{ "type": "genome", "identifier": "GCF_025822965.1", "organism": "Mycobacterium parmense", "title": "Mycobacterium parmense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025822965.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568931", "wgs_master": "JACKUX000000000.1", "refseq_category": "na", "taxid": "185642", "species_taxid": "185642", "organism_name": "Mycobacterium parmense", "infraspecific_name": "strain=DSM 44553", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582296v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025822965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/822/965/GCF_025822965.1_ASM2582296v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5913836", "genome_size_ungapped": "5913703", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025822965.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "5549", "protein_coding_gene_count": "5321", "non_coding_gene_count": "53", "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 parmense" ], "sample_taxid": [ "185642" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland: Panacea, Halichondria boweranki" ], "sample_host_location_id": [], "data_size": "1.617 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)": "5913836", "Number of Sequences": "39", "Longest Sequences (bp)": "1775703", "N50 (bp)": "511154", "Gap Ratio (%)": "0.003652", "GCcontent (%)": "68.4", "Number of CDSs": "5500", "Average Protein Length": "324.6", "Coding Ratio (%)": "90.6", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium parmense", "strain": "strain=JCM 14742", "accession": "GCA_010730575.1", "taxid": 185642, "species_taxid": 185642, "relation_to_type": "type", "validated": true, "ani": 99.9943, "matched_fragments": 1950, 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"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": 83.7647, "matched_fragments": 1187, "total_fragments": 1951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraense", "strain": "strain=IEC26", "accession": "GCA_002101815.1", "taxid": 767916, "species_taxid": 767916, "relation_to_type": "type", "validated": true, "ani": 83.7575, "matched_fragments": 1262, "total_fragments": 1951, "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": 83.7499, "matched_fragments": 1156, "total_fragments": 1951, "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": 83.5668, "matched_fragments": 1205, "total_fragments": 1951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium avium subsp. avium", "strain": "strain=ATCC 25291", "accession": "GCA_000174035.1", "taxid": 44454, "species_taxid": 1764, "relation_to_type": "type", "validated": true, "ani": 83.5478, "matched_fragments": 1110, "total_fragments": 1951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium seoulense", "strain": "strain=JCM 16018", "accession": "GCA_010731595.1", "taxid": 386911, "species_taxid": 386911, "relation_to_type": "type", "validated": true, "ani": 83.3974, "matched_fragments": 1261, "total_fragments": 1951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium bohemicum", "strain": 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"accession": "GCA_010731675.1", "taxid": 701042, "species_taxid": 701042, "relation_to_type": "type", "validated": true, "ani": 82.8754, "matched_fragments": 1226, "total_fragments": 1951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium ahvazicum", "strain": "strain=AFP003", "accession": "GCA_900176255.2", "taxid": 1964395, "species_taxid": 1964395, "relation_to_type": "type", "validated": true, "ani": 81.9853, "matched_fragments": 1220, "total_fragments": 1951, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010730575.1", "gtdb_species": "s__Mycobacterium parmense", "ani": 99.9943, "matched_fragments": 1950, "total_fragments": 1951, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, 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