{ "type": "genome", "identifier": "GCF_018501225.1", "organism": "Geobacter hydrogenophilus", "title": "Geobacter hydrogenophilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018501225.1", "bioproject": "PRJNA224116", "biosample": "SAMN19238708", "wgs_master": "JAHCZI000000000.1", "refseq_category": "na", "taxid": "40983", "species_taxid": "40983", "organism_name": "Geobacter hydrogenophilus", "infraspecific_name": "strain=DSM 13691", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/25", "asm_name": "ASM1850122v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_018501225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/501/225/GCF_018501225.1_ASM1850122v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4015526", "genome_size_ungapped": "4015526", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "50", "contig_count": "50", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018501225.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "3702", "protein_coding_gene_count": "3603", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-25", "dateModified": "2021-05-25", "datePublished": "2021-05-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Geobacter hydrogenophilus" ], "sample_taxid": [ "40983" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Defense Fuel Supply Center, Hanahan, SC" ], "sample_host_location_id": [], "data_size": "1.134 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 94.03, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4015526", "Number of Sequences": "50", "Longest Sequences (bp)": "788862", "N50 (bp)": "325008", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.6", "Number of CDSs": "3601", "Average Protein Length": "333.7", "Coding Ratio (%)": "89.8", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Geobacter hydrogenophilus", "strain": "strain=DSM 13691", "accession": "GCA_018501225.1", "taxid": 40983, "species_taxid": 40983, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1317, "total_fragments": 1320, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Geobacter grbiciae", "strain": "strain=DSM 13689", "accession": "GCA_018531165.1", "taxid": 155042, "species_taxid": 155042, "relation_to_type": "type", "validated": true, "ani": 92.2543, "matched_fragments": 1016, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geobacter metallireducens", "strain": "strain=GS-15", "accession": "GCA_000012925.1", "taxid": 28232, "species_taxid": 28232, "relation_to_type": "type", "validated": true, "ani": 92.0745, "matched_fragments": 1033, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geobacter benzoatilyticus", "strain": "strain=Jerry-YX", "accession": "GCA_017338855.1", "taxid": 2815309, "species_taxid": 2815309, "relation_to_type": "type", "validated": true, "ani": 83.0271, "matched_fragments": 747, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geobacter pickeringii", "strain": "strain=G13", "accession": "GCA_000817955.1", "taxid": 345632, "species_taxid": 345632, "relation_to_type": "type", "validated": true, "ani": 82.2153, "matched_fragments": 641, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geobacter sulfurreducens", "strain": "strain=PCA", "accession": "GCA_000007985.2", "taxid": 35554, "species_taxid": 35554, "relation_to_type": "type", "validated": true, "ani": 80.6219, "matched_fragments": 580, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geoalkalibacter halelectricus", "strain": "strain=SAP-1", "accession": "GCA_025263685.1", "taxid": 2847045, "species_taxid": 2847045, "relation_to_type": "type", "validated": true, "ani": 77.0115, "matched_fragments": 98, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces toxytricini", "strain": "strain=JCM 4421", "accession": "GCA_014649915.1", "taxid": 67369, "species_taxid": 67369, "relation_to_type": "type", "validated": true, "ani": 74.9807, "matched_fragments": 52, "total_fragments": 1320, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 94.03, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018501225.1", "gtdb_species": "s__Geobacter hydrogenophilus", "ani": 100.0, "matched_fragments": 1317, "total_fragments": 1320, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter", "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_000012925.1", "gtdb_species": "s__Geobacter metallireducens", "ani": 92.0917, "matched_fragments": 1032, "total_fragments": 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"d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter", "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_001628815.1", "gtdb_species": "s__Geobacter anodireducens", "ani": 80.6942, "matched_fragments": 574, "total_fragments": 1320, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.24", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000007985.2", "gtdb_species": "s__Geobacter sulfurreducens", "ani": 80.6146, "matched_fragments": 581, "total_fragments": 1320, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 8, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.0, "doubling_h": 0.943, "growth_tmp": 30.0, "optimum_tmp": 29.979, "optimum_ph": 6.912, "genome_size": 4017962.234, "gc_content": 59.39, "coding_genes": 3407.194, "rRNA16S_genes": 2.5, "tRNA_genes": 49.916, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.666, "range_salinity": 0.0, "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": [ "Geobacter", "hydrogenophilus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }