{ "type": "genome", "identifier": "GCF_004339575.1", "organism": "Phorcysia thermohydrogeniphila", "title": "Phorcysia thermohydrogeniphila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004339575.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621466", "wgs_master": "SMFV00000000.1", "refseq_category": "reference genome", "taxid": "936138", "species_taxid": "936138", "organism_name": "Phorcysia thermohydrogeniphila", "infraspecific_name": "strain=DSM 24425", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM433957v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004339575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/339/575/GCF_004339575.1_ASM433957v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1621410", "genome_size_ungapped": "1621139", "gc_percent": "45.000000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004339575.1-RS_2024_05_12", "annotation_date": "2024-05-12", "total_gene_count": "1705", "protein_coding_gene_count": "1650", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Phorcysia thermohydrogeniphila" ], "sample_taxid": [ "936138" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.456 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.54, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1621410", "Number of Sequences": "8", "Longest Sequences (bp)": "525043", "N50 (bp)": "327746", "Gap Ratio (%)": "0.016714", "GCcontent (%)": "44.9", "Number of CDSs": "1656", "Average Protein Length": "309.5", "Coding Ratio (%)": "94.8", "Number of rRNAs": "2", "Number of tRNAs": "42", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phorcysia thermohydrogeniphila", "strain": "strain=DSM 24425", "accession": "GCA_004339575.1", "taxid": 936138, "species_taxid": 936138, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 536, "total_fragments": 537, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thermovibrio guaymasensis", "strain": "strain=DSM 15521", "accession": "GCA_003633715.1", "taxid": 240167, "species_taxid": 240167, "relation_to_type": "type", "validated": true, "ani": 77.7617, "matched_fragments": 134, "total_fragments": 537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfurobacterium thermolithotrophum", "strain": "strain=DSM 11699", "accession": "GCA_000191045.1", "taxid": 64160, "species_taxid": 64160, "relation_to_type": "type", "validated": true, "ani": 77.4198, "matched_fragments": 64, "total_fragments": 537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Balnearium lithotrophicum", "strain": "strain=DSM 16304", "accession": "GCA_900182585.1", "taxid": 223788, "species_taxid": 223788, "relation_to_type": "type", "validated": true, "ani": 77.2958, "matched_fragments": 121, "total_fragments": 537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermovibrio ammonificans", "strain": "strain=HB-1", "accession": "GCA_000185805.1", "taxid": 228745, "species_taxid": 228745, "relation_to_type": "type", "validated": true, "ani": 77.1887, "matched_fragments": 121, "total_fragments": 537, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.54, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004339575.1", "gtdb_species": "s__Phorcysia thermohydrogeniphila", "ani": 100.0, "matched_fragments": 537, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Phorcysia", "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": "GCA_003978805.1", "gtdb_species": "s__Phorcysia sp003978805", "ani": 82.5792, "matched_fragments": 206, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Phorcysia", "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_015488335.1", "gtdb_species": "s__Balnearium sp015488335", "ani": 77.9528, "matched_fragments": 148, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium", "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_015490195.1", "gtdb_species": "s__Balnearium sp015490195", "ani": 77.782, "matched_fragments": 152, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium", "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_003633715.1", "gtdb_species": "s__Thermovibrio guaymasensis", "ani": 77.7559, "matched_fragments": 135, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Thermovibrio", "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_000191045.1", "gtdb_species": "s__Desulfurobacterium thermolithotrophum", "ani": 77.4198, "matched_fragments": 64, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.79", "min_intra_species_ani": "95.79", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900182585.1", "gtdb_species": "s__Balnearium lithotrophicum", "ani": 77.2719, "matched_fragments": 122, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium", "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_000185805.1", "gtdb_species": "s__Thermovibrio ammonificans", "ani": 77.1887, "matched_fragments": 121, "total_fragments": 537, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Thermovibrio", "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": -0.302, "cell_length": 0.096, "doubling_h": null, "growth_tmp": 75.0, "optimum_tmp": 75.0, "optimum_ph": 6.0, "genome_size": 1621410.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": 0.0, "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": [ "Phorcysia", "thermohydrogeniphila" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }