{ "type": "genome", "identifier": "GCA_020721065.1", "organism": "Thiocystis violascens", "title": "Thiocystis violascens", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University Duisburg-Essen", "publication": [ {} ], "properties": { "assembly_accession": "GCA_020721065.1", "bioproject": "PRJNA767587", "biosample": "SAMN22209500", "wgs_master": "DYNM00000000.1", "refseq_category": "na", "taxid": "73141", "species_taxid": "73141", "organism_name": "Thiocystis violascens", "infraspecific_name": "", "isolate": "SulCav_FS08_3_52_29", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/11/02", "asm_name": "ASM2072106v1", "submitter": "University Duisburg-Essen", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/721/065/GCA_020721065.1_ASM2072106v1", "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": "2021-11-02", "dateModified": "2021-11-02", "datePublished": "2021-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Thiocystis violascens" ], "sample_taxid": [ "73141" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy: Frasassi cave" ], "sample_host_location_id": [], "data_size": "0.862 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3056930", "Number of Sequences": "113", "Longest Sequences (bp)": "344366", "N50 (bp)": "90446", "Gap Ratio (%)": "0.019628", "GCcontent (%)": "51.7", "Number of CDSs": "2609", "Average Protein Length": "341.0", "Coding Ratio (%)": "87.3", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Chromatium okenii", "strain": "strain=DSM 169", "accession": "GCA_016583745.1", "taxid": 61644, "species_taxid": 61644, "relation_to_type": "type", "validated": true, "ani": 93.0026, "matched_fragments": 833, "total_fragments": 965, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocystis violascens", "strain": "strain=DSM 198", "accession": "GCA_000227745.3", "taxid": 73141, "species_taxid": 73141, "relation_to_type": "type", "validated": true, "ani": 76.6466, "matched_fragments": 121, "total_fragments": 965, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allochromatium warmingii", "strain": "strain=DSM 173", "accession": "GCA_900107145.1", "taxid": 61595, "species_taxid": 61595, "relation_to_type": "type", "validated": true, "ani": 76.5477, "matched_fragments": 164, "total_fragments": 965, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocystis minor", "strain": "strain=DSM 178", "accession": "GCA_016653465.1", "taxid": 61597, "species_taxid": 61597, "relation_to_type": "type", "validated": true, "ani": 76.5448, "matched_fragments": 112, "total_fragments": 965, "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": 75.9464, "matched_fragments": 77, "total_fragments": 965, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016583745.1", "gtdb_species": "s__Chromatium okenii", "ani": 93.0245, "matched_fragments": 832, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium", "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_002958735.1", "gtdb_species": "s__Chromatium okenii_A", "ani": 82.5115, "matched_fragments": 528, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016583765.1", "gtdb_species": "s__Chromatium weissei", "ani": 80.022, "matched_fragments": 478, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium", "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_903897335.1", "gtdb_species": "s__Chromatium sp903897335", "ani": 77.3393, "matched_fragments": 125, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012276755.1", "gtdb_species": "s__Marichromatium bheemlicum", "ani": 76.7545, "matched_fragments": 55, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium", "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_000227745.2", "gtdb_species": "s__Chromatium violascens", "ani": 76.665, "matched_fragments": 120, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium", "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_903866365.1", "gtdb_species": "s__Chromatium sp903866365", "ani": 76.631, "matched_fragments": 97, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium", "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_900107145.1", "gtdb_species": "s__Allochromatium warmingii", "ani": 76.5477, "matched_fragments": 164, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium", "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_000025485.1", "gtdb_species": "s__Allochromatium vinosum", "ani": 76.078, "matched_fragments": 77, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004343155.1", "gtdb_species": "s__Marichromatium gracile", "ani": 75.9778, "matched_fragments": 66, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "96.74", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_018409545.1", "gtdb_species": "s__Allochromatium tepidum", "ani": 75.9464, "matched_fragments": 77, "total_fragments": 965, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium", "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": 0.301, "cell_length": 0.397, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": null, "optimum_ph": 7.15, "genome_size": 5017070.75, "gc_content": 62.6, "coding_genes": 4302.667, "rRNA16S_genes": 3.0, "tRNA_genes": 50.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Chromatiales", "f__Chromatiaceae", "g__Chromatium", "s__Chromatium violascens_A" ], "_genome_taxon": [ "Thiocystis", "violascens", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Chromatiales", "f__Chromatiaceae", "g__Chromatium", "s__Chromatium violascens_A", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Chromatiales", "Chromatiaceae", "Chromatium", "Chromatium", "violascens", "A" ], "_meo": [ { "id": "MEO_0000366", "label": "ground water" }, { "id": "MEO_0000116", "label": "biofilm" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }