{ "type": "genome", "identifier": "GCF_003385235.1", "organism": "Amycolatopsis circi", "title": "Amycolatopsis circi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northumbria University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003385235.1", "bioproject": "PRJNA224116", "biosample": "SAMN08435653", "wgs_master": "PQIA00000000.1", "refseq_category": "reference genome", "taxid": "871959", "species_taxid": "871959", "organism_name": "Amycolatopsis circi", "infraspecific_name": "strain=DSM 45561", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/14", "asm_name": "ASM338523v1", "asm_submitter": "Northumbria University", "gbrs_paired_asm": "GCA_003385235.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/385/235/GCF_003385235.1_ASM338523v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9804613", "genome_size_ungapped": "9804613", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "305", "contig_count": "305", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003385235.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "9241", "protein_coding_gene_count": "9022", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-14", "dateModified": "2018-08-14", "datePublished": "2018-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis circi" ], "sample_taxid": [ "871959" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Africa: Cape Town" ], "sample_host_location_id": [], "data_size": "2.678 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.55, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9804613", "Number of Sequences": "305", "Longest Sequences (bp)": "202078", "N50 (bp)": "54985", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.0", "Number of CDSs": "9117", "Average Protein Length": "311.1", "Coding Ratio (%)": "86.8", "Number of rRNAs": "2", "Number of tRNAs": "80", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis circi", "strain": "strain=DSM 45561", "accession": "GCA_003385235.1", "taxid": 871959, "species_taxid": 871959, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3086, "total_fragments": 3107, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis dendrobii", "strain": "strain=DR6-1", "accession": "GCA_014145675.1", "taxid": 2760662, "species_taxid": 2760662, "relation_to_type": "type", "validated": true, "ani": 92.1931, "matched_fragments": 2510, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis nivea", "strain": "strain=CFH S0261", "accession": "GCA_004522235.1", "taxid": 1644109, "species_taxid": 1644109, "relation_to_type": "type", "validated": true, "ani": 92.1748, "matched_fragments": 2478, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rubida", "strain": "strain=DSM 44637", "accession": "GCA_900115345.1", "taxid": 112413, "species_taxid": 112413, "relation_to_type": "type", "validated": true, "ani": 91.8969, "matched_fragments": 2368, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis benzoatilytica", "strain": "strain=AK 16/65", "accession": "GCA_000383915.1", "taxid": 346045, "species_taxid": 346045, "relation_to_type": "type", "validated": true, "ani": 86.6184, "matched_fragments": 1953, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis jejuensis", "strain": "strain=NRRL B-24427", "accession": "GCA_000717335.1", "taxid": 330084, "species_taxid": 330084, "relation_to_type": "type", "validated": true, "ani": 85.295, "matched_fragments": 1776, "total_fragments": 3107, "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": 81.4849, "matched_fragments": 1560, "total_fragments": 3107, "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": 79.8587, "matched_fragments": 1094, "total_fragments": 3107, "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": 78.9907, "matched_fragments": 897, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prauserella isguenensis", "strain": "strain=CECT 8577", "accession": "GCA_014191605.1", "taxid": 1470180, "species_taxid": 1470180, "relation_to_type": "type", "validated": true, "ani": 78.6933, "matched_fragments": 676, "total_fragments": 3107, "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": 78.0642, "matched_fragments": 772, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kibdelosporangium philippinense", "strain": "strain=ATCC 49844", "accession": "GCA_021390435.3", "taxid": 211113, "species_taxid": 211113, "relation_to_type": "type", "validated": true, "ani": 77.6829, "matched_fragments": 738, "total_fragments": 3107, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.55, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003385235.1", "gtdb_species": "s__Amycolatopsis circi", "ani": 100.0, "matched_fragments": 3087, "total_fragments": 3107, "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_014145675.1", "gtdb_species": "s__Amycolatopsis sp014145675", "ani": 92.2195, "matched_fragments": 2506, "total_fragments": 3107, "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_004522235.1", "gtdb_species": "s__Amycolatopsis nivea", "ani": 92.1818, "matched_fragments": 2477, "total_fragments": 3107, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "97.28", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002796545.1", "gtdb_species": "s__Amycolatopsis sp002796545", "ani": 91.9393, "matched_fragments": 2357, "total_fragments": 3107, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900115345.1", "gtdb_species": "s__Amycolatopsis rubida", "ani": 91.8626, "matched_fragments": 2372, "total_fragments": 3107, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", 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