{ "type": "genome", "identifier": "GCF_900107045.1", "organism": "Amycolatopsis xylanica", "title": "Amycolatopsis xylanica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900107045.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421504", "wgs_master": "FNON00000000.1", "refseq_category": "reference genome", "taxid": "589385", "species_taxid": "589385", "organism_name": "Amycolatopsis xylanica", "infraspecific_name": "strain=CPCC 202699", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/22", "asm_name": "IMG-taxon 2675903050 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900107045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/107/045/GCF_900107045.1_IMG-taxon_2675903050_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": "9406090", "genome_size_ungapped": "9406080", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900107045.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "8598", "protein_coding_gene_count": "8474", "non_coding_gene_count": "84", "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 xylanica" ], "sample_taxid": [ "589385" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Qinghai Province" ], "sample_host_location_id": [], "data_size": "2.544 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)": "9406090", "Number of Sequences": "25", "Longest Sequences (bp)": "1745265", "N50 (bp)": "884467", "Gap Ratio (%)": "0.000106", "GCcontent (%)": "68.9", "Number of CDSs": "8600", "Average Protein Length": "335.8", "Coding Ratio (%)": "92.1", "Number of rRNAs": "4", "Number of tRNAs": "84", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amycolatopsis xylanica", "strain": "strain=CPCC 202699", "accession": "GCA_900107045.1", "taxid": 589385, "species_taxid": 589385, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3124, "total_fragments": 3124, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amycolatopsis pittospori", "strain": "strain=PIP199", "accession": "GCA_013870525.1", "taxid": 2749434, "species_taxid": 2749434, "relation_to_type": "type", "validated": true, "ani": 81.3786, "matched_fragments": 1441, "total_fragments": 3124, "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": 81.2885, "matched_fragments": 1523, "total_fragments": 3124, "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": 81.2847, "matched_fragments": 1521, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis thailandensis", "strain": "strain=JCM 16380", "accession": "GCA_002234405.1", "taxid": 589330, "species_taxid": 589330, "relation_to_type": "type", "validated": true, "ani": 81.2549, "matched_fragments": 1418, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis orientalis", "strain": "strain=KCTC 9412", "accession": "GCA_000478275.1", "taxid": 31958, "species_taxid": 31958, "relation_to_type": "type", "validated": true, "ani": 81.2424, "matched_fragments": 1511, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=NRRL B-24131", "accession": "GCA_002156005.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 81.1793, "matched_fragments": 1501, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_000384215.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 81.1629, "matched_fragments": 1537, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis eburnea", "strain": "strain=GLM-1", "accession": "GCA_003937945.1", "taxid": 2267691, "species_taxid": 2267691, "relation_to_type": "type", "validated": true, "ani": 81.1563, "matched_fragments": 1676, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis alba", "strain": "strain=DSM 44262", "accession": "GCA_002234385.1", "taxid": 76020, "species_taxid": 76020, "relation_to_type": "type", "validated": true, "ani": 81.1523, "matched_fragments": 1431, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis kentuckyensis", "strain": "strain=NRRL B-24129", "accession": "GCA_002155975.1", "taxid": 218823, "species_taxid": 218823, "relation_to_type": "type", "validated": true, "ani": 81.1019, "matched_fragments": 1448, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis lexingtonensis", "strain": "strain=DSM 44653", "accession": "GCA_014873755.1", "taxid": 218822, "species_taxid": 218822, "relation_to_type": "type", "validated": true, "ani": 81.0676, "matched_fragments": 1673, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vastitatis", "strain": "strain=H5", "accession": "GCA_002234595.1", "taxid": 1905142, "species_taxid": 1905142, "relation_to_type": "type", "validated": true, "ani": 81.0612, "matched_fragments": 1547, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vancoresmycina", "strain": "strain=DSM 44592", "accession": "GCA_000388135.1", "taxid": 208444, "species_taxid": 208444, "relation_to_type": "type", "validated": true, "ani": 81.0494, "matched_fragments": 1437, "total_fragments": 3124, "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": 80.9634, "matched_fragments": 1660, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis vancoresmycina", "strain": "strain=NRRL B-24208", "accession": "GCA_000716785.1", "taxid": 