{ "type": "genome", "identifier": "GCF_900155575.1", "organism": "Actinotignum timonense", "title": "Actinotignum timonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900155575.1", "bioproject": "PRJNA224116", "biosample": "SAMEA47263918", "wgs_master": "FTLO00000000.1", "refseq_category": "na", "taxid": "1870995", "species_taxid": "1870995", "organism_name": "Actinotignum timonense", "infraspecific_name": "strain=Marseille-P2803T", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/13", "asm_name": "ASM90015557v1", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900155575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/155/575/GCF_900155575.1_ASM90015557v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2295680", "genome_size_ungapped": "2287264", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-26", "total_gene_count": "1952", "protein_coding_gene_count": "1863", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-13", "dateModified": "2017-01-13", "datePublished": "2017-01-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinotignum timonense" ], "sample_taxid": [ "1870995" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.641 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)": "2295680", "Number of Sequences": "19", "Longest Sequences (bp)": "2263001", "N50 (bp)": "2263001", "Gap Ratio (%)": "0.370958", "GCcontent (%)": "61.8", "Number of CDSs": "1906", "Average Protein Length": "348.9", "Coding Ratio (%)": "86.9", "Number of rRNAs": "6", "Number of tRNAs": "47", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinotignum timonense", "strain": "strain=type strain: Marseille-P2803", "accession": "GCA_900155575.1", "taxid": 1870995, "species_taxid": 1870995, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 754, "total_fragments": 756, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinotignum schaalii", "strain": "strain=DSM 15541", "accession": "GCA_000429205.1", "taxid": 59505, "species_taxid": 59505, "relation_to_type": "type", "validated": true, "ani": 94.8002, "matched_fragments": 638, "total_fragments": 756, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotignum schaalii", "strain": "strain=CCUG 27420", "accession": "GCA_000724605.1", "taxid": 59505, "species_taxid": 59505, "relation_to_type": "type", "validated": true, "ani": 94.7238, "matched_fragments": 653, "total_fragments": 756, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotignum sanguinis", "strain": "strain=DSM 26039", "accession": "GCA_003957255.1", "taxid": 1445614, "species_taxid": 1445614, "relation_to_type": "type", "validated": true, "ani": 89.7109, "matched_fragments": 605, "total_fragments": 756, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinobaculum 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"gtdb_result": [ { "accession": "GCF_900155575.1", "gtdb_species": "s__Actinotignum timonense", "ani": 99.9999, "matched_fragments": 754, "total_fragments": 756, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.14", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_000724605.1", "gtdb_species": "s__Actinotignum schaalii", "ani": 94.7238, "matched_fragments": 653, "total_fragments": 756, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum", "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": "-" }, { 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"gtdb_species": "s__Actinobaculum massiliense", "ani": 77.7561, "matched_fragments": 101, "total_fragments": 756, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinobaculum", "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_900604955.1", "gtdb_species": "s__Neoactinobaculum massilliense", "ani": 76.9485, "matched_fragments": 81, "total_fragments": 756, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Neoactinobaculum", "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_001469025.1", "gtdb_species": "s__Trueperella bernardiae", "ani": 76.6067, "matched_fragments": 56, "total_fragments": 756, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001278845.1", "gtdb_species": "s__Actinomyces sp001278845", "ani": 76.5899, "matched_fragments": 54, "total_fragments": 756, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2024501.937, "gc_content": 56.333, "coding_genes": 1603.0, "rRNA16S_genes": 3.0, "tRNA_genes": 46.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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": [ "Actinotignum", "timonense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }