{ "type": "genome", "identifier": "GCF_900103065.1", "organism": "Geoalkalibacter ferrihydriticus", "title": "Geoalkalibacter ferrihydriticus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900103065.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660860", "wgs_master": "FNGU00000000.1", "refseq_category": "reference genome", "taxid": "392333", "species_taxid": "392333", "organism_name": "Geoalkalibacter ferrihydriticus", "infraspecific_name": "strain=DSM 17813", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/21", "asm_name": "IMG-taxon 2599185148 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900103065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/103/065/GCF_900103065.1_IMG-taxon_2599185148_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3818286", "genome_size_ungapped": "3813811", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "22", "contig_count": "22", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900103065.1-RS_2024_04_21", "annotation_date": "2024-04-21", "total_gene_count": "3489", "protein_coding_gene_count": "3413", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-21", "dateModified": "2016-10-21", "datePublished": "2016-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Geoalkalibacter ferrihydriticus DSM 17813" ], "sample_taxid": [ "1121915" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia:Lake Khadyn, Tuva Region, Russian Federation" ], "sample_host_location_id": [], "data_size": "1.078 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)": "3818286", "Number of Sequences": "22", "Longest Sequences (bp)": "967273", "N50 (bp)": "471483", "Gap Ratio (%)": "0.117199", "GCcontent (%)": "57.9", "Number of CDSs": "3441", "Average Protein Length": "325.8", "Coding Ratio (%)": "88.1", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Geoalkalibacter ferrihydriticus", "strain": "strain=DSM 17813", "accession": "GCA_900103065.1", "taxid": 392333, "species_taxid": 392333, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1261, "total_fragments": 1262, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Geoalkalibacter ferrihydriticus", "strain": "strain=DSM 17813", "accession": "GCA_000820505.1", "taxid": 392333, "species_taxid": 392333, "relation_to_type": "type", "validated": true, "ani": 99.9888, "matched_fragments": 1253, "total_fragments": 1262, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Geoalkalibacter halelectricus", "strain": "strain=SAP-1", "accession": "GCA_025263685.1", "taxid": 2847045, "species_taxid": 2847045, "relation_to_type": "type", "validated": true, "ani": 81.2157, "matched_fragments": 842, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geoalkalibacter subterraneus", "strain": "strain=Red1", "accession": "GCA_000827125.1", "taxid": 483547, "species_taxid": 483547, "relation_to_type": "type", "validated": true, "ani": 77.7866, "matched_fragments": 278, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas versatilis", "strain": "strain=NIT-T3", "accession": "GCA_019704135.1", "taxid": 2802975, "species_taxid": 2802975, "relation_to_type": "type", "validated": true, "ani": 77.4747, "matched_fragments": 272, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas soudanensis", "strain": "strain=WTL", "accession": "GCA_001278055.1", "taxid": 1603606, "species_taxid": 1603606, "relation_to_type": "type", "validated": true, "ani": 77.1822, "matched_fragments": 180, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geothermobacter ehrlichii", "strain": "strain=SS015", "accession": "GCA_008124615.1", "taxid": 213224, "species_taxid": 213224, "relation_to_type": "type", "validated": true, "ani": 76.8782, "matched_fragments": 149, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfuromonas thiophila", "strain": "strain=DSM 8987", "accession": "GCA_900101955.1", "taxid": 57664, "species_taxid": 57664, "relation_to_type": "type", "validated": true, "ani": 76.7951, "matched_fragments": 104, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Syntrophotalea acetylenica", "strain": "strain=DSM 3246", "accession": "GCA_001888165.1", "taxid": 29542, "species_taxid": 29542, "relation_to_type": "type", "validated": true, "ani": 76.5392, "matched_fragments": 86, "total_fragments": 1262, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000820505.1", "gtdb_species": "s__Geoalkalibacter ferrihydriticus", 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151, "total_fragments": 1262, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter", "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_900101955.1", "gtdb_species": "s__Pseudodesulfuromonas thiophila", "ani": 76.7971, "matched_fragments": 105, "total_fragments": 1262, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Desulfuromonadaceae;g__Pseudodesulfuromonas", "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_002898515.1", "gtdb_species": "s__PPFX01 sp002898515", "ani": 76.6944, "matched_fragments": 134, 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"gc_content": 57.94, "coding_genes": 3309.667, "rRNA16S_genes": 3.0, "tRNA_genes": 52.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "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": [ "Geoalkalibacter", "ferrihydriticus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }