{ "type": "genome", "identifier": "GCF_002846615.1", "organism": "Amycolatopsis echigonensis", "title": "Amycolatopsis echigonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002846615.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489734", "wgs_master": "PJMY00000000.1", "refseq_category": "reference genome", "taxid": "369930", "species_taxid": "369930", "organism_name": "Amycolatopsis echigonensis", "infraspecific_name": "strain=DSM 45165", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/21", "asm_name": "ASM284661v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_002846615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/846/615/GCF_002846615.1_ASM284661v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from synonym type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9312963", "genome_size_ungapped": "9312963", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002846615.1-RS_2024_08_07", "annotation_date": "2024-08-07", "total_gene_count": "8998", "protein_coding_gene_count": "8766", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-12-21", "dateModified": "2017-12-21", "datePublished": "2017-12-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis echigonensis" ], "sample_taxid": [ "369930" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.515 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9312963", "Number of Sequences": "3", "Longest Sequences (bp)": "8366534", "N50 (bp)": "8366534", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.5", "Number of CDSs": "9033", "Average Protein Length": "306.5", "Coding Ratio (%)": "89.2", "Number of rRNAs": "12", "Number of tRNAs": "74", "Number of CRISPRs": "0" }, "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": 92.5297, "matched_fragments": 2336, "total_fragments": 3102, "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": 92.4125, "matched_fragments": 2334, "total_fragments": 3102, "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": 92.0671, "matched_fragments": 2277, "total_fragments": 3102, "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": 91.8651, "matched_fragments": 2201, "total_fragments": 3102, "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": 87.0073, "matched_fragments": 2057, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis sulphurea", "strain": "strain=DSM 46092", "accession": "GCA_002564045.1", "taxid": 76022, "species_taxid": 76022, "relation_to_type": "type", "validated": true, "ani": 83.2014, "matched_fragments": 1419, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis panacis", "strain": "strain=YIM PH21725", "accession": "GCA_003600245.1", "taxid": 2340917, "species_taxid": 2340917, "relation_to_type": "type", "validated": true, "ani": 83.0069, "matched_fragments": 1403, "total_fragments": 3102, "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": 81.606, "matched_fragments": 1610, "total_fragments": 3102, "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": 79.9967, "matched_fragments": 1168, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis alkalitolerans", "strain": "strain=SYSUP0005", "accession": "GCA_006152065.1", "taxid": 2547244, "species_taxid": 2547244, "relation_to_type": "type", "validated": true, "ani": 79.6042, "matched_fragments": 1078, "total_fragments": 3102, "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": 79.1307, "matched_fragments": 983, "total_fragments": 3102, "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": 78.6898, "matched_fragments": 742, "total_fragments": 3102, "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": 78.2183, "matched_fragments": 795, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia bannensis", "strain": "strain=DSM 45300", "accession": "GCA_012911875.1", "taxid": 630973, "species_taxid": 630973, "relation_to_type": "type", "validated": true, "ani": 77.3237, "matched_fragments": 618, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium luteum", "strain": "strain=A18JL200", "accession": "GCA_015277875.1", "taxid": 2782167, "species_taxid": 2782167, "relation_to_type": "type", "validated": true, "ani": 75.8248, "matched_fragments": 231, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Symbiobacterium terraclitae", "strain": "strain=DSM 27138", "accession": "GCA_017874315.1", "taxid": 557451, "species_taxid": 557451, "relation_to_type": "type", "validated": true, "ani": 75.0075, "matched_fragments": 129, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Solimonas terrae", "strain": "strain=KIS83-12", "accession": "GCA_011067135.1", "taxid": 1396819, "species_taxid": 1396819, "relation_to_type": "type", "validated": true, "ani": 74.8402, "matched_fragments": 175, "total_fragments": 3102, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014174495.1", "gtdb_species": "s__Amycolatopsis echigonensis", "ani": 98.5982, "matched_fragments": 2701, "total_fragments": 3102, "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", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000411975.1", "gtdb_species": "s__Amycolatopsis orientalis_D", "ani": 92.7044, "matched_fragments": 2392, "total_fragments": 3102, "gtdb_taxonomy": 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