604, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopolyspora algeriensis", "strain": "strain=DSM 46680", "accession": "GCA_006716575.1", "taxid": 1500506, "species_taxid": 1500506, "relation_to_type": "type", "validated": true, "ani": 79.0568, "matched_fragments": 586, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora rectivirgula", "strain": "strain=DSM 43747", "accession": "GCA_000497205.1", "taxid": 28042, "species_taxid": 28042, "relation_to_type": "type", "validated": true, "ani": 78.2079, "matched_fragments": 474, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia hydrocarbonoxydans", "strain": "strain=NBRC 14498", "accession": "GCA_006539565.1", "taxid": 76726, "species_taxid": 76726, "relation_to_type": "type", "validated": true, "ani": 76.6605, "matched_fragments": 348, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia petroleophila", "strain": "strain=CGMCC 4.1532", "accession": "GCA_014235185.1", "taxid": 37331, "species_taxid": 37331, "relation_to_type": "type", "validated": true, "ani": 76.3987, "matched_fragments": 353, "total_fragments": 1639, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013408175.1", "gtdb_species": "s__Actinopolyspora biskrensis", "ani": 100.0, "matched_fragments": 1638, "total_fragments": 1639, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora", "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_000371785.1", "gtdb_species": "s__Actinopolyspora halophila", "ani": 93.4682, "matched_fragments": 1411, "total_fragments": 1639, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora", "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_006716775.1", "gtdb_species": "s__Actinopolyspora sp006716775", "ani": 92.9382, "matched_fragments": 1363, "total_fragments": 1639, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora", "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_900100925.1", "gtdb_species": "s__Actinopolyspora saharensis", "ani": 91.6514, "matched_fragments": 1329, "total_fragments": 1639, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { 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"GCF_900101095.1", "gtdb_species": "s__Actinopolyspora mzabensis", "ani": 81.6604, "matched_fragments": 982, "total_fragments": 1639, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora", "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_003337235.1", "gtdb_species": "s__Halopolyspora algeriensis", "ani": 79.0938, "matched_fragments": 603, "total_fragments": 1639, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halopolyspora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": 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