{ "type": "genome", "identifier": "GCF_025821785.1", "organism": "Mycobacterium stomatepiae", "title": "Mycobacterium stomatepiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025821785.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568992", "wgs_master": "JACKSO000000000.1", "refseq_category": "na", "taxid": "470076", "species_taxid": "470076", "organism_name": "Mycobacterium stomatepiae", "infraspecific_name": "strain=DSM 45059", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582178v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025821785.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/821/785/GCF_025821785.1_ASM2582178v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6223474", "genome_size_ungapped": "6223474", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "203", "contig_count": "203", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025821785.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "6103", "protein_coding_gene_count": "5499", "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": [ "Mycobacterium stomatepiae" ], "sample_taxid": [ "470076" ], "sample_host_organism": [ "Stomatepia mariae" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: London Zoo Aquarium" ], "sample_host_location_id": [], "data_size": "1.728 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 28.0, "max": 28.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6223474", "Number of Sequences": "203", "Longest Sequences (bp)": "534046", "N50 (bp)": "227753", "Gap Ratio (%)": "0.001237", "GCcontent (%)": "66.0", "Number of CDSs": "6028", "Average Protein Length": "307.1", "Coding Ratio (%)": "89.2", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium stomatepiae", "strain": "strain=JCM 17783", "accession": "GCA_010731715.1", "taxid": 470076, "species_taxid": 470076, "relation_to_type": "type", "validated": true, "ani": 99.998, "matched_fragments": 2025, "total_fragments": 2025, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium florentinum", "strain": "strain=DSM 44852", "accession": "GCA_002101635.1", "taxid": 292462, "species_taxid": 292462, "relation_to_type": "type", "validated": true, "ani": 90.36, "matched_fragments": 1682, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium florentinum", "strain": "strain=JCM 14740", "accession": "GCA_010730355.1", "taxid": 292462, "species_taxid": 292462, "relation_to_type": "type", "validated": true, "ani": 90.3292, "matched_fragments": 1701, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium triplex", "strain": "strain=DSM 44626", "accession": "GCA_002102415.1", "taxid": 47839, "species_taxid": 47839, "relation_to_type": "type", "validated": true, "ani": 88.1685, "matched_fragments": 1594, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium triplex", "strain": "strain=DSM 44626", "accession": "GCA_000689255.1", "taxid": 47839, "species_taxid": 47839, "relation_to_type": "type", "validated": true, "ani": 88.13, "matched_fragments": 1584, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium lentiflavum", "strain": "strain=ATCC 51985", "accession": "GCA_022374895.2", "taxid": 141349, "species_taxid": 141349, "relation_to_type": "type", "validated": true, "ani": 87.4991, "matched_fragments": 1584, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium ahvazicum", "strain": "strain=AFP003", "accession": "GCA_900176255.2", "taxid": 1964395, "species_taxid": 1964395, "relation_to_type": "type", "validated": true, "ani": 87.3677, "matched_fragments": 1613, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium genavense", "strain": "strain=ATCC 51234", "accession": "GCA_000526915.1", "taxid": 36812, "species_taxid": 36812, "relation_to_type": "type", "validated": true, "ani": 87.0991, "matched_fragments": 1388, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium simiae", "strain": "strain=JCM 12377", "accession": "GCA_010727605.1", "taxid": 1784, "species_taxid": 1784, "relation_to_type": "type", "validated": true, "ani": 83.1938, "matched_fragments": 1399, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium numidiamassiliense", "strain": "strain=AB215", "accession": "GCA_900157365.1", "taxid": 1841861, "species_taxid": 1841861, "relation_to_type": "type", "validated": true, "ani": 82.8731, "matched_fragments": 1316, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium mantenii", "strain": "strain=DSM 45255", "accession": "GCA_002086335.1", "taxid": 560555, "species_taxid": 560555, "relation_to_type": "type", "validated": true, "ani": 82.2893, "matched_fragments": 1197, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium nebraskense", "strain": "strain=DSM 44803", "accession": "GCA_002102255.1", "taxid": 244292, "species_taxid": 244292, "relation_to_type": "type", "validated": true, "ani": 82.265, "matched_fragments": 1222, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium mantenii", "strain": "strain=JCM 18113", "accession": "GCA_010731775.1", "taxid": 560555, "species_taxid": 560555, "relation_to_type": "type", "validated": true, "ani": 82.1563, "matched_fragments": 1219, "total_fragments": 2025, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, 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{ "accession": "GCF_000689255.1", "gtdb_species": "s__Mycobacterium triplex", "ani": 88.1214, "matched_fragments": 1585, "total_fragments": 2025, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_001373395.1", "gtdb_species": "s__Mycobacterium lentiflavum", "ani": 87.5152, "matched_fragments": 1600, "total_fragments": 2025, "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": 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