{ "type": "genome", "identifier": "GCF_025821845.1", "organism": "Mycobacterium nebraskense", "title": "Mycobacterium nebraskense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025821845.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568988", "wgs_master": "JACKSS000000000.1", "refseq_category": "na", "taxid": "244292", "species_taxid": "244292", "organism_name": "Mycobacterium nebraskense", "infraspecific_name": "strain=DSM 44803", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582184v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025821845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/821/845/GCF_025821845.1_ASM2582184v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6648069", "genome_size_ungapped": "6646844", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "171", "contig_count": "171", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025821845.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "6372", "protein_coding_gene_count": "5908", "non_coding_gene_count": "54", "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 nebraskense" ], "sample_taxid": [ "244292" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: State of Nebraska" ], "sample_host_location_id": [], "data_size": "1.846 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 37.0, "max": 37.0 }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6648069", "Number of Sequences": "171", "Longest Sequences (bp)": "263747", "N50 (bp)": "85633", "Gap Ratio (%)": "0.023240", "GCcontent (%)": "66.6", "Number of CDSs": "6335", "Average Protein Length": "310.6", "Coding Ratio (%)": "88.8", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium nebraskense", "strain": "strain=DSM 44803", "accession": "GCA_002102255.1", "taxid": 244292, "species_taxid": 244292, "relation_to_type": "type", "validated": true, "ani": 99.9489, "matched_fragments": 2061, 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"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": 84.4091, "matched_fragments": 1426, "total_fragments": 2138, "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": 84.4043, "matched_fragments": 1444, "total_fragments": 2138, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraintracellulare", "strain": "strain=JCM 30622", "accession": "GCA_010731935.1", "taxid": 1138383, "species_taxid": 1138383, "relation_to_type": "suspected-type", "validated": true, "ani": 84.3926, "matched_fragments": 1348, "total_fragments": 2138, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium avium subsp. avium", "strain": "strain=DSM 44156", "accession": "GCA_009741445.1", "taxid": 44454, "species_taxid": 1764, "relation_to_type": "type", "validated": true, "ani": 84.3562, "matched_fragments": 1281, "total_fragments": 2138, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium marseillense", "strain": "strain=JCM 17324", "accession": "GCA_010731675.1", "taxid": 701042, "species_taxid": 701042, "relation_to_type": "type", "validated": true, "ani": 84.1156, "matched_fragments": 1321, "total_fragments": 2138, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium bohemicum", "strain": "strain=DSM 44277", "accession": "GCA_002102025.1", "taxid": 56425, "species_taxid": 56425, "relation_to_type": "type", "validated": true, "ani": 83.1267, "matched_fragments": 1246, "total_fragments": 2138, "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": 82.4714, "matched_fragments": 1273, "total_fragments": 2138, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002102255.1", "gtdb_species": "s__Mycobacterium nebraskense", "ani": 99.9489, "matched_fragments": 2061, "total_fragments": 2138, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_001665605.1", "gtdb_species": "s__Mycobacterium sp001665605", "ani": 90.3526, 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