{ "type": "genome", "identifier": "GCF_002086575.1", "organism": "Mycobacterium branderi", "title": "Mycobacterium branderi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "San Raffaele Scientific Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002086575.1", "bioproject": "PRJNA224116", "biosample": "SAMN06064235", "wgs_master": "MVHM00000000.1", "refseq_category": "na", "taxid": "43348", "species_taxid": "43348", "organism_name": "Mycobacterium branderi", "infraspecific_name": "strain=DSM 44624", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/11", "asm_name": "ASM208657v1", "asm_submitter": "San Raffaele Scientific Institute", "gbrs_paired_asm": "GCA_002086575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/086/575/GCF_002086575.1_ASM208657v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5903509", "genome_size_ungapped": "5903509", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "63", "contig_count": "63", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002086575.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "5796", "protein_coding_gene_count": "5606", "non_coding_gene_count": "53", "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 branderi" ], "sample_taxid": [ "43348" ], "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": "1.630 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)": "5903509", "Number of Sequences": "63", "Longest Sequences (bp)": "1194910", "N50 (bp)": "198498", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.5", "Number of CDSs": "5730", "Average Protein Length": "312.8", "Coding Ratio (%)": "91.1", "Number of rRNAs": "2", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium branderi", "strain": "strain=DSM 44624", "accession": "GCA_002086575.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1935, "total_fragments": 1938, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium branderi", "strain": "strain=JCM 12687", "accession": "GCA_010728725.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 99.9975, "matched_fragments": 1938, "total_fragments": 1938, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium celatum", "strain": "strain=DSM 44243", "accession": "GCA_002101595.1", "taxid": 28045, "species_taxid": 28045, "relation_to_type": "type", "validated": true, "ani": 90.9005, "matched_fragments": 1325, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kyorinense", "strain": "strain=DSM 45166", "accession": "GCA_002101735.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 90.8487, "matched_fragments": 1366, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kyorinense", "strain": "strain=KUM060204T", "accession": "GCA_000759695.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 90.8255, "matched_fragments": 1345, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium celatum", "strain": "strain=ATCC 51131", "accession": "GCA_000974705.1", "taxid": 28045, "species_taxid": 28045, "relation_to_type": "type", "validated": true, "ani": 90.5198, "matched_fragments": 1018, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium fragae", "strain": "strain=DSM 45731", "accession": "GCA_002102185.1", "taxid": 1260918, "species_taxid": 1260918, "relation_to_type": "type", "validated": true, "ani": 82.7057, "matched_fragments": 1111, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium noviomagense", "strain": "strain=DSM 45145", "accession": "GCA_002086415.1", "taxid": 459858, "species_taxid": 459858, "relation_to_type": "type", "validated": true, "ani": 81.6667, "matched_fragments": 1049, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=DSM 45093", "accession": "GCA_002086285.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 80.2843, "matched_fragments": 787, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter senuensis", "strain": "strain=JCM 16017", "accession": "GCA_010723225.1", "taxid": 386913, "species_taxid": 386913, "relation_to_type": "type", "validated": true, "ani": 80.1788, "matched_fragments": 802, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter senuensis", "strain": "strain=DSM 44999", "accession": "GCA_002101885.1", "taxid": 386913, "species_taxid": 386913, "relation_to_type": "type", "validated": true, "ani": 80.173, "matched_fragments": 785, "total_fragments": 1938, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010728725.1", "gtdb_species": "s__Mycobacterium branderi", "ani": 99.9975, "matched_fragments": 1938, "total_fragments": 1938, "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": "conclusive" }, { "accession": "GCF_002101595.1", "gtdb_species": "s__Mycobacterium celatum", "ani": 90.8935, "matched_fragments": 1326, "total_fragments": 1938, "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": "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_001672775.1", "gtdb_species": "s__Mycobacterium kyorinense_A", "ani": 83.0583, "matched_fragments": 1105, "total_fragments": 1938, "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": "GCA_002101905.1", "gtdb_species": "s__Mycobacterium shimoidei", "ani": 82.7625, "matched_fragments": 1043, "total_fragments": 1938, "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": "97.51", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002101885.1", "gtdb_species": "s__Mycobacterium senuense", "ani": 80.1756, "matched_fragments": 785, "total_fragments": 1938, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.079, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 37.0, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 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