{ "type": "genome", "identifier": "GCF_002086635.1", "organism": "Mycobacterium alsense", "title": "Mycobacterium alsense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "San Raffaele Scientific Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002086635.1", "bioproject": "PRJNA224116", "biosample": "SAMN06064226", "wgs_master": "MVHD00000000.1", "refseq_category": "reference genome", "taxid": "324058", "species_taxid": "324058", "organism_name": "Mycobacterium alsense", "infraspecific_name": "strain=DSM 45230", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/11", "asm_name": "ASM208663v1", "asm_submitter": "San Raffaele Scientific Institute", "gbrs_paired_asm": "GCA_002086635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/086/635/GCF_002086635.1_ASM208663v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5692845", "genome_size_ungapped": "5692845", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "157", "contig_count": "157", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002086635.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "5427", "protein_coding_gene_count": "5184", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-11", "dateModified": "2017-04-11", "datePublished": "2017-04-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium alsense" ], "sample_taxid": [ "324058" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.560 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5692845", "Number of Sequences": "157", "Longest Sequences (bp)": "287483", "N50 (bp)": "76856", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.3", "Number of CDSs": "5234", "Average Protein Length": "326.5", "Coding Ratio (%)": "90.1", "Number of rRNAs": "3", "Number of tRNAs": "73", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium paraense", "strain": "strain=IEC26", "accession": "GCA_002101815.1", "taxid": 767916, "species_taxid": 767916, "relation_to_type": "type", "validated": true, "ani": 86.3818, "matched_fragments": 1427, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium heidelbergense", "strain": "strain=DSM 44471", "accession": "GCA_002086215.1", "taxid": 53376, "species_taxid": 53376, "relation_to_type": "type", "validated": true, "ani": 85.9727, "matched_fragments": 1200, "total_fragments": 1831, "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": 85.9305, "matched_fragments": 1226, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium palustre", "strain": "strain=DSM 44572", "accession": "GCA_002101785.1", "taxid": 153971, "species_taxid": 153971, "relation_to_type": "type", "validated": true, "ani": 85.2663, "matched_fragments": 1272, "total_fragments": 1831, "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": 83.8477, "matched_fragments": 1298, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium intracellulare", "strain": "strain=ATCC 13950", "accession": "GCA_000172115.1", "taxid": 1767, "species_taxid": 1767, "relation_to_type": "suspected-type", "validated": true, "ani": 83.8232, "matched_fragments": 1153, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraintracellulare", "strain": "strain=MOTT64", "accession": "GCA_000276825.1", "taxid": 1138383, "species_taxid": 1138383, "relation_to_type": "suspected-type", "validated": true, "ani": 83.8064, "matched_fragments": 1300, "total_fragments": 1831, "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": 83.7092, "matched_fragments": 1257, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium helveticum", "strain": "strain=16-83", "accession": "GCA_007714205.1", "taxid": 2592811, "species_taxid": 2592811, "relation_to_type": "type", "validated": true, "ani": 83.6849, "matched_fragments": 1089, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium bohemicum", "strain": "strain=DSM 44277", "accession": "GCA_001053185.1", "taxid": 56425, "species_taxid": 56425, "relation_to_type": "type", "validated": true, "ani": 83.6424, "matched_fragments": 1221, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium colombiense", "strain": "strain=CECT 3035", "accession": "GCA_002105755.1", "taxid": 339268, "species_taxid": 339268, "relation_to_type": "suspected-type", "validated": true, "ani": 83.5858, "matched_fragments": 1287, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium conspicuum", "strain": "strain=DSM 44136", "accession": "GCA_002102095.1", "taxid": 44010, "species_taxid": 44010, "relation_to_type": "type", "validated": true, "ani": 82.8612, "matched_fragments": 1264, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium conspicuum", "strain": "strain=JCM 14738", "accession": "GCA_010730195.1", "taxid": 44010, "species_taxid": 44010, "relation_to_type": "type", "validated": true, "ani": 82.8323, "matched_fragments": 1285, "total_fragments": 1831, "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": 82.3301, "matched_fragments": 1014, "total_fragments": 1831, "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": 82.2178, "matched_fragments": 1045, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium riyadhense", "strain": "strain=DSM 45176", "accession": "GCA_002101845.1", "taxid": 486698, "species_taxid": 486698, "relation_to_type": "type", "validated": true, "ani": 81.1247, "matched_fragments": 1014, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant africanum", "strain": "strain=ATCC 25420", "accession": "GCA_002982335.1", "taxid": 33894, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 80.9848, "matched_fragments": 860, "total_fragments": 1831, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002086635.1", "gtdb_species": "s__Mycobacterium alsense", "ani": 100.0, "matched_fragments": 1825, "total_fragments": 1831, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.76", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_002101815.1", "gtdb_species": "s__Mycobacterium paraense", "ani": 86.3744, "matched_fragments": 1429, "total_fragments": 1831, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002102225.1", "gtdb_species": "s__Mycobacterium interjectum_B", "ani": 86.2956, "matched_fragments": 1433, "total_fragments": 1831, "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_001673535.1", "gtdb_species": "s__Mycobacterium sp001673535", "ani": 86.2853, "matched_fragments": 1345, "total_fragments": 1831, "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_900157385.1", "gtdb_species": "s__Mycobacterium terramassiliense", "ani": 86.1902, "matched_fragments": 1443, "total_fragments": 1831, "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_001667015.1", "gtdb_species": "s__Mycobacterium sp001667015", "ani": 86.1581, "matched_fragments": 1392, "total_fragments": 1831, "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_900078675.2", "gtdb_species": "s__Mycobacterium interjectum", "ani": 86.1564, "matched_fragments": 1411, "total_fragments": 1831, "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_001672915.1", "gtdb_species": "s__Mycobacterium sp001672915", "ani": 86.0803, "matched_fragments": 1362, "total_fragments": 1831, "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_010730745.1", "gtdb_species": "s__Mycobacterium heidelbergense", "ani": 85.9472, "matched_fragments": 1224, "total_fragments": 1831, "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_001665295.1", "gtdb_species": "s__Mycobacterium sp001665295", "ani": 85.9316, "matched_fragments": 1357, "total_fragments": 1831, "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_000455205.1", "gtdb_species": "s__Mycobacterium sp000455205", "ani": 85.6354, "matched_fragments": 1357, "total_fragments": 1831, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.16", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001672815.1", "gtdb_species": "s__Mycobacterium sp001672815", "ani": 85.6032, "matched_fragments": 1314, "total_fragments": 1831, "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_002101785.1", "gtdb_species": "s__Mycobacterium palustre", "ani": 85.2852, "matched_fragments": 1270, "total_fragments": 1831, "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_002086305.1", "gtdb_species": "s__Mycobacterium malmoense_B", "ani": 85.2257, "matched_fragments": 1231, "total_fragments": 1831, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001053185.1", "gtdb_species": "s__Mycobacterium bohemicum", "ani": 83.6819, "matched_fragments": 1214, "total_fragments": 1831, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007714205.1", "gtdb_species": "s__Mycobacterium helveticum", "ani": 83.6772, "matched_fragments": 1090, "total_fragments": 1831, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002101845.1", "gtdb_species": "s__Mycobacterium riyadhense", "ani": 81.1427, "matched_fragments": 1012, "total_fragments": 1831, "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": "-" }, { "accession": "GCF_010723735.1", "gtdb_species": "s__Mycobacterium hippocampi_B", "ani": 79.0706, "matched_fragments": 766, "total_fragments": 1831, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.117, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 34.928, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 5658460.823, "gc_content": 66.422, "coding_genes": 4941.245, "rRNA16S_genes": 1.504, "tRNA_genes": 48.184, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.2, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.842, "coccus_cell_shape": 0.057, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.1, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycobacterium", "alsense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }