{ "type": "genome", "identifier": "GCF_003002815.1", "organism": "Umezawaea tangerina", "title": "Umezawaea tangerina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003002815.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621133", "wgs_master": "PVTF00000000.1", "refseq_category": "reference genome", "taxid": "84725", "species_taxid": "84725", "organism_name": "Umezawaea tangerina", "infraspecific_name": "strain=DSM 44720", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/15", "asm_name": "ASM300281v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003002815.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/002/815/GCF_003002815.1_ASM300281v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10685010", "genome_size_ungapped": "10684747", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "34", "contig_count": "34", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003002815.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "9483", "protein_coding_gene_count": "9322", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-15", "dateModified": "2018-03-15", "datePublished": "2018-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Umezawaea tangerina" ], "sample_taxid": [ "84725" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "2.833 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10685010", "Number of Sequences": "34", "Longest Sequences (bp)": "1278869", "N50 (bp)": "610673", "Gap Ratio (%)": "0.002461", "GCcontent (%)": "71.6", "Number of CDSs": "9520", "Average Protein Length": "337.2", "Coding Ratio (%)": "90.1", "Number of rRNAs": "5", "Number of tRNAs": "67", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Saccharothrix coeruleofusca", "strain": "strain=JCM 3313", "accession": "GCA_014648515.1", "taxid": 33919, "species_taxid": 33919, "relation_to_type": "type", "validated": true, "ani": 81.5215, "matched_fragments": 1527, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix coeruleofusca", "strain": "strain=DSM 43679", "accession": "GCA_017876325.1", "taxid": 33919, "species_taxid": 33919, "relation_to_type": "type", "validated": true, "ani": 81.4239, "matched_fragments": 1566, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix texasensis", "strain": "strain=DSM 44231", "accession": "GCA_003752005.1", "taxid": 103734, "species_taxid": 103734, "relation_to_type": "type", "validated": true, "ani": 81.1809, "matched_fragments": 1718, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix saharensis", "strain": "strain=DSM 45456", "accession": "GCA_006716745.1", "taxid": 571190, "species_taxid": 571190, "relation_to_type": "type", "validated": true, "ani": 81.0804, "matched_fragments": 1648, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix deserti", "strain": "strain=BMP B8144", "accession": "GCA_009769385.1", "taxid": 2593674, "species_taxid": 2593674, "relation_to_type": "type", "validated": true, "ani": 81.0712, "matched_fragments": 1631, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix carnea", "strain": "strain=CGMCC 4.7097", "accession": "GCA_003014735.1", "taxid": 1280637, "species_taxid": 1280637, "relation_to_type": "type", "validated": true, "ani": 80.9954, "matched_fragments": 1625, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix syringae", "strain": "strain=NRRL B-16468", "accession": "GCA_009498035.1", "taxid": 103733, "species_taxid": 103733, "relation_to_type": "type", "validated": true, "ani": 80.8424, "matched_fragments": 1813, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix syringae", "strain": "strain=NRRL B-16468", "accession": "GCA_000716755.1", "taxid": 103733, "species_taxid": 103733, "relation_to_type": "type", "validated": true, "ani": 80.8, "matched_fragments": 1788, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea tibetensis", "strain": "strain=FXJ1.1311", "accession": "GCA_007845675.1", "taxid": 2591470, "species_taxid": 2591470, "relation_to_type": "type", "validated": true, "ani": 80.5279, "matched_fragments": 1528, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix obliqua", "strain": "strain=SC076", "accession": "GCA_019375475.1", "taxid": 2861747, "species_taxid": 2861747, "relation_to_type": "type", "validated": true, "ani": 80.3743, "matched_fragments": 1407, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea xinjiangensis", "strain": "strain=CGMCC 4.3525", "accession": "GCA_900110955.1", "taxid": 402600, "species_taxid": 402600, "relation_to_type": "type", "validated": true, "ani": 80.3332, "matched_fragments": 1509, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea fradiae", "strain": "strain=CGMCC 4.3506", "accession": "GCA_900100955.1", "taxid": 200378, "species_taxid": 200378, "relation_to_type": "type", "validated": true, "ani": 80.3081, "matched_fragments": 1482, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea guizhouensis", "strain": "strain=DHS C013", "accession": "GCA_001701025.1", "taxid": 1586287, "species_taxid": 1586287, "relation_to_type": "type", "validated": true, "ani": 80.3077, "matched_fragments": 1597, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix violaceirubra", "strain": "strain=DSM 45084", "accession": "GCA_014203755.1", "taxid": 413306, "species_taxid": 413306, "relation_to_type": "type", "validated": true, "ani": 80.2055, "matched_fragments": 1292, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea flava", "strain": "strain=JCM 3296", "accession": "GCA_014648475.1", "taxid": 103732, "species_taxid": 103732, "relation_to_type": "type", "validated": true, "ani": 80.1105, "matched_fragments": 1461, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea flava", "strain": "strain=DSM 43885", "accession": "GCA_024171845.1", "taxid": 103732, "species_taxid": 103732, "relation_to_type": "type", "validated": true, "ani": 80.0785, "matched_fragments": 1486, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea cavernae", "strain": "strain=CGMCC 4.7367", "accession": "GCA_014653695.1", "taxid": 2020703, "species_taxid": 2020703, "relation_to_type": "type", "validated": true, "ani": 80.0783, "matched_fragments": 1572, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea albidocapillata", "strain": "strain=NRRL B-24057", "accession": "GCA_000719115.1", "taxid": 40571, "species_taxid": 40571, "relation_to_type": "type", "validated": true, "ani": 80.0418, "matched_fragments": 1404, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea pudingi", "strain": "strain=CGMCC 4.7319", "accession": "GCA_014646255.1", "taxid": 1789439, "species_taxid": 1789439, "relation_to_type": "type", "validated": true, "ani": 80.0348, "matched_fragments": 1460, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea indica", "strain": "strain=PSKA42", "accession": "GCA_012184385.1", "taxid": 2604800, "species_taxid": 2604800, "relation_to_type": "type", "validated": true, "ani": 80.0172, "matched_fragments": 1334, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea flaviverrucosa", "strain": "strain=DSM 44664", "accession": "GCA_003350445.1", "taxid": 200379, "species_taxid": 200379, "relation_to_type": "type", "validated": true, "ani": 79.9915, "matched_fragments": 1504, "total_fragments": 3541, "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": 79.9661, "matched_fragments": 1500, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea waywayandensis", "strain": "strain=DSM 44232", "accession": "GCA_900115955.1", "taxid": 84724, "species_taxid": 84724, "relation_to_type": "type", "validated": true, "ani": 79.956, "matched_fragments": 1558, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentzea terrae", "strain": "strain=NEAU-LZS 42", "accession": "GCA_003265345.1", "taxid": 2200761, "species_taxid": 2200761, "relation_to_type": "type", "validated": true, "ani": 79.9226, "matched_fragments": 1476, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinokineospora diospyrosa", "strain": "strain=DSM 44255", "accession": "GCA_024171925.1", "taxid": 103728, "species_taxid": 103728, "relation_to_type": "type", "validated": true, "ani": 78.3065, "matched_fragments": 1100, "total_fragments": 3541, "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": 77.8944, "matched_fragments": 1059, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leifsonia aquatica", "strain": "strain=ATCC 14665", "accession": "GCA_000469485.1", "taxid": 144185, "species_taxid": 144185, "relation_to_type": "type", "validated": true, "ani": 76.1235, "matched_fragments": 301, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pimelobacter simplex", "strain": "strain=NBRC 12069", "accession": "GCA_006538965.1", "taxid": 2045, "species_taxid": 2045, "relation_to_type": "type", "validated": true, "ani": 75.8904, "matched_fragments": 708, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pimelobacter simplex", "strain": "strain=ATCC 6946", "accession": "GCA_900114845.1", "taxid": 2045, "species_taxid": 2045, "relation_to_type": "type", "validated": true, "ani": 75.8843, "matched_fragments": 707, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leifsonia aquatica", "strain": "strain=DSM 20146", "accession": "GCA_014190775.1", "taxid": 144185, "species_taxid": 144185, "relation_to_type": "type", "validated": true, "ani": 75.7766, "matched_fragments": 430, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amnibacterium kyonggiense", "strain": "strain=DSM 24782", "accession": "GCA_004364555.1", "taxid": 595671, "species_taxid": 595671, "relation_to_type": "type", "validated": true, "ani": 75.5417, "matched_fragments": 449, "total_fragments": 3541, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003002815.1", "gtdb_species": "s__Umezawaea tangerina", "ani": 100.0, "matched_fragments": 3538, "total_fragments": 3541, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea", "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_014648515.1", "gtdb_species": "s__Actinosynnema coeruleofuscum", "ani": 81.4634, "matched_fragments": 1540, "total_fragments": 3541, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.37", "min_intra_species_ani": "99.37", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016464305.1", "gtdb_species": "s__REN6 sp016464305", "ani": 81.2798, "matched_fragments": 1397, "total_fragments": 3541, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": 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