{ "type": "genome", "identifier": "GCF_900105055.1", "organism": "Amycolatopsis lurida", "title": "Amycolatopsis lurida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900105055.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489729", "wgs_master": "FNTA00000000.1", "refseq_category": "reference genome", "taxid": "31959", "species_taxid": "31959", "organism_name": "Amycolatopsis lurida", "infraspecific_name": "strain=DSM 43134", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/22", "asm_name": "IMG-taxon 2634166339 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900105055.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/105/055/GCF_900105055.1_IMG-taxon_2634166339_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": "9047228", "genome_size_ungapped": "9047228", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900105055.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "8508", "protein_coding_gene_count": "8351", "non_coding_gene_count": "70", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-22", "dateModified": "2016-10-22", "datePublished": "2016-10-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis lurida" ], "sample_taxid": [ "31959" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "2.448 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9047228", "Number of Sequences": "4", "Longest Sequences (bp)": "7823100", "N50 (bp)": "7823100", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.7", "Number of CDSs": "8581", "Average Protein Length": "319.5", "Coding Ratio (%)": "90.9", "Number of rRNAs": "12", "Number of tRNAs": "64", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis lurida", "strain": "strain=DSM 43134", "accession": "GCA_900105055.1", "taxid": 31959, "species_taxid": 31959, 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92.223, "matched_fragments": 2458, "total_fragments": 3014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis keratiniphila subsp. keratiniphila", "strain": "strain=DSM 44409", "accession": "GCA_001620365.2", "taxid": 227715, "species_taxid": 129921, "relation_to_type": "type", "validated": true, "ani": 92.2063, "matched_fragments": 2448, "total_fragments": 3014, "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": 92.1969, "matched_fragments": 2396, "total_fragments": 3014, "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": 90.9294, 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"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": 81.5602, "matched_fragments": 1635, "total_fragments": 3014, "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": 80.0249, "matched_fragments": 1074, "total_fragments": 3014, "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": 79.1039, "matched_fragments": 993, "total_fragments": 3014, "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": 78.7646, "matched_fragments": 1024, "total_fragments": 3014, "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": 78.1036, "matched_fragments": 801, "total_fragments": 3014, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900105055.1", "gtdb_species": "s__Amycolatopsis lurida", "ani": 100.0, "matched_fragments": 3012, "total_fragments": 3014, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.56", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_014873915.1", "gtdb_species": "s__Amycolatopsis roodepoortensis", "ani": 94.3567, "matched_fragments": 2507, "total_fragments": 3014, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000342005.1", "gtdb_species": "s__Amycolatopsis decaplanina", "ani": 92.3899, "matched_fragments": 2255, "total_fragments": 3014, "gtdb_taxonomy": 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