{ "type": "genome", "identifier": "GCF_010723415.1", "organism": "Mycobacterium paragordonae", "title": "Mycobacterium paragordonae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Department of Infection Metagenomics, Osaka University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010723415.1", "bioproject": "PRJNA224116", "biosample": "SAMD00153214", "wgs_master": "BLKX00000000.1", "refseq_category": "na", "taxid": "1389713", "species_taxid": "1389713", "organism_name": "Mycobacterium paragordonae", "infraspecific_name": "strain=JCM 18565", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/06", "asm_name": "ASM1072341v1", "asm_submitter": "Department of Infection Metagenomics, Osaka University", "gbrs_paired_asm": "GCA_010723415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/723/415/GCF_010723415.1_ASM1072341v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7218455", "genome_size_ungapped": "7218455", "gc_percent": "67.000000", "replicon_count": "1", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010723415.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "6611", "protein_coding_gene_count": "6381", "non_coding_gene_count": "54", "pubmed_id": "31287781" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-06", "dateModified": "2020-02-06", "datePublished": "2020-02-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium paragordonae" ], "sample_taxid": [ "1389713" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.976 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)": "7218455", "Number of Sequences": "5", "Longest Sequences (bp)": "6719917", "N50 (bp)": "6719917", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "6600", "Average Protein Length": "333.3", "Coding Ratio (%)": "91.4", "Number of rRNAs": "3", "Number of tRNAs": "60", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium paragordonae", "strain": "strain=JCM 18565", "accession": "GCA_010723415.1", "taxid": 1389713, "species_taxid": 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"total_fragments": 2403, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kubicae", "strain": "strain=JCM 13573", "accession": "GCA_015689175.1", "taxid": 120959, "species_taxid": 120959, "relation_to_type": "type", "validated": true, "ani": 80.9868, "matched_fragments": 1150, "total_fragments": 2403, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kubicae", "strain": "strain=CIP 106428", "accession": "GCA_002101745.1", "taxid": 120959, "species_taxid": 120959, "relation_to_type": "type", "validated": true, "ani": 80.9621, "matched_fragments": 1155, "total_fragments": 2403, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kubicae", "strain": "strain=JCM 13573", "accession": "GCA_010723135.1", "taxid": 120959, "species_taxid": 120959, "relation_to_type": "type", "validated": true, "ani": 80.9556, "matched_fragments": 1161, "total_fragments": 2403, "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": 80.86, "matched_fragments": 1255, "total_fragments": 2403, "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": 80.8563, "matched_fragments": 1113, "total_fragments": 2403, "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": 80.6987, "matched_fragments": 1079, "total_fragments": 2403, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { 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"status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.117, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 34.928, "optimum_tmp": 27.5, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycobacterium", "paragordonae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }