{ "type": "genome", "identifier": "GCF_004365925.1", "organism": "Amycolatopsis arida", "title": "Amycolatopsis arida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004365925.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621706", "wgs_master": "SOEP00000000.1", "refseq_category": "na", "taxid": "587909", "species_taxid": "587909", "organism_name": "Amycolatopsis arida", "infraspecific_name": "strain=DSM 45648", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436592v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004365925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/365/925/GCF_004365925.1_ASM436592v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6002460", "genome_size_ungapped": "6002460", "gc_percent": "72.500000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004365925.1-RS_2024_04_19", "annotation_date": "2024-04-19", "total_gene_count": "5782", "protein_coding_gene_count": "5624", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis arida" ], "sample_taxid": [ "587909" ], "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": "1.589 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)": "6002460", "Number of Sequences": "28", "Longest Sequences (bp)": "977085", "N50 (bp)": "652511", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.7", "Number of CDSs": "5826", "Average Protein Length": "301.9", "Coding Ratio (%)": "87.9", "Number of rRNAs": "2", "Number of tRNAs": "66", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis arida", "strain": "strain=DSM 45648", "accession": "GCA_004365925.1", "taxid": 587909, "species_taxid": 587909, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1985, "total_fragments": 1986, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis arida", "strain": "strain=CGMCC 4.5579", "accession": "GCA_900115565.1", "taxid": 587909, "species_taxid": 587909, "relation_to_type": "type", "validated": true, "ani": 99.9973, "matched_fragments": 1964, "total_fragments": 1986, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis aidingensis", "strain": "strain=YIM 96748", "accession": "GCA_018885265.1", "taxid": 2842453, "species_taxid": 2842453, "relation_to_type": "type", "validated": true, "ani": 81.0426, "matched_fragments": 1208, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella muralis", "strain": "strain=DSM 45305", "accession": "GCA_007993965.1", "taxid": 588067, "species_taxid": 588067, "relation_to_type": "type", "validated": true, "ani": 80.9549, "matched_fragments": 1144, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella muralis", "strain": "strain=DSM 45305", "accession": "GCA_003202285.1", "taxid": 588067, "species_taxid": 588067, "relation_to_type": "type", "validated": true, "ani": 80.954, "matched_fragments": 1122, "total_fragments": 1986, "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": 80.7547, "matched_fragments": 1052, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis granulosa", "strain": "strain=DSM 45669", "accession": "GCA_011758745.1", "taxid": 185684, "species_taxid": 185684, "relation_to_type": "type", "validated": true, "ani": 80.6763, "matched_fragments": 966, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis anabasis", "strain": "strain=EGI 650086", "accession": "GCA_009765355.1", "taxid": 1840409, "species_taxid": 1840409, "relation_to_type": "type", "validated": true, "ani": 80.6427, "matched_fragments": 1184, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis nigrescens", "strain": "strain=CSC17Ta-90", "accession": "GCA_000384315.1", "taxid": 381445, "species_taxid": 381445, "relation_to_type": "type", "validated": true, "ani": 80.6025, "matched_fragments": 1209, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis viridis", "strain": "strain=DSM 45668", "accession": "GCA_011758765.1", "taxid": 185678, "species_taxid": 185678, "relation_to_type": "type", "validated": true, "ani": 80.5898, "matched_fragments": 980, "total_fragments": 1986, "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": 80.3355, "matched_fragments": 991, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acidiphila", "strain": "strain=JCM 30562", "accession": "GCA_007713745.1", "taxid": 715473, "species_taxid": 715473, "relation_to_type": "type", "validated": true, "ani": 80.3348, "matched_fragments": 961, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis palatopharyngis", "strain": "strain=DSM 44832", "accession": "GCA_003385185.1", "taxid": 187982, "species_taxid": 187982, "relation_to_type": "type", "validated": true, "ani": 80.2876, "matched_fragments": 1015, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acidiphila", "strain": "strain=KCTC 39523", "accession": "GCA_021391495.1", "taxid": 715473, "species_taxid": 715473, "relation_to_type": "type", "validated": true, "ani": 80.2747, "matched_fragments": 998, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis endophytica", "strain": "strain=DSM 104006", "accession": "GCA_013410405.1", "taxid": 860233, "species_taxid": 860233, "relation_to_type": "type", "validated": true, "ani": 80.0789, "matched_fragments": 988, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rhizosphaerae", "strain": "strain=TBRC 6029", "accession": "GCA_007713715.1", "taxid": 2053003, "species_taxid": 2053003, "relation_to_type": "type", "validated": true, "ani": 79.8393, "matched_fragments": 808, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acidicola", "strain": "strain=K81G1", "accession": "GCA_007713735.2", "taxid": 2596893, "species_taxid": 2596893, "relation_to_type": "type", "validated": true, "ani": 79.6452, "matched_fragments": 953, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharomonospora piscinae", "strain": "strain=KCTC 19743", "accession": "GCA_005862235.1", "taxid": 687388, "species_taxid": 687388, "relation_to_type": "type", "validated": true, "ani": 79.3553, "matched_fragments": 805, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella aidingensis", "strain": "strain=DSM 45266", "accession": "GCA_024171865.1", "taxid": 387890, "species_taxid": 387890, "relation_to_type": "type", "validated": true, "ani": 79.3467, "matched_fragments": 776, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis taiwanensis", "strain": "strain=DSM 45107", "accession": "GCA_000519205.1", "taxid": 342230, "species_taxid": 342230, "relation_to_type": "type", "validated": true, "ani": 79.318, "matched_fragments": 884, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea tibetensis", "strain": "strain=FXJ1.1311", "accession": "GCA_007845675.1", "taxid": 2591470, "species_taxid": 2591470, "relation_to_type": "type", "validated": true, "ani": 77.8976, "matched_fragments": 842, "total_fragments": 1986, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900115565.1", "gtdb_species": "s__Yuhushiella arida", "ani": 99.9973, "matched_fragments": 1964, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003001955.1", "gtdb_species": "s__Saccharomonospora shujinwangii", "ani": 81.1312, "matched_fragments": 1106, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora", "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_018885265.1", "gtdb_species": "s__Amycolatopsis_D sp018885265", "ani": 81.0256, "matched_fragments": 1211, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D", "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_006715045.1", "gtdb_species": "s__Amycolatopsis_D cihanbeyliensis", "ani": 80.9707, "matched_fragments": 1185, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D", "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_003202285.1", "gtdb_species": "s__Saccharomonospora muralis", "ani": 80.9301, "matched_fragments": 1126, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003385215.1", "gtdb_species": "s__Amycolatopsis thermalba", "ani": 80.7534, "matched_fragments": 1052, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_011758745.1", "gtdb_species": "s__Amycolatopsis granulosa", "ani": 80.6632, "matched_fragments": 968, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.9842, "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_009765355.1", "gtdb_species": "s__Amycolatopsis anabasis", "ani": 80.6427, "matched_fragments": 1183, "total_fragments": 1986, "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_003202235.1", "gtdb_species": "s__Saccharomonospora sp003202235", "ani": 80.6281, "matched_fragments": 1112, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora", "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_000384315.1", "gtdb_species": "s__Amycolatopsis nigrescens", "ani": 80.5963, "matched_fragments": 1210, "total_fragments": 1986, "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_011758765.1", "gtdb_species": "s__Amycolatopsis viridis", "ani": 80.58, "matched_fragments": 982, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.9842, "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_000231075.2", "gtdb_species": "s__Amycolatopsis sp000231075", "ani": 80.5131, "matched_fragments": 1104, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.4849, "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_007713745.1", "gtdb_species": "s__Amycolatopsis acidiphila", "ani": 80.3298, "matched_fragments": 963, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003385185.1", "gtdb_species": "s__Amycolatopsis_D palatopharyngis", "ani": 80.3175, "matched_fragments": 1010, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D", "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_014191255.1", "gtdb_species": "s__Amycolatopsis bartoniae", "ani": 80.1235, "matched_fragments": 977, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013410405.1", "gtdb_species": "s__Amycolatopsis endophytica", "ani": 80.1075, "matched_fragments": 983, "total_fragments": 1986, "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_007713715.1", "gtdb_species": "s__Amycolatopsis rhizosphaerae", "ani": 79.8733, "matched_fragments": 803, "total_fragments": 1986, "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_018736145.1", "gtdb_species": "s__Amycolatopsis sp018736145", "ani": 79.7219, "matched_fragments": 1105, "total_fragments": 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"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_005862235.1", "gtdb_species": "s__Saccharomonospora piscinae", "ani": 79.3755, "matched_fragments": 802, "total_fragments": 1986, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000519205.1", "gtdb_species": "s__Amycolatopsis taiwanensis", "ani": 79.3278, "matched_fragments": 882, "total_fragments": 1986, "gtdb_taxonomy": 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