{ "type": "genome", "identifier": "GCF_001907975.1", "organism": "Silvanigrella aquatica", "title": "Silvanigrella aquatica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Innsbruck", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001907975.1", "bioproject": "PRJNA224116", "biosample": "SAMN04451922", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1915309", "species_taxid": "1915309", "organism_name": "Silvanigrella aquatica", "infraspecific_name": "strain=MWH-Nonnen-W8red", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/13", "asm_name": "ASM190797v2", "asm_submitter": "University of Innsbruck", "gbrs_paired_asm": "GCA_001907975.2", "paired_asm_comp": "different", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/907/975/GCF_001907975.1_ASM190797v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3421598", "genome_size_ungapped": "3403211", "gc_percent": "33.000000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001907975.1-RS_2024_03_12", "annotation_date": "2024-03-12", "total_gene_count": "2959", "protein_coding_gene_count": "2888", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-13", "dateModified": "2016-12-13", "datePublished": "2016-12-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Silvanigrella aquatica" ], "sample_taxid": [ "1915309" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Black Forest (Schwarzwald), Baden-Wuertemberg" ], "sample_host_location_id": [], "data_size": "0.947 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.62, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3421598", "Number of Sequences": "3", "Longest Sequences (bp)": "3342382", "N50 (bp)": "3342382", "Gap Ratio (%)": "0.537468", "GCcontent (%)": "32.8", "Number of CDSs": "2949", "Average Protein Length": "344.8", "Coding Ratio (%)": "89.2", "Number of rRNAs": "12", "Number of tRNAs": "38", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Silvanigrella aquatica", "strain": "strain=MWH-Nonnen-W8red", "accession": "GCA_001907975.2", "taxid": 1915309, "species_taxid": 1915309, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1137, "total_fragments": 1140, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Silvanigrella paludirubra", "strain": "strain=SP-Ram-0.45-NSY-1", "accession": "GCA_009208775.1", "taxid": 2499159, "species_taxid": 2499159, "relation_to_type": "type", "validated": true, "ani": 79.146, "matched_fragments": 481, "total_fragments": 1140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fluviispira sanaruensis", "strain": "strain=RF1110005", "accession": "GCA_004295685.1", "taxid": 2493639, "species_taxid": 2493639, "relation_to_type": "type", "validated": true, "ani": 77.6915, "matched_fragments": 253, "total_fragments": 1140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pigmentibacter ruber", "strain": "strain=HNSRY-1", "accession": "GCA_009792895.1", "taxid": 2683196, "species_taxid": 2683196, "relation_to_type": "type", "validated": true, "ani": 77.5034, "matched_fragments": 289, "total_fragments": 1140, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fluviispira multicolorata", "strain": "strain=33A1-SZDP", "accession": "GCA_009208585.1", "taxid": 2654512, "species_taxid": 2654512, "relation_to_type": "type", "validated": true, "ani": 77.3379, "matched_fragments": 280, "total_fragments": 1140, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.62, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001907975.1", "gtdb_species": "s__Silvanigrella aquatica", "ani": 100.0, "matched_fragments": 1137, "total_fragments": 1140, "gtdb_taxonomy": "d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella", "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_009208775.1", "gtdb_species": "s__Silvanigrella paludirubra", "ani": 79.1254, "matched_fragments": 479, "total_fragments": 1140, "gtdb_taxonomy": "d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella", "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_004295685.1", "gtdb_species": "s__Silvanigrella sanaruensis", "ani": 77.7139, "matched_fragments": 254, "total_fragments": 1140, "gtdb_taxonomy": "d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "99.33", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009208585.1", "gtdb_species": "s__Silvanigrella multicolorata", "ani": 77.3422, "matched_fragments": 279, "total_fragments": 1140, "gtdb_taxonomy": "d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella", "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_003339605.1", "gtdb_species": "s__Silvanigrella cienkowskii", "ani": 77.2581, "matched_fragments": 236, "total_fragments": 1140, "gtdb_taxonomy": "d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella", "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_014281055.1", "gtdb_species": "s__Silvanigrella sp014281055", "ani": 77.0874, "matched_fragments": 252, "total_fragments": 1140, "gtdb_taxonomy": "d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella", "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": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": 3506707.0, "gc_content": 30.27, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Silvanigrella", "aquatica" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }