{ "type": "genome", "identifier": "GCF_003333315.1", "organism": "Acidiferrobacter thiooxydans", "title": "Acidiferrobacter thiooxydans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Fundacion Ciencia & Vida", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003333315.1", "bioproject": "PRJNA224116", "biosample": "SAMN08523060", "wgs_master": "PSYR00000000.1", "refseq_category": "na", "taxid": "163359", "species_taxid": "163359", "organism_name": "Acidiferrobacter thiooxydans", "infraspecific_name": "strain=m-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/21", "asm_name": "ASM333331v1", "asm_submitter": "Fundacion Ciencia & Vida", "gbrs_paired_asm": "GCA_003333315.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/333/315/GCF_003333315.1_ASM333331v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3251406", "genome_size_ungapped": "3251406", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-17", "total_gene_count": "3094", "protein_coding_gene_count": "2981", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-21", "dateModified": "2018-07-21", "datePublished": "2018-07-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Acidiferrobacter thiooxydans" ], "sample_taxid": [ "163359" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Mississipi, Calloway County" ], "sample_host_location_id": [], "data_size": "0.907 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)": "3251406", "Number of Sequences": "4", "Longest Sequences (bp)": "1759369", "N50 (bp)": "1759369", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.7", "Number of CDSs": "3166", "Average Protein Length": "297.3", "Coding Ratio (%)": "86.8", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Acidiferrobacter thiooxydans", "strain": "strain=m-1", "accession": "GCA_003333315.1", "taxid": 163359, "species_taxid": 163359, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1074, "total_fragments": 1082, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thioalbus denitrificans", "strain": "strain=DSM 26407", "accession": "GCA_003337735.1", "taxid": 547122, "species_taxid": 547122, "relation_to_type": "type", "validated": true, "ani": 76.8692, "matched_fragments": 73, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfurifustis variabilis", "strain": "strain=skN76", "accession": "GCA_002355415.1", "taxid": 1675686, "species_taxid": 1675686, "relation_to_type": "type", "validated": true, "ani": 76.6187, "matched_fragments": 95, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuritortus calidifontis", "strain": "strain=J1A", "accession": "GCA_003967275.1", "taxid": 1914471, "species_taxid": 1914471, "relation_to_type": "type", "validated": true, "ani": 76.5611, "matched_fragments": 54, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuricaulis limicola", "strain": "strain=HA5", "accession": "GCA_002355735.1", "taxid": 1620215, "species_taxid": 1620215, "relation_to_type": "type", "validated": true, "ani": 76.354, "matched_fragments": 83, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Inmirania thermothiophila", "strain": "strain=DSM 100275", "accession": "GCA_003751635.1", "taxid": 1750597, "species_taxid": 1750597, "relation_to_type": "type", "validated": true, "ani": 76.2232, "matched_fragments": 81, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allochromatium tepidum", "strain": "strain=NZ", "accession": "GCA_018409545.1", "taxid": 553982, "species_taxid": 553982, "relation_to_type": "type", "validated": true, "ani": 76.2211, "matched_fragments": 68, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuritortus calidifontis", "strain": "strain=DSM 103923", "accession": "GCA_004346085.1", "taxid": 1914471, "species_taxid": 1914471, "relation_to_type": "type", "validated": true, "ani": 76.2058, "matched_fragments": 53, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiohalobacter thiocyanaticus", "strain": "strain=Hrh1", "accession": "GCA_003932505.1", "taxid": 585455, "species_taxid": 585455, "relation_to_type": "type", "validated": true, "ani": 76.0605, "matched_fragments": 60, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorhodospira neutriphila", "strain": "strain=DSM 15116", "accession": "GCA_016584055.1", "taxid": 168379, "species_taxid": 168379, "relation_to_type": "type", "validated": true, "ani": 75.859, "matched_fragments": 58, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus nantongensis", "strain": "strain=X1", "accession": "GCA_001598055.1", "taxid": 1796606, "species_taxid": 1796606, "relation_to_type": "type", "validated": true, "ani": 75.8122, "matched_fragments": 62, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiohalocapsa halophila", "strain": "strain=DSM 6210", "accession": "GCA_016583825.1", "taxid": 69359, "species_taxid": 69359, "relation_to_type": "type", "validated": true, "ani": 75.7583, "matched_fragments": 59, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 75.606, "matched_fragments": 56, "total_fragments": 1082, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003333315.1", "gtdb_species": "s__Acidiferrobacter thiooxydans", "ani": 100.0, "matched_fragments": 1074, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Acidiferrobacteraceae;g__Acidiferrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "99.34", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003184265.1", "gtdb_species": "s__Acidiferrobacter sp003184265", "ani": 91.2791, "matched_fragments": 845, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Acidiferrobacteraceae;g__Acidiferrobacter", "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_001785115.1", "gtdb_species": "s__RBG-16-65-34 sp001785115", "ani": 76.7294, "matched_fragments": 63, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__RBG-16-65-34", "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_001753165.1", "gtdb_species": "s__Acidihalobacter aeolianus", "ani": 76.5286, "matched_fragments": 53, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter", "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_016218345.1", "gtdb_species": "s__JACREH01 sp016218345", "ani": 76.3655, "matched_fragments": 95, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__UBA6901;g__JACREH01", "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_001785175.1", "gtdb_species": "s__MFSY01 sp001785175", "ani": 76.3619, "matched_fragments": 76, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__MFSY01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.76", "min_intra_species_af": "0.76", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013348725.1", "gtdb_species": "s__GCA-013348725 sp013348725", "ani": 76.323, "matched_fragments": 84, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725", "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_003751635.1", "gtdb_species": "s__Inmirania thermothiophila", "ani": 76.2232, "matched_fragments": 81, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania", "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_002897735.1", "gtdb_species": "s__BMS3Abin12 sp002897735", "ani": 75.7952, "matched_fragments": 59, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__21-64-14;f__21-64-14;g__BMS3Abin12", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.73", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_015494165.1", "gtdb_species": "s__S144-34 sp015494165", "ani": 75.6472, "matched_fragments": 68, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34", "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_018623495.1", "gtdb_species": "s__JAAZVP01 sp018623495", "ani": 75.6422, "matched_fragments": 52, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01", "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_018240295.1", "gtdb_species": "s__Plasticicumulans sp003962905", "ani": 75.5654, "matched_fragments": 63, "total_fragments": 1082, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Acidiferrobacter", "thiooxydans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }