{ "type": "genome", "identifier": "GCF_003368535.1", "organism": "Ammonifex thiophilus", "title": "Ammonifex thiophilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Winogradsky Institute of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003368535.1", "bioproject": "PRJNA224116", "biosample": "SAMN09763181", "wgs_master": "QSLN00000000.1", "refseq_category": "reference genome", "taxid": "444093", "species_taxid": "444093", "organism_name": "Ammonifex thiophilus", "infraspecific_name": "strain=SR", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/09", "asm_name": "ASM336853v1", "asm_submitter": "Winogradsky Institute of Microbiology", "gbrs_paired_asm": "GCA_003368535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/368/535/GCF_003368535.1_ASM336853v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2111834", "genome_size_ungapped": "2111834", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "111", "contig_count": "111", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003368535.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2277", "protein_coding_gene_count": "2179", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-09", "dateModified": "2018-08-09", "datePublished": "2018-08-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Ammonifex thiophilus" ], "sample_taxid": [ "444093" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: Uzon Caldera, Kamchatka" ], "sample_host_location_id": [], "data_size": "0.600 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)": "2111834", "Number of Sequences": "111", "Longest Sequences (bp)": "430452", "N50 (bp)": "87296", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.5", "Number of CDSs": "2156", "Average Protein Length": "293.4", "Coding Ratio (%)": "89.9", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "7" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ammonifex thiophilus", "strain": "strain=SR", "accession": "GCA_003368535.1", "taxid": 444093, "species_taxid": 444093, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 670, "total_fragments": 674, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ammonifex degensii", "strain": "strain=KC4", "accession": "GCA_000024605.1", "taxid": 42838, "species_taxid": 42838, "relation_to_type": "type", "validated": true, "ani": 88.5222, "matched_fragments": 538, "total_fragments": 674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovirgula thermocuniculi", "strain": "strain=DSM 16036", "accession": "GCA_000429345.1", "taxid": 348842, "species_taxid": 348842, "relation_to_type": "type", "validated": true, "ani": 76.636, "matched_fragments": 72, "total_fragments": 674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermodesulfitimonas autotrophica", "strain": "strain=DSM 102936", "accession": "GCA_003815015.1", "taxid": 1894989, "species_taxid": 1894989, "relation_to_type": "type", "validated": true, "ani": 76.5674, "matched_fragments": 51, "total_fragments": 674, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003368535.1", "gtdb_species": "s__Ammonifex thiophilus", "ani": 100.0, "matched_fragments": 670, "total_fragments": 674, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Ammonifex", "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": "conclusive" }, { "accession": "GCF_000024605.1", "gtdb_species": "s__Ammonifex degensii", "ani": 88.4984, "matched_fragments": 538, "total_fragments": 674, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Ammonifex", "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_000429345.1", "gtdb_species": "s__Desulfovirgula thermocuniculi", "ani": 76.5899, "matched_fragments": 71, "total_fragments": 674, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfovirgula", "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_003815015.1", "gtdb_species": "s__Thermodesulfitimonas autotrophica", "ani": 76.5674, "matched_fragments": 51, "total_fragments": 674, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__Thermodesulfitimonas", "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": -0.222, "cell_length": 0.477, "doubling_h": null, "growth_tmp": 70.0, "optimum_tmp": 75.0, "optimum_ph": 6.9, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Ammonifex", "thiophilus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }