{ "type": "genome", "identifier": "GCA_013335435.1", "organism": "Thiobacillus sp.", "title": "Thiobacillus sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Univerisity of Wisconsin--Madison", "publication": [ {} ], "properties": { "assembly_accession": "GCA_013335435.1", "bioproject": "PRJNA615962", "biosample": "SAMN14482947", "wgs_master": "JAAXVP000000000.1", "refseq_category": "na", "taxid": "924", "species_taxid": "924", "organism_name": "Thiobacillus sp.", "infraspecific_name": "", "isolate": "W9_Combined_metabat1_065", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/11", "asm_name": "ASM1333543v1", "submitter": "Univerisity of Wisconsin--Madison", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/335/435/GCA_013335435.1_ASM1333543v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-11", "dateModified": "2020-06-11", "datePublished": "2020-06-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Thiobacillus sp." ], "sample_taxid": [ "924" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Wisconsin, near Picnic Point on the coast of Lake Mendota" ], "sample_host_location_id": [], "data_size": "1.022 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3689125", "Number of Sequences": "537", "Longest Sequences (bp)": "46808", "N50 (bp)": "10073", "Gap Ratio (%)": "0.004066", "GCcontent (%)": "65.9", "Number of CDSs": "3071", "Average Protein Length": "299.5", "Coding Ratio (%)": "74.8", "Number of rRNAs": "1", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sulfuritortus calidifontis", "strain": "strain=DSM 103923", "accession": "GCA_004346085.1", "taxid": 1914471, "species_taxid": 1914471, "relation_to_type": "type", "validated": true, "ani": 81.0726, "matched_fragments": 406, "total_fragments": 945, "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": 81.0606, "matched_fragments": 409, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiobacillus denitrificans", "strain": "strain=DSM 12475", "accession": "GCA_000376425.1", "taxid": 36861, "species_taxid": 36861, "relation_to_type": "type", "validated": true, "ani": 78.1007, "matched_fragments": 262, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospira oryzae", "strain": "strain=DSM 21223", "accession": "GCA_004217225.1", "taxid": 146939, "species_taxid": 146939, "relation_to_type": "type", "validated": true, "ani": 78.0715, "matched_fragments": 286, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azoarcus rhizosphaerae", "strain": "strain=CC-YHH848", "accession": "GCA_004801305.1", "taxid": 2565932, "species_taxid": 2565932, "relation_to_type": "type", "validated": true, "ani": 77.8981, "matched_fragments": 300, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera phenylacetica", "strain": "strain=B4P", "accession": "GCA_000310225.1", "taxid": 164400, "species_taxid": 164400, "relation_to_type": "type", "validated": true, "ani": 77.8762, "matched_fragments": 264, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera chlorobenzoica", "strain": "strain=3CB-1", "accession": "GCA_900108255.1", "taxid": 96773, "species_taxid": 96773, "relation_to_type": "type", "validated": true, "ani": 77.8713, "matched_fragments": 226, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera aromatica", "strain": "strain=K172", "accession": "GCA_003030465.1", "taxid": 59405, "species_taxid": 59405, "relation_to_type": "type", "validated": true, "ani": 77.8398, "matched_fragments": 228, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera phenolivorans", "strain": "strain=ZV1C", "accession": "GCA_001696715.1", "taxid": 1792543, "species_taxid": 1792543, "relation_to_type": "type", "validated": true, "ani": 77.747, "matched_fragments": 239, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinimonas koreensis", "strain": "strain=DSM 17726", "accession": "GCA_000428465.1", "taxid": 356302, "species_taxid": 356302, "relation_to_type": "type", "validated": true, "ani": 77.7049, "matched_fragments": 303, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrogeniibacter mangrovi", "strain": "strain=M9-3-2", "accession": "GCA_010983895.1", "taxid": 2016596, "species_taxid": 2016596, "relation_to_type": "type", "validated": true, "ani": 77.6989, "matched_fragments": 262, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crenobacter luteus", "strain": "strain=DSM 27258", "accession": "GCA_004345725.1", "taxid": 1452487, "species_taxid": 1452487, "relation_to_type": "type", "validated": true, "ani": 77.6891, "matched_fragments": 212, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ferrigenium kumadai", "strain": "strain=An22", "accession": "GCA_018324385.1", "taxid": 1682490, "species_taxid": 1682490, "relation_to_type": "type", "validated": true, "ani": 77.5127, "matched_fragments": 168, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azoarcus indigens", "strain": "strain=VB32", "accession": "GCA_012910835.1", "taxid": 29545, "species_taxid": 29545, "relation_to_type": "type", "validated": true, "ani": 77.5085, "matched_fragments": 269, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Schlegelella thermodepolymerans", "strain": "strain=DSM 15344", "accession": "GCA_015476235.1", "taxid": 215580, "species_taxid": 215580, "relation_to_type": "type", "validated": true, "ani": 77.4352, "matched_fragments": 224, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium amazonense", "strain": "strain=DSM 26508", "accession": "GCA_001855565.1", "taxid": 1382803, "species_taxid": 1382803, "relation_to_type": "type", "validated": true, "ani": 77.3172, "matched_fragments": 181, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphaerotilus hippei", "strain": "strain=DSM 566", "accession": "GCA_003201595.1", "taxid": 744406, "species_taxid": 744406, "relation_to_type": "type", "validated": true, "ani": 77.1656, "matched_fragments": 218, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula plumbiphila", "strain": "strain=Gro7", "accession": "GCA_009938015.1", "taxid": 171865, "species_taxid": 171865, "relation_to_type": "type", "validated": true, "ani": 77.1305, "matched_fragments": 149, "total_fragments": 945, "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": 77.1174, "matched_fragments": 174, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula plumbiphila", "strain": "strain=NBRC 107929", "accession": "GCA_007992375.1", "taxid": 171865, "species_taxid": 171865, "relation_to_type": "type", "validated": true, "ani": 77.0684, "matched_fragments": 145, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidimonas alkaliphilus", "strain": "strain=YIM 72238", "accession": "GCA_007556595.1", "taxid": 2588942, "species_taxid": 2588942, "relation_to_type": "type", "validated": true, "ani": 77.058, "matched_fragments": 124, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidimonas fonticaldi", "strain": "strain=AT-A2", "accession": "GCA_007556755.1", "taxid": 1101373, "species_taxid": 1101373, "relation_to_type": "type", "validated": true, "ani": 77.0445, "matched_fragments": 155, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jeongeupia chitinilytica", "strain": "strain=KCTC 23701", "accession": "GCA_014652315.1", "taxid": 1041641, "species_taxid": 1041641, "relation_to_type": "type", "validated": true, "ani": 76.915, "matched_fragments": 166, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfuriferula multivorans", "strain": "strain=TTN", "accession": "GCA_003851125.1", "taxid": 1559896, "species_taxid": 1559896, "relation_to_type": "type", "validated": true, "ani": 76.8, "matched_fragments": 119, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novimethylophilus kurashikiensis", "strain": "strain=La2-4", "accession": "GCA_003112435.1", "taxid": 1825523, "species_taxid": 1825523, "relation_to_type": "type", "validated": true, "ani": 76.6691, "matched_fragments": 94, "total_fragments": 945, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_013335435.1", "gtdb_species": "s__Parasulfuritortus sp013335435", "ani": 100.0, "matched_fragments": 930, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus", "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_004337445.1", "gtdb_species": "s__Parasulfuritortus cantonensis", "ani": 85.9132, "matched_fragments": 610, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus", "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_003967275.1", "gtdb_species": "s__Sulfuritortus calidifontis", "ani": 81.0553, "matched_fragments": 408, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002782005.1", "gtdb_species": "s__Parasulfuritortus sp002782005", "ani": 80.9113, "matched_fragments": 350, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.86", "min_intra_species_ani": "99.81", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_016719465.1", "gtdb_species": "s__PFJX01 sp016719465", "ani": 80.6016, "matched_fragments": 422, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.31", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_009772925.1", "gtdb_species": "s__PFJX01 sp009772925", "ani": 80.4887, "matched_fragments": 413, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002339725.1", "gtdb_species": "s__Sulfuritortus sp002339725", "ani": 80.4525, "matched_fragments": 356, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus", "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_013389055.1", "gtdb_species": "s__Sulfuritortus sp013389055", "ani": 80.3879, "matched_fragments": 336, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus", "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_016234655.1", "gtdb_species": "s__Sulfuritortus sp016234655", "ani": 80.3787, "matched_fragments": 384, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus", "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_016219425.1", "gtdb_species": "s__PFJX01 sp016219425", "ani": 80.1447, "matched_fragments": 396, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01", "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_002360535.1", "gtdb_species": "s__UBA3361 sp002360535", "ani": 80.1335, "matched_fragments": 424, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA3361", "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_016703155.1", "gtdb_species": "s__JADJCP01 sp016703155", "ani": 80.064, "matched_fragments": 419, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__JADJCP01", "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_002347615.1", "gtdb_species": "s__UBA9220 sp002347615", "ani": 78.1758, "matched_fragments": 279, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA9220;g__UBA9220", "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_016208415.1", "gtdb_species": "s__JACQYB01 sp016208415", "ani": 77.6654, "matched_fragments": 248, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYB01", "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_006212015.1", "gtdb_species": "s__28-57-27 sp006212015", "ani": 77.1881, "matched_fragments": 144, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__28-57-27", "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_011391275.1", "gtdb_species": "s__FEB-7 sp011391275", "ani": 76.9076, "matched_fragments": 128, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7", "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_013824755.1", "gtdb_species": "s__PNOJ01 sp013824755", "ani": 75.4792, "matched_fragments": 70, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__PNOJ01", "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_016719645.1", "gtdb_species": "s__PNOJ01 sp016719645", "ani": 75.4064, "matched_fragments": 94, "total_fragments": 945, "gtdb_taxonomy": "d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__PNOJ01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.99", "min_intra_species_ani": "95.77", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.375, "cell_length": 0.033, "doubling_h": 1.144, "growth_tmp": 28.2, "optimum_tmp": 28.687, "optimum_ph": 7.4, "genome_size": 3132411.714, "gc_content": 66.1, "coding_genes": 2784.667, "rRNA16S_genes": 2.0, "tRNA_genes": 43.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.666, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.333, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Thiobacillaceae", "g__Parasulfuritortus", "s__Parasulfuritortus sp013335435" ], "_genome_taxon": [ "Thiobacillus", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Thiobacillaceae", "g__Parasulfuritortus", "s__Parasulfuritortus sp013335435", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Thiobacillaceae", "Parasulfuritortus", "Parasulfuritortus", "sp013335435" ], "_meo": [ { "id": "MEO_0000116", "label": "biofilm" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }