{ "type": "genome", "identifier": "GCF_025822705.1", "organism": "Mycolicibacterium flavescens", "title": "Mycolicibacterium flavescens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025822705.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568943", "wgs_master": "JACKUL000000000.1", "refseq_category": "reference genome", "taxid": "1776", "species_taxid": "1776", "organism_name": "Mycolicibacterium flavescens", "infraspecific_name": "strain=DSM 43991", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582270v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025822705.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/822/705/GCF_025822705.1_ASM2582270v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5973602", "genome_size_ungapped": "5973038", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "47", "contig_count": "47", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025822705.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "5889", "protein_coding_gene_count": "5721", "non_coding_gene_count": "55", "pubmed_id": "36243697" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-10-24", "dateModified": "2022-10-24", "datePublished": "2022-10-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacterium flavescens" ], "sample_taxid": [ "1776" ], "sample_host_organism": [ "guinea pig" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not collected" ], "sample_host_location_id": [], "data_size": "1.620 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 37.0, "max": 37.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5973602", "Number of Sequences": "47", "Longest Sequences (bp)": "1062037", "N50 (bp)": "232585", "Gap Ratio (%)": "0.011049", "GCcontent (%)": "68.5", "Number of CDSs": "5828", "Average Protein Length": "317.1", "Coding Ratio (%)": "92.8", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacterium rutilum", "strain": "strain=DSM 45405", "accession": "GCA_900108565.1", "taxid": 370526, "species_taxid": 370526, "relation_to_type": "type", "validated": true, "ani": 88.2001, "matched_fragments": 1558, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium phlei", "strain": "strain=DSM 43239 = CCUG 21000", "accession": "GCA_001582015.1", "taxid": 1771, "species_taxid": 1771, "relation_to_type": "type", "validated": true, "ani": 84.9243, "matched_fragments": 1343, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium phlei", "strain": "strain=CCUG 21000", "accession": "GCA_001583415.1", "taxid": 1771, "species_taxid": 1771, "relation_to_type": "type", "validated": true, "ani": 84.8921, "matched_fragments": 1343, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium phlei", "strain": "strain=CCUG 21000", "accession": "GCA_009192875.1", "taxid": 1771, "species_taxid": 1771, "relation_to_type": "type", "validated": true, "ani": 84.8773, "matched_fragments": 1335, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium lehmannii", "strain": "strain=CECT 8763", "accession": "GCA_002245535.1", "taxid": 2048550, "species_taxid": 2048550, "relation_to_type": "type", "validated": true, "ani": 84.1471, "matched_fragments": 1296, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium malmesburyense", "strain": "strain=WCM 7299", "accession": "GCA_001050015.1", "taxid": 1566886, "species_taxid": 1566886, "relation_to_type": "type", "validated": true, "ani": 84.0389, "matched_fragments": 1267, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium komanii", "strain": "strain=GPK 1020", "accession": "GCA_001050035.1", "taxid": 1566885, "species_taxid": 1566885, "relation_to_type": "type", "validated": true, "ani": 84.0098, "matched_fragments": 1303, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium neumannii", "strain": "strain=CECT 8766", "accession": "GCA_002245615.1", "taxid": 2048551, "species_taxid": 2048551, "relation_to_type": "type", "validated": true, "ani": 83.8724, "matched_fragments": 1277, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium celeriflavum", "strain": "strain=DSM 46765", "accession": "GCA_002086175.1", "taxid": 1249101, "species_taxid": 1249101, "relation_to_type": "type", "validated": true, "ani": 83.8667, "matched_fragments": 1184, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium celeriflavum", "strain": "strain=JCM 18439", "accession": "GCA_010731795.1", "taxid": 1249101, "species_taxid": 1249101, "relation_to_type": "type", "validated": true, "ani": 83.813, "matched_fragments": 1228, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium elephantis", "strain": "strain=DSM 44368", "accession": "GCA_004014805.1", "taxid": 81858, "species_taxid": 81858, "relation_to_type": "type", "validated": true, "ani": 82.7732, "matched_fragments": 1176, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium moriokaense", "strain": "strain=CIP105393", "accession": "GCA_002086395.1", "taxid": 39691, "species_taxid": 39691, "relation_to_type": "type", "validated": true, "ani": 81.5219, "matched_fragments": 1113, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium moriokaense", "strain": "strain=JCM 6375", "accession": "GCA_010726085.1", "taxid": 39691, "species_taxid": 39691, "relation_to_type": "type", "validated": true, "ani": 81.4983, "matched_fragments": 1129, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium gadium", "strain": "strain=JCM 12688", "accession": "GCA_010728925.1", "taxid": 1794, "species_taxid": 1794, "relation_to_type": "type", "validated": true, "ani": 81.2419, "matched_fragments": 1111, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium thermoresistibile", "strain": "strain=ATCC 19527", "accession": "GCA_000234585.2", "taxid": 1797, "species_taxid": 1797, "relation_to_type": "type", "validated": true, "ani": 81.0004, "matched_fragments": 990, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium thermoresistibile", "strain": "strain=NCTC10409", "accession": "GCA_900187065.1", "taxid": 1797, "species_taxid": 1797, "relation_to_type": "type", "validated": true, "ani": 80.9683, "matched_fragments": 1002, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium neworleansense", "strain": "strain=type strain: ATCC 49404", "accession": "GCA_001245615.1", "taxid": 146018, "species_taxid": 146018, "relation_to_type": "type", "validated": true, "ani": 80.591, "matched_fragments": 1031, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium mageritense", "strain": "strain=CIP 104973", "accession": "GCA_000612825.1", "taxid": 53462, "species_taxid": 53462, "relation_to_type": "type", "validated": true, "ani": 80.5856, "matched_fragments": 1033, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium pallens", "strain": "strain=JCM 16370", "accession": "GCA_019456675.1", "taxid": 370524, "species_taxid": 370524, "relation_to_type": "type", "validated": true, "ani": 80.5741, "matched_fragments": 973, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium mageritense", "strain": "strain=JCM 12375", "accession": "GCA_010727475.1", "taxid": 53462, "species_taxid": 53462, "relation_to_type": "type", "validated": true, "ani": 80.545, "matched_fragments": 1037, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium dioxanotrophicus", "strain": "strain=PH-06", "accession": "GCA_002157835.1", "taxid": 482462, "species_taxid": 482462, "relation_to_type": "type", "validated": true, "ani": 80.391, "matched_fragments": 1019, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium aquaticum", "strain": "strain=RW6", "accession": "GCA_002086485.1", "taxid": 1927124, "species_taxid": 1927124, "relation_to_type": "type", "validated": true, "ani": 80.2864, "matched_fragments": 1018, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium crocinum", "strain": "strain=JCM 16369", "accession": "GCA_022370635.3", "taxid": 388459, "species_taxid": 388459, "relation_to_type": "type", "validated": true, "ani": 80.26, "matched_fragments": 970, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fortuitum subsp. fortuitum", "strain": "strain=JCM 6387", "accession": "GCA_022179545.1", "taxid": 144549, "species_taxid": 1766, "relation_to_type": "type", "validated": true, "ani": 80.2356, "matched_fragments": 973, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium anyangense", "strain": "strain=JCM 30275", "accession": "GCA_010731855.1", "taxid": 1431246, "species_taxid": 1431246, "relation_to_type": "type", "validated": true, "ani": 80.0923, "matched_fragments": 869, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium mengxianglii", "strain": "strain=Z-34", "accession": "GCA_015710575.2", "taxid": 2736649, "species_taxid": 2736649, "relation_to_type": "type", "validated": true, "ani": 79.4148, "matched_fragments": 887, "total_fragments": 1970, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001722335.1", "gtdb_species": "s__Mycobacterium flavescens_A", "ani": 99.9829, "matched_fragments": 1953, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_900108565.1", "gtdb_species": "s__Mycobacterium rutilum", "ani": 88.1969, "matched_fragments": 1559, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_001583415.1", "gtdb_species": "s__Mycobacterium phlei", "ani": 84.8892, "matched_fragments": 1344, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.86", "min_intra_species_ani": "99.38", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002245535.1", "gtdb_species": "s__Mycobacterium lehmannii", "ani": 84.1495, "matched_fragments": 1295, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.2034, "mean_intra_species_ani": "97.95", "min_intra_species_ani": "97.72", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001050015.1", "gtdb_species": "s__Mycobacterium malmesburyense", "ani": 84.0616, "matched_fragments": 1264, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_001570485.1", "gtdb_species": "s__Mycobacterium novocastrense", "ani": 83.9712, "matched_fragments": 1328, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.10", "min_intra_species_ani": "95.11", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900637135.1", "gtdb_species": "s__Mycobacterium flavescens", "ani": 83.9217, "matched_fragments": 1286, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.2034, "mean_intra_species_ani": "98.19", "min_intra_species_ani": "96.77", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001665535.1", "gtdb_species": "s__Mycobacterium sp001665535", "ani": 83.8393, "matched_fragments": 1275, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.97", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001500025.1", "gtdb_species": "s__Mycobacterium sp001500025", "ani": 83.7815, "matched_fragments": 1297, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_001668575.1", "gtdb_species": "s__Mycobacterium sp001668575", "ani": 83.6708, "matched_fragments": 1249, "total_fragments": 1970, "gtdb_taxonomy": 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"d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.23", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_010725725.1", "gtdb_species": "s__Mycobacterium pulveris", "ani": 82.6545, "matched_fragments": 1187, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_010726645.1", "gtdb_species": "s__Mycobacterium duvalii", "ani": 82.309, "matched_fragments": 1094, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_900240945.1", "gtdb_species": "s__Mycobacterium sp900240945", "ani": 81.6189, "matched_fragments": 1196, "total_fragments": 1970, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_010726085.1", "gtdb_species": "s__Mycobacterium moriokaense", "ani": 81.5107, "matched_fragments": 1127, "total_fragments": 1970, "gtdb_taxonomy": 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