{ "type": "genome", "identifier": "GCF_900105945.1", "organism": "Amycolatopsis tolypomycina", "title": "Amycolatopsis tolypomycina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900105945.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489727", "wgs_master": "FNSO00000000.1", "refseq_category": "reference genome", "taxid": "208445", "species_taxid": "208445", "organism_name": "Amycolatopsis tolypomycina", "infraspecific_name": "strain=DSM 44544", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/22", "asm_name": "IMG-taxon 2634166899 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900105945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/105/945/GCF_900105945.1_IMG-taxon_2634166899_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": "10363431", "genome_size_ungapped": "10363431", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900105945.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "9598", "protein_coding_gene_count": "9410", "non_coding_gene_count": "67", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-22", "dateModified": "2016-10-22", "datePublished": "2016-10-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis tolypomycina" ], "sample_taxid": [ "208445" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.745 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 6.94, "strain_heterogeneity": 81.82, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10363431", "Number of Sequences": "4", "Longest Sequences (bp)": "8172406", "N50 (bp)": "8172406", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.7", "Number of CDSs": "9641", "Average Protein Length": "329.3", "Coding Ratio (%)": "91.9", "Number of rRNAs": "12", "Number of tRNAs": "83", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis tolypomycina", "strain": "strain=DSM 44544", "accession": "GCA_900105945.1", "taxid": 208445, "species_taxid": 208445, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3445, "total_fragments": 3453, "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": 92.0294, "matched_fragments": 2306, "total_fragments": 3453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rifamycinica", "strain": "strain=DSM 46095", "accession": "GCA_000695625.1", "taxid": 287986, "species_taxid": 287986, "relation_to_type": "type", "validated": true, "ani": 91.7783, "matched_fragments": 2505, "total_fragments": 3453, "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": 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89.6962, "matched_fragments": 2451, "total_fragments": 3453, "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": 89.531, "matched_fragments": 2456, "total_fragments": 3453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis eburnea", "strain": "strain=GLM-1", "accession": "GCA_003937945.1", "taxid": 2267691, "species_taxid": 2267691, "relation_to_type": "type", "validated": true, "ani": 88.9494, "matched_fragments": 2423, "total_fragments": 3453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=DSM 44653", "accession": "GCA_014873755.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 88.8072, "matched_fragments": 2523, "total_fragments": 3453, "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": 88.7583, "matched_fragments": 2215, "total_fragments": 3453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis pretoriensis", "strain": "strain=NRRL B-24133", "accession": "GCA_002156025.1", "taxid": 218821, "species_taxid": 218821, "relation_to_type": "type", "validated": true, "ani": 88.5787, "matched_fragments": 2201, "total_fragments": 3453, "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": 88.492, "matched_fragments": 2463, "total_fragments": 3453, "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": 80.2036, "matched_fragments": 1292, "total_fragments": 3453, "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": 79.0719, "matched_fragments": 1148, "total_fragments": 3453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis aidingensis", "strain": "strain=YIM 96748", "accession": "GCA_018885265.1", "taxid": 2842453, "species_taxid": 2842453, "relation_to_type": "type", "validated": true, "ani": 78.7372, "matched_fragments": 1154, "total_fragments": 3453, "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": 78.1204, "matched_fragments": 1010, "total_fragments": 3453, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 6.94, "strain_heterogeneity": 81.82 }, "gtdb_result": [ { "accession": "GCF_900105945.1", "gtdb_species": "s__Amycolatopsis tolypomycina", "ani": 100.0, "matched_fragments": 3447, "total_fragments": 3453, "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_017308975.1", "gtdb_species": 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