208444, "species_taxid": 208444, "relation_to_type": "type", "validated": true, "ani": 80.9221, "matched_fragments": 1637, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis mediterranei", "strain": "strain=S699", "accession": "GCA_000220945.1", "taxid": 33910, "species_taxid": 33910, "relation_to_type": "type", "validated": true, "ani": 80.9097, "matched_fragments": 1594, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis saalfeldensis", "strain": "strain=DSM 44993", "accession": "GCA_900110575.1", "taxid": 394193, "species_taxid": 394193, "relation_to_type": "type", "validated": true, "ani": 80.7948, "matched_fragments": 1492, "total_fragments": 3124, "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": 80.2202, "matched_fragments": 1305, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis acidiphila", "strain": "strain=JCM 30562", "accession": "GCA_007713745.1", "taxid": 715473, "species_taxid": 715473, "relation_to_type": "type", "validated": true, "ani": 79.8989, "matched_fragments": 1109, "total_fragments": 3124, "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": 79.8711, "matched_fragments": 1111, "total_fragments": 3124, "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": 79.8552, "matched_fragments": 1162, "total_fragments": 3124, "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": 79.6045, "matched_fragments": 1154, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis endophytica", "strain": "strain=DSM 104006", "accession": "GCA_013410405.1", "taxid": 860233, "species_taxid": 860233, "relation_to_type": "type", "validated": true, "ani": 79.4953, "matched_fragments": 1084, "total_fragments": 3124, "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": 79.2684, "matched_fragments": 1041, "total_fragments": 3124, "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": 78.8776, "matched_fragments": 1019, "total_fragments": 3124, "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": 78.2823, "matched_fragments": 899, "total_fragments": 3124, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900107045.1", "gtdb_species": "s__Amycolatopsis xylanica", "ani": 100.0, "matched_fragments": 3124, "total_fragments": 3124, "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": "conclusive" }, { "accession": "GCF_001620365.2", "gtdb_species": "s__Amycolatopsis keratiniphila", "ani": 81.3012, "matched_fragments": 1519, "total_fragments": 3124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000732925.1", "gtdb_species": "s__Amycolatopsis japonica", "ani": 81.2873, "matched_fragments": 1549, "total_fragments": 3124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.30", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014654365.1", "gtdb_species": "s__Amycolatopsis oliviviridis", "ani": 81.2695, "matched_fragments": 1539, "total_fragments": 3124, "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_002234405.1", "gtdb_species": "s__Amycolatopsis thailandensis", "ani": 81.2637, "matched_fragments": 1417, "total_fragments": 3124, "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_000478275.1", "gtdb_species": "s__Amycolatopsis orientalis", "ani": 81.2547, "matched_fragments": 1510, "total_fragments": 3124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "96.64", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000342005.1", "gtdb_species": "s__Amycolatopsis decaplanina", "ani": 81.2079, "matched_fragments": 1456, "total_fragments": 3124, "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_000384215.1", "gtdb_species": "s__Amycolatopsis alba", "ani": 81.1671, "matched_fragments": 1535, "total_fragments": 3124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003937945.1", "gtdb_species": "s__Amycolatopsis eburnea", "ani": 81.148, "matched_fragments": 1678, "total_fragments": 3124, "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_002155975.1", "gtdb_species": "s__Amycolatopsis kentuckyensis", "ani": 81.0879, "matched_fragments": 1453, "total_fragments": 3124, "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_014873755.1", "gtdb_species": "s__Amycolatopsis lexingtonensis", "ani": 81.0741, "matched_fragments": 1672, "total_fragments": 3124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002234595.1", "gtdb_species": "s__Amycolatopsis vastitatis", "ani": 81.0635, "matched_fragments": 1547, "total_fragments": 3124, "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_001953865.1", "gtdb_species": "s__Amycolatopsis coloradensis", "ani": 81.0233, "matched_fragments": 1409, "total_fragments": 3124, "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_002904335.1", "gtdb_species": "s__Amycolatopsis sp002904335", "ani": 80.9754, "matched_fragments": 1561, "total_fragments": 3124, "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_000384295.1", "gtdb_species": "s__Amycolatopsis balhimycina", "ani": 80.9713, "matched_fragments": 1567, "total_fragments": 3124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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