{ "type": "genome", "identifier": "GCF_016583575.1", "organism": "Thiocystis violacea", "title": "Thiocystis violacea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "GEOMAR Helmholtz Centre for Ocean Research Kiel", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016583575.1", "bioproject": "PRJNA224116", "biosample": "SAMN07535003", "wgs_master": "NRRG00000000.1", "refseq_category": "reference genome", "taxid": "13725", "species_taxid": "13725", "organism_name": "Thiocystis violacea", "infraspecific_name": "strain=DSM 207", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/01/08", "asm_name": "ASM1658357v1", "asm_submitter": "GEOMAR Helmholtz Centre for Ocean Research Kiel", "gbrs_paired_asm": "GCA_016583575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/583/575/GCF_016583575.1_ASM1658357v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5368928", "genome_size_ungapped": "5368928", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "207", "contig_count": "207", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016583575.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "4869", "protein_coding_gene_count": "4695", "non_coding_gene_count": "57", "pubmed_id": "33375353" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-01-08", "dateModified": "2021-01-08", "datePublished": "2021-01-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Thiocystis violacea" ], "sample_taxid": [ "13725" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: near Gruenenplan" ], "sample_host_location_id": [], "data_size": "1.498 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)": "5368928", "Number of Sequences": "207", "Longest Sequences (bp)": "257745", "N50 (bp)": "75551", "Gap Ratio (%)": "0.000075", "GCcontent (%)": "64.0", "Number of CDSs": "4700", "Average Protein Length": "323.8", "Coding Ratio (%)": "85.0", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thiocystis violacea", "strain": "strain=DSM 207", "accession": "GCA_016583575.1", "taxid": 13725, "species_taxid": 13725, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1689, "total_fragments": 1698, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thiocystis minor", "strain": "strain=DSM 178", "accession": "GCA_016653465.1", "taxid": 61597, "species_taxid": 61597, "relation_to_type": "type", "validated": true, "ani": 81.3414, "matched_fragments": 782, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allochromatium humboldtianum", "strain": "strain=DSM 21881", "accession": "GCA_013385175.1", "taxid": 504901, "species_taxid": 504901, "relation_to_type": "type", "validated": true, "ani": 81.0367, "matched_fragments": 730, "total_fragments": 1698, "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": 81.0288, "matched_fragments": 661, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allochromatium vinosum", "strain": "strain=DSM 180", "accession": "GCA_000025485.1", "taxid": 1049, "species_taxid": 1049, "relation_to_type": "type", "validated": true, "ani": 80.985, "matched_fragments": 691, "total_fragments": 1698, "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": 80.9578, "matched_fragments": 767, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiorhodococcus minor", "strain": "strain=DSM 11518", "accession": "GCA_010820565.1", "taxid": 57489, "species_taxid": 57489, "relation_to_type": "type", "validated": true, "ani": 79.6441, "matched_fragments": 714, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiorhodococcus mannitoliphagus", "strain": "strain=DSM 18266", "accession": "GCA_010915725.1", "taxid": 329406, "species_taxid": 329406, "relation_to_type": "type", "validated": true, "ani": 79.5494, "matched_fragments": 665, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocapsa roseopersicina", "strain": "strain=DSM 217", "accession": "GCA_900106925.1", "taxid": 1058, "species_taxid": 1058, "relation_to_type": "type", "validated": true, "ani": 79.4234, "matched_fragments": 521, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocapsa rosea", "strain": "strain=DSM 235", "accession": "GCA_003634315.1", "taxid": 69360, "species_taxid": 69360, "relation_to_type": "type", "validated": true, "ani": 79.2468, "matched_fragments": 514, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marichromatium gracile", "strain": "strain=DSM 203", "accession": "GCA_004343155.1", "taxid": 1048, "species_taxid": 1048, "relation_to_type": "type", "validated": true, "ani": 79.1521, "matched_fragments": 560, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocapsa marina", "strain": "strain=5811", "accession": "GCA_000223985.2", "taxid": 244573, "species_taxid": 244573, "relation_to_type": "type", "validated": true, "ani": 79.1475, "matched_fragments": 479, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marichromatium gracile", "strain": "strain=DSM 203", "accession": "GCA_016583515.1", "taxid": 1048, "species_taxid": 1048, "relation_to_type": "type", "validated": true, "ani": 79.1175, "matched_fragments": 556, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocapsa bogorovii", "strain": "strain=BBS", "accession": "GCA_021228795.1", "taxid": 521689, "species_taxid": 521689, "relation_to_type": "type", "validated": true, "ani": 78.7731, "matched_fragments": 467, "total_fragments": 1698, "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": 77.9016, "matched_fragments": 162, "total_fragments": 1698, "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": 77.206, "matched_fragments": 201, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=JCM 5962", "accession": "GCA_022496575.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.1353, "matched_fragments": 160, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_024169805.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.0761, "matched_fragments": 159, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylocystis heyeri", "strain": "strain=H2", "accession": "GCA_004802635.2", "taxid": 391905, "species_taxid": 391905, "relation_to_type": "type", "validated": true, "ani": 75.7397, "matched_fragments": 52, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylocystis parvus", "strain": "strain=OBBP", "accession": "GCA_000283235.1", "taxid": 134, "species_taxid": 134, "relation_to_type": "type", "validated": true, "ani": 75.2951, "matched_fragments": 72, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas morindae", "strain": "strain=NBD5", "accession": "GCA_023822065.1", "taxid": 1541170, "species_taxid": 1541170, "relation_to_type": "type", "validated": true, "ani": 75.2558, "matched_fragments": 101, "total_fragments": 1698, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016583575.1", "gtdb_species": "s__Thiocystis violacea", "ani": 100.0, "matched_fragments": 1689, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis", "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_016653465.1", "gtdb_species": "s__Chromatium minus", "ani": 81.3357, "matched_fragments": 784, "total_fragments": 1698, "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_013385175.1", "gtdb_species": "s__Allochromatium humboldtianum", "ani": 81.0348, "matched_fragments": 730, "total_fragments": 1698, "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_018409545.1", "gtdb_species": "s__Allochromatium tepidum", "ani": 81.0188, "matched_fragments": 662, "total_fragments": 1698, "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": 80.9955, "matched_fragments": 690, "total_fragments": 1698, "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_000227745.2", "gtdb_species": "s__Chromatium violascens", "ani": 80.9341, "matched_fragments": 768, "total_fragments": 1698, "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": 80.6916, "matched_fragments": 693, "total_fragments": 1698, "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_016583565.1", "gtdb_species": "s__Thiorhodococcus violacea_A", "ani": 80.2987, "matched_fragments": 785, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus", "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_000585215.1", "gtdb_species": "s__Imhoffiella purpurea", "ani": 80.2764, "matched_fragments": 689, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella", "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_009720725.1", "gtdb_species": "s__Allochromatium palmeri", "ani": 80.2746, "matched_fragments": 684, "total_fragments": 1698, "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_004342175.1", "gtdb_species": "s__Thiobaca trueperi", "ani": 80.2212, "matched_fragments": 638, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca", "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_000224065.1", "gtdb_species": "s__Imhoffiella drewsii", "ani": 79.7582, "matched_fragments": 669, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella", "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_010820565.1", "gtdb_species": "s__Thiorhodococcus minor", "ani": 79.6405, "matched_fragments": 713, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus", "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_900106925.1", "gtdb_species": "s__Thiocapsa roseopersicina", "ani": 79.4137, "matched_fragments": 522, "total_fragments": 1698, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa", "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_004343155.1", "gtdb_species": "s__Marichromatium gracile", "ani": 79.1566, "matched_fragments": 560, "total_fragments": 1698, "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_900107145.1", "gtdb_species": "s__Allochromatium warmingii", "ani": 77.8811, "matched_fragments": 163, "total_fragments": 1698, "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": 0.397, "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 }, "_genome_taxon": [ "Thiocystis", "violacea" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }