{ "type": "genome", "identifier": "GCF_014205155.1", "organism": "Amycolatopsis umgeniensis", "title": "Amycolatopsis umgeniensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014205155.1", "bioproject": "PRJNA224116", "biosample": "SAMN14502812", "wgs_master": "JACHMX000000000.1", "refseq_category": "reference genome", "taxid": "336628", "species_taxid": "336628", "organism_name": "Amycolatopsis umgeniensis", "infraspecific_name": "strain=DSM 45272", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1420515v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014205155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/205/155/GCF_014205155.1_ASM1420515v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9225930", "genome_size_ungapped": "9225930", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014205155.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "8451", "protein_coding_gene_count": "8326", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis umgeniensis" ], "sample_taxid": [ "336628" ], "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": "2.497 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 6.94, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9225930", "Number of Sequences": "1", "Longest Sequences (bp)": "9225930", "N50 (bp)": "9225930", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.7", "Number of CDSs": "8493", "Average Protein Length": "329.9", "Coding Ratio (%)": "91.1", "Number of rRNAs": "12", "Number of tRNAs": "75", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis umgeniensis", "strain": "strain=DSM 45272", "accession": "GCA_014205155.1", "taxid": 336628, "species_taxid": 336628, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3074, "total_fragments": 3075, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_000384215.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 91.6728, "matched_fragments": 2466, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_002234385.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 91.5772, "matched_fragments": 2315, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis azurea", "strain": "strain=DSM 43854", "accession": "GCA_001995215.1", "taxid": 36819, "species_taxid": 36819, "relation_to_type": "type", "validated": true, "ani": 91.5541, "matched_fragments": 2496, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis azurea", "strain": "strain=DSM 43854", "accession": "GCA_000340415.1", "taxid": 36819, "species_taxid": 36819, "relation_to_type": "type", "validated": true, "ani": 91.5109, "matched_fragments": 2471, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis thailandensis", "strain": "strain=JCM 16380", "accession": "GCA_002234405.1", "taxid": 589330, "species_taxid": 589330, "relation_to_type": "type", "validated": true, "ani": 91.4179, "matched_fragments": 2287, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis coloradensis", "strain": "strain=DSM 44225", "accession": "GCA_001953865.1", "taxid": 76021, "species_taxid": 76021, "relation_to_type": "type", "validated": true, "ani": 90.8876, "matched_fragments": 2293, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis keratiniphila subsp. nogabecina", "strain": "strain=FH 1893", "accession": "GCA_001953855.1", "taxid": 208442, "species_taxid": 129921, "relation_to_type": "type", "validated": true, "ani": 90.5824, "matched_fragments": 2413, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis orientalis", "strain": "strain=KCTC 9412", "accession": "GCA_000478275.1", "taxid": 31958, "species_taxid": 31958, "relation_to_type": "type", "validated": true, "ani": 90.4284, "matched_fragments": 2309, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis pittospori", "strain": "strain=PIP199", "accession": "GCA_013870525.1", "taxid": 2749434, "species_taxid": 2749434, "relation_to_type": "type", "validated": true, "ani": 90.2517, "matched_fragments": 2206, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=GY080", "accession": "GCA_001558125.2", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 90.1254, "matched_fragments": 2183, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis regifaucium", "strain": "strain=GY080", "accession": "GCA_001613935.1", "taxid": 546365, "species_taxid": 546365, "relation_to_type": "type", "validated": true, "ani": 90.083, "matched_fragments": 2198, "total_fragments": 3075, "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": 81.4726, "matched_fragments": 1717, "total_fragments": 3075, "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": 79.6723, "matched_fragments": 1080, "total_fragments": 3075, "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": 78.9007, "matched_fragments": 1018, "total_fragments": 3075, "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": 78.7663, "matched_fragments": 1036, "total_fragments": 3075, "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": 77.891, "matched_fragments": 824, "total_fragments": 3075, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 6.94, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014205155.1", "gtdb_species": "s__Amycolatopsis umgeniensis", "ani": 100.0, "matched_fragments": 3075, "total_fragments": 3075, "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_002849735.1", "gtdb_species": "s__Amycolatopsis sp002849735", "ani": 93.2183, "matched_fragments": 2597, "total_fragments": 3075, "gtdb_taxonomy": 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