{ "type": "genome", "identifier": "GCF_004522235.1", "organism": "Amycolatopsis nivea", "title": "Amycolatopsis nivea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Xinxiang Medical University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004522235.1", "bioproject": "PRJNA224116", "biosample": "SAMN10511189", "wgs_master": "SDLT00000000.1", "refseq_category": "reference genome", "taxid": "1644109", "species_taxid": "1644109", "organism_name": "Amycolatopsis nivea", "infraspecific_name": "strain=CFH S0261", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/29", "asm_name": "ASM452223v1", "asm_submitter": "Xinxiang Medical University", "gbrs_paired_asm": "GCA_004522235.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/522/235/GCF_004522235.1_ASM452223v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9571567", "genome_size_ungapped": "9571386", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "133", "contig_count": "133", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004522235.1-RS_2024_08_06", "annotation_date": "2024-08-06", "total_gene_count": "8934", "protein_coding_gene_count": "8794", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-29", "dateModified": "2019-03-29", "datePublished": "2019-03-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis nivea" ], "sample_taxid": [ "1644109" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Henan" ], "sample_host_location_id": [], "data_size": "2.592 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9571567", "Number of Sequences": "133", "Longest Sequences (bp)": "434569", "N50 (bp)": "181068", "Gap Ratio (%)": "0.002413", "GCcontent (%)": "69.5", "Number of CDSs": "8985", "Average Protein Length": "319.2", "Coding Ratio (%)": "89.9", "Number of rRNAs": "2", "Number of tRNAs": "82", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis nivea", "strain": "strain=CFH S0261", "accession": "GCA_004522235.1", "taxid": 1644109, "species_taxid": 1644109, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3124, "total_fragments": 3130, "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": 93.8995, "matched_fragments": 2640, "total_fragments": 3130, "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": 93.6656, "matched_fragments": 2476, "total_fragments": 3130, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis circi", "strain": "strain=DSM 45561", "accession": "GCA_003385235.1", "taxid": 871959, "species_taxid": 871959, "relation_to_type": "type", "validated": true, "ani": 92.1896, "matched_fragments": 2450, "total_fragments": 3130, "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": 86.7529, "matched_fragments": 2046, "total_fragments": 3130, "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": 85.3331, "matched_fragments": 1841, "total_fragments": 3130, "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": 81.56, "matched_fragments": 1639, "total_fragments": 3130, "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": 79.6748, "matched_fragments": 1166, "total_fragments": 3130, "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": 78.6113, "matched_fragments": 763, "total_fragments": 3130, "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": 77.9387, "matched_fragments": 915, "total_fragments": 3130, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea californiensis", "strain": "strain=DSM 43393", "accession": "GCA_024648825.1", "taxid": 438851, "species_taxid": 438851, "relation_to_type": "type", "validated": true, "ani": 77.778, "matched_fragments": 863, "total_fragments": 3130, "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": 77.591, "matched_fragments": 761, "total_fragments": 3130, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004522235.1", "gtdb_species": "s__Amycolatopsis nivea", "ani": 100.0, "matched_fragments": 3124, "total_fragments": 3130, "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": "conclusive" }, { "accession": "GCF_014145675.1", "gtdb_species": "s__Amycolatopsis sp014145675", "ani": 93.8849, "matched_fragments": 2642, "total_fragments": 3130, "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_900115345.1", "gtdb_species": "s__Amycolatopsis rubida", "ani": 93.6517, "matched_fragments": 2478, "total_fragments": 3130, "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", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002796545.1", "gtdb_species": "s__Amycolatopsis sp002796545", "ani": 92.7417, "matched_fragments": 2458, "total_fragments": 3130, "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_014174495.1", "gtdb_species": "s__Amycolatopsis echigonensis", "ani": 92.2588, "matched_fragments": 2267, "total_fragments": 3130, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", 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