{ "type": "genome", "identifier": "GCF_900115345.1", "organism": "Amycolatopsis rubida", "title": "Amycolatopsis rubida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900115345.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421854", "wgs_master": "FOWC00000000.1", "refseq_category": "reference genome", "taxid": "112413", "species_taxid": "112413", "organism_name": "Amycolatopsis rubida", "infraspecific_name": "strain=DSM 44637", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/05", "asm_name": "IMG-taxon 2675903692 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900115345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/115/345/GCF_900115345.1_IMG-taxon_2675903692_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": "9873592", "genome_size_ungapped": "9873592", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "45", "contig_count": "45", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900115345.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "9325", "protein_coding_gene_count": "9096", "non_coding_gene_count": "67", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-05", "dateModified": "2016-11-05", "datePublished": "2016-11-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis rubida" ], "sample_taxid": [ "112413" ], "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": "2.664 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.76, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9873592", "Number of Sequences": "45", "Longest Sequences (bp)": "1806213", "N50 (bp)": "540869", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.8", "Number of CDSs": "9390", "Average Protein Length": "309.4", "Coding Ratio (%)": "88.3", "Number of rRNAs": "3", "Number of tRNAs": "80", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis rubida", "strain": "strain=DSM 44637", "accession": "GCA_900115345.1", "taxid": 112413, "species_taxid": 112413, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3262, "total_fragments": 3268, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis nivea", "strain": "strain=CFH S0261", "accession": "GCA_004522235.1", "taxid": 1644109, "species_taxid": 1644109, "relation_to_type": "type", "validated": true, "ani": 93.756, "matched_fragments": 2470, "total_fragments": 3268, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis dendrobii", "strain": "strain=DR6-1", "accession": "GCA_014145675.1", "taxid": 2760662, "species_taxid": 2760662, "relation_to_type": "type", "validated": true, "ani": 93.7205, "matched_fragments": 2509, "total_fragments": 3268, "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", 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"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": 77.6629, "matched_fragments": 857, "total_fragments": 3268, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.76, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900115345.1", "gtdb_species": "s__Amycolatopsis rubida", "ani": 100.0, "matched_fragments": 3262, "total_fragments": 3268, "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": "conclusive" }, { "accession": 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"gtdb_species": "s__Amycolatopsis sp002796545", "ani": 92.2452, "matched_fragments": 2430, "total_fragments": 3268, "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_003385235.1", "gtdb_species": "s__Amycolatopsis circi", "ani": 91.8899, "matched_fragments": 2331, "total_fragments": 3268, "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_014174495.1", "gtdb_species": 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83.3632, "matched_fragments": 1674, "total_fragments": 3268, "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_900119165.1", "gtdb_species": "s__Amycolatopsis australiensis", "ani": 81.591, "matched_fragments": 1599, "total_fragments": 3268, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.398, "cell_length": 0.079, "doubling_h": null, 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