{ "type": "genome", "identifier": "GCF_002101845.1", "organism": "Mycobacterium riyadhense", "title": "Mycobacterium riyadhense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Trento", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002101845.1", "bioproject": "PRJNA224116", "biosample": "SAMN04216947", "wgs_master": "LQPQ00000000.1", "refseq_category": "na", "taxid": "486698", "species_taxid": "486698", "organism_name": "Mycobacterium riyadhense", "infraspecific_name": "strain=DSM 45176", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/20", "asm_name": "ASM210184v1", "asm_submitter": "University of Trento", "gbrs_paired_asm": "GCA_002101845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/101/845/GCF_002101845.1_ASM210184v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6269850", "genome_size_ungapped": "6269850", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "263", "contig_count": "263", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002101845.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "5740", "protein_coding_gene_count": "5307", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-20", "dateModified": "2017-04-20", "datePublished": "2017-04-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium riyadhense" ], "sample_taxid": [ "486698" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Saudi Arabia: Riyadh" ], "sample_host_location_id": [], "data_size": "1.751 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6269850", "Number of Sequences": "263", "Longest Sequences (bp)": "255189", "N50 (bp)": "56910", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.3", "Number of CDSs": "5405", "Average Protein Length": "327.9", "Coding Ratio (%)": "84.8", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "9" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium riyadhense", "strain": "strain=DSM 45176", "accession": "GCA_002101845.1", "taxid": 486698, "species_taxid": 486698, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1945, "total_fragments": 1961, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium simulans", "strain": "strain=FI-09026", "accession": "GCA_900232995.1", "taxid": 627089, "species_taxid": 627089, "relation_to_type": "type", "validated": true, "ani": 91.6972, "matched_fragments": 1586, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium lacus", "strain": "strain=DSM 44577", "accession": "GCA_002102215.1", "taxid": 169765, "species_taxid": 169765, "relation_to_type": "type", "validated": true, "ani": 83.0903, "matched_fragments": 1198, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium lacus", "strain": "strain=JCM 15657", "accession": "GCA_010731535.1", "taxid": 169765, "species_taxid": 169765, "relation_to_type": "type", "validated": true, "ani": 82.9403, "matched_fragments": 1264, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium angelicum", "strain": "strain=DSM 45057", "accession": "GCA_002086155.1", "taxid": 470074, "species_taxid": 470074, "relation_to_type": "type", "validated": true, "ani": 82.7319, "matched_fragments": 1315, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium szulgai", "strain": "strain=DSM 44166", "accession": "GCA_002116635.1", "taxid": 1787, "species_taxid": 1787, "relation_to_type": "type", "validated": true, "ani": 82.5004, "matched_fragments": 1327, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium shinjukuense", "strain": "strain=JCM 14233", "accession": "GCA_010730055.1", "taxid": 398694, "species_taxid": 398694, "relation_to_type": "type", "validated": true, "ani": 82.4849, "matched_fragments": 1111, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium shinjukuense", "strain": "strain=CCUG 53584", "accession": "GCA_002086755.1", "taxid": 398694, "species_taxid": 398694, "relation_to_type": "type", "validated": true, "ani": 82.4719, "matched_fragments": 1077, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium heidelbergense", "strain": "strain=JCM 14842", "accession": "GCA_010730745.1", "taxid": 53376, "species_taxid": 53376, "relation_to_type": "type", "validated": true, "ani": 81.8459, "matched_fragments": 1014, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant pinnipedii", "strain": "strain=ATCC BAA-688", "accession": "GCA_002982275.1", "taxid": 194542, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 81.7148, "matched_fragments": 996, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis", "strain": "strain=H37Rv", "accession": "GCA_000195955.2", "taxid": 1773, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 81.6401, "matched_fragments": 1050, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant microti", "strain": "strain=ATCC 19422", "accession": "GCA_002982215.1", "taxid": 1806, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 81.5547, "matched_fragments": 956, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium innocens", "strain": "strain=MK13", "accession": "GCA_900566055.1", "taxid": 2341083, "species_taxid": 2341083, "relation_to_type": "type", "validated": true, "ani": 81.4168, "matched_fragments": 1121, "total_fragments": 1961, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraense", "strain": "strain=IEC26", "accession": "GCA_002101815.1", 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"s__Mycobacterium riyadhense", "ani": 100.0, "matched_fragments": 1945, "total_fragments": 1961, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.30", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 10, "status": "conclusive" }, { "accession": "GCF_900232995.1", "gtdb_species": "s__Mycobacterium simulans", "ani": 91.6762, "matched_fragments": 1588, "total_fragments": 1961, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "97.78", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010731535.1", "gtdb_species": 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