{ "type": "genome", "identifier": "GCF_007713745.1", "organism": "Amycolatopsis acidiphila", "title": "Amycolatopsis acidiphila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kasetsart University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007713745.1", "bioproject": "PRJNA224116", "biosample": "SAMN12240872", "wgs_master": "VJZA00000000.1", "refseq_category": "na", "taxid": "715473", "species_taxid": "715473", "organism_name": "Amycolatopsis acidiphila", "infraspecific_name": "strain=JCM 30562", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/30", "asm_name": "ASM771374v1", "asm_submitter": "Kasetsart University", "gbrs_paired_asm": "GCA_007713745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/713/745/GCF_007713745.1_ASM771374v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8076958", "genome_size_ungapped": "8076958", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "212", "contig_count": "212", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-17", "total_gene_count": "8075", "protein_coding_gene_count": "7789", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-30", "dateModified": "2019-07-30", "datePublished": "2019-07-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Amycolatopsis acidiphila" ], "sample_taxid": [ "715473" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mongolia: Nalaikh coal mine" ], "sample_host_location_id": [], "data_size": "2.190 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8076958", "Number of Sequences": "212", "Longest Sequences (bp)": "276703", "N50 (bp)": "75437", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.5", "Number of CDSs": "7918", "Average Protein Length": "303.7", "Coding Ratio (%)": "89.3", "Number of rRNAs": "5", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis acidiphila", "strain": "strain=JCM 30562", "accession": "GCA_007713745.1", "taxid": 715473, "species_taxid": 715473, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2580, "total_fragments": 2591, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis acidiphila", "strain": "strain=KCTC 39523", "accession": "GCA_021391495.1", "taxid": 715473, "species_taxid": 715473, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 2589, "total_fragments": 2591, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis bartoniae", "strain": "strain=DSM 45807", "accession": "GCA_007713755.1", "taxid": 941986, "species_taxid": 941986, "relation_to_type": "type", "validated": true, "ani": 85.3621, "matched_fragments": 1547, "total_fragments": 2591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis bartoniae", "strain": "strain=DSM 45807", "accession": "GCA_014191255.1", "taxid": 941986, "species_taxid": 941986, "relation_to_type": "type", "validated": true, "ani": 85.3596, "matched_fragments": 1589, "total_fragments": 2591, "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": 85.2887, "matched_fragments": 1452, "total_fragments": 2591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis sacchari", "strain": "strain=DSM 44468", "accession": "GCA_900114035.1", "taxid": 115433, "species_taxid": 115433, "relation_to_type": "type", "validated": true, "ani": 85.2095, "matched_fragments": 1529, "total_fragments": 2591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis pithecellobii", "strain": "strain=RM579", "accession": "GCA_009707865.1", "taxid": 664692, "species_taxid": 664692, "relation_to_type": "type", "validated": true, "ani": 83.8614, "matched_fragments": 1229, "total_fragments": 2591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acididurans", "strain": "strain=K13G38", "accession": "GCA_012328925.1", "taxid": 2724524, "species_taxid": 2724524, "relation_to_type": "type", "validated": true, "ani": 82.7822, "matched_fragments": 1384, "total_fragments": 2591, "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": 82.3605, "matched_fragments": 1291, "total_fragments": 2591, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis rhizosphaerae", "strain": "strain=TBRC 6029", "accession": "GCA_007713715.1", "taxid": 2053003, "species_taxid": 2053003, "relation_to_type": "type", "validated": true, "ani": 82.2919, "matched_fragments": 1041, "total_fragments": 2591, "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": 79.9767, "matched_fragments": 1012, "total_fragments": 2591, "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": 79.1034, "matched_fragments": 790, "total_fragments": 2591, "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": 77.8811, "matched_fragments": 784, "total_fragments": 2591, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 0.0 }, "gtdb_result": 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"GCF_009707865.1", "gtdb_species": "s__Amycolatopsis pithecellobii", "ani": 83.854, "matched_fragments": 1230, "total_fragments": 2591, "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_007713735.2", "gtdb_species": "s__Amycolatopsis acidicola", "ani": 83.0104, "matched_fragments": 1401, "total_fragments": 2591, "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_012328925.1", "gtdb_species": "s__Amycolatopsis acididurans", "ani": 82.7717, "matched_fragments": 1387, "total_fragments": 2591, "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_003385215.1", "gtdb_species": "s__Amycolatopsis thermalba", "ani": 82.4127, "matched_fragments": 1281, "total_fragments": 2591, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_007713715.1", "gtdb_species": 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taiwanensis", "ani": 80.691, "matched_fragments": 1137, "total_fragments": 2591, "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": 80.2787, "matched_fragments": 1289, "total_fragments": 2591, "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": -0.304, "cell_length": 0.239, "doubling_h": null, "growth_tmp": 28.508, "optimum_tmp": 29.166, "optimum_ph": 7.391, "genome_size": 9093664.233, "gc_content": 70.207, "coding_genes": 8151.527, "rRNA16S_genes": 3.75, "tRNA_genes": 51.4, "gram_stain": 1.0, "sporulation": 0.88, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.022, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.977, "mesophilic_range_tmp": 0.909, "thermophilic_range_tmp": 0.09, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.586, "coccus_cell_shape": 0.068, "filament_cell_shape": 0.344, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Amycolatopsis", "acidiphila" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }