{ "type": "genome", "identifier": "GCF_000695625.1", "organism": "Amycolatopsis rifamycinica", "title": "Amycolatopsis rifamycinica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Delhi", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000695625.1", "bioproject": "PRJNA224116", "biosample": "SAMN02745639", "wgs_master": "JMQI00000000.1", "refseq_category": "reference genome", "taxid": "287986", "species_taxid": "287986", "organism_name": "Amycolatopsis rifamycinica", "infraspecific_name": "strain=DSM 46095", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/05/22", "asm_name": "ASM69562v1", "asm_submitter": "University of Delhi", "gbrs_paired_asm": "GCA_000695625.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/695/625/GCF_000695625.1_ASM69562v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9202418", "genome_size_ungapped": "9202418", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "88", "contig_count": "88", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000695625.1-RS_2024_12_16", "annotation_date": "2024-12-16", "total_gene_count": "8686", "protein_coding_gene_count": "8519", "non_coding_gene_count": "79", "pubmed_id": "24994803" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-05-22", "dateModified": "2014-05-22", "datePublished": "2014-05-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis rifamycinica" ], "sample_taxid": [ "287986" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia" ], "sample_host_location_id": [], "data_size": "2.452 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9202418", "Number of Sequences": "88", "Longest Sequences (bp)": "400030", "N50 (bp)": "210173", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.8", "Number of CDSs": "8678", "Average Protein Length": "320.1", "Coding Ratio (%)": "90.5", "Number of rRNAs": "4", "Number of tRNAs": "73", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis rifamycinica", "strain": "strain=DSM 46095", "accession": "GCA_000695625.1", "taxid": 287986, "species_taxid": 287986, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3025, "total_fragments": 3032, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis kentuckyensis", "strain": "strain=NRRL B-24129", "accession": "GCA_002155975.1", "taxid": 218823, "species_taxid": 218823, "relation_to_type": "type", "validated": true, "ani": 92.041, "matched_fragments": 2212, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis tolypomycina", "strain": "strain=DSM 44544", "accession": "GCA_900105945.1", "taxid": 208445, "species_taxid": 208445, "relation_to_type": "type", "validated": true, "ani": 91.8264, "matched_fragments": 2492, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis mediterranei", "strain": "strain=S699", "accession": "GCA_000220945.1", "taxid": 33910, "species_taxid": 33910, "relation_to_type": "type", "validated": true, "ani": 91.7405, "matched_fragments": 2453, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vancoresmycina", "strain": "strain=NRRL B-24208", "accession": "GCA_000716785.1", "taxid": 208444, "species_taxid": 208444, "relation_to_type": "type", "validated": true, "ani": 90.6926, "matched_fragments": 2414, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vancoresmycina", "strain": "strain=DSM 44592", "accession": "GCA_000388135.1", "taxid": 208444, "species_taxid": 208444, "relation_to_type": "type", "validated": true, "ani": 90.5263, "matched_fragments": 2042, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vastitatis", "strain": "strain=H5", "accession": "GCA_002234595.1", "taxid": 1905142, "species_taxid": 1905142, "relation_to_type": "type", "validated": true, "ani": 89.8951, "matched_fragments": 2305, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis balhimycina", "strain": "strain=DSM 44591", "accession": "GCA_000384295.1", "taxid": 208443, "species_taxid": 208443, "relation_to_type": "type", "validated": true, "ani": 89.6737, "matched_fragments": 2295, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=NRRL B-24131", "accession": "GCA_002156005.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 88.947, "matched_fragments": 2094, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis camponoti", "strain": "strain=A23", "accession": "GCA_902497555.1", "taxid": 2606593, "species_taxid": 2606593, "relation_to_type": "type", "validated": true, "ani": 88.6005, "matched_fragments": 2352, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis thermalba", "strain": "strain=NRRL B-24845", "accession": "GCA_003385215.1", "taxid": 944492, "species_taxid": 944492, "relation_to_type": "type", "validated": true, "ani": 80.2758, "matched_fragments": 1253, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella cavernicola", "strain": "strain=ASG 168", "accession": "GCA_016595675.1", "taxid": 2800127, "species_taxid": 2800127, "relation_to_type": "type", "validated": true, "ani": 79.1314, "matched_fragments": 1103, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora globicatena", "strain": "strain=DSM 44256", "accession": "GCA_024171945.1", "taxid": 103729, "species_taxid": 103729, "relation_to_type": "type", "validated": true, "ani": 78.1778, "matched_fragments": 950, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea aerocolonigenes", "strain": "strain=DSM 40034", "accession": "GCA_024171805.1", "taxid": 68170, "species_taxid": 68170, "relation_to_type": "type", "validated": true, "ani": 78.0807, "matched_fragments": 1101, "total_fragments": 3032, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000695625.1", "gtdb_species": "s__Amycolatopsis rifamycinica", "ani": 100.0, "matched_fragments": 3025, "total_fragments": 3032, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_002155975.1", "gtdb_species": "s__Amycolatopsis kentuckyensis", "ani": 92.0349, "matched_fragments": 2213, "total_fragments": 3032, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_900105945.1", "gtdb_species": "s__Amycolatopsis tolypomycina", "ani": 91.8409, "matched_fragments": 2490, "total_fragments": 3032, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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_017308975.1", "gtdb_species": "s__Amycolatopsis sp017308975", "ani": 91.8358, "matched_fragments": 2434, "total_fragments": 3032, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "rifamycinica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }