{ "type": "genome", "identifier": "GCF_010820565.1", "organism": "Thiorhodococcus minor", "title": "Thiorhodococcus minor", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bellevue University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010820565.1", "bioproject": "PRJNA224116", "biosample": "SAMN14084852", "wgs_master": "JAAIJQ000000000.1", "refseq_category": "reference genome", "taxid": "57489", "species_taxid": "57489", "organism_name": "Thiorhodococcus minor", "infraspecific_name": "strain=DSM 11518", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/20", "asm_name": "ASM1082056v1", "asm_submitter": "Bellevue University", "gbrs_paired_asm": "GCA_010820565.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/820/565/GCF_010820565.1_ASM1082056v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6204626", "genome_size_ungapped": "6204626", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "389", "contig_count": "389", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010820565.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "5506", "protein_coding_gene_count": "5316", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-20", "dateModified": "2020-02-20", "datePublished": "2020-02-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Thiorhodococcus minor" ], "sample_taxid": [ "57489" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Arcachon Bay" ], "sample_host_location_id": [], "data_size": "1.740 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)": "6204626", "Number of Sequences": "389", "Longest Sequences (bp)": "160947", "N50 (bp)": "60973", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.8", "Number of CDSs": "5273", "Average Protein Length": "318.2", "Coding Ratio (%)": "81.1", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thiorhodococcus minor", "strain": "strain=DSM 11518", "accession": "GCA_010820565.1", "taxid": 57489, "species_taxid": 57489, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1893, "total_fragments": 1908, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thiorhodococcus mannitoliphagus", "strain": "strain=DSM 18266", "accession": "GCA_010915725.1", "taxid": 329406, "species_taxid": 329406, "relation_to_type": "type", "validated": true, "ani": 83.5642, "matched_fragments": 1161, "total_fragments": 1908, "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": 79.6635, "matched_fragments": 539, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocystis violacea", "strain": "strain=DSM 207", "accession": "GCA_016583575.1", "taxid": 13725, "species_taxid": 13725, "relation_to_type": "type", "validated": true, "ani": 79.6543, "matched_fragments": 709, "total_fragments": 1908, "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": 79.6331, "matched_fragments": 561, "total_fragments": 1908, "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": 79.5842, "matched_fragments": 600, "total_fragments": 1908, "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": 79.3313, "matched_fragments": 549, "total_fragments": 1908, "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": 79.2509, "matched_fragments": 561, "total_fragments": 1908, "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": 78.873, "matched_fragments": 492, "total_fragments": 1908, "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": 78.6644, "matched_fragments": 535, "total_fragments": 1908, "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": 78.5691, "matched_fragments": 527, "total_fragments": 1908, "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": 78.438, "matched_fragments": 548, "total_fragments": 1908, "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": 78.2332, "matched_fragments": 471, "total_fragments": 1908, "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": 76.2562, "matched_fragments": 168, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas guguanensis", "strain": "strain=JCM 18416", "accession": "GCA_900104265.1", "taxid": 1198456, "species_taxid": 1198456, "relation_to_type": "type", "validated": true, "ani": 76.0024, "matched_fragments": 139, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas yangonensis", "strain": "strain=MY50", "accession": "GCA_009932725.1", "taxid": 2579922, "species_taxid": 2579922, "relation_to_type": "type", "validated": true, "ani": 75.9677, "matched_fragments": 134, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cavernae", "strain": "strain=K2W31S-8", "accession": "GCA_003595175.1", "taxid": 2320867, "species_taxid": 2320867, "relation_to_type": "type", "validated": true, "ani": 75.7856, "matched_fragments": 122, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010820565.1", "gtdb_species": "s__Thiorhodococcus minor", "ani": 100.0, "matched_fragments": 1893, "total_fragments": 1908, "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": "conclusive" }, { "accession": "GCF_010915725.1", "gtdb_species": "s__Thiorhodococcus mannitoliphagus", "ani": 83.5579, "matched_fragments": 1162, "total_fragments": 1908, "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", 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"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": 79.6639, "matched_fragments": 539, "total_fragments": 1908, "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_016583575.1", "gtdb_species": "s__Thiocystis violacea", "ani": 79.6476, "matched_fragments": 710, "total_fragments": 1908, "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": "-" }, { "accession": "GCF_000025485.1", "gtdb_species": "s__Allochromatium vinosum", "ani": 79.6057, "matched_fragments": 564, "total_fragments": 1908, "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_013385175.1", "gtdb_species": "s__Allochromatium humboldtianum", "ani": 79.5995, "matched_fragments": 598, "total_fragments": 1908, "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_004343155.1", "gtdb_species": "s__Marichromatium gracile", "ani": 79.226, "matched_fragments": 564, "total_fragments": 1908, "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_009720725.1", "gtdb_species": "s__Allochromatium palmeri", "ani": 79.2124, "matched_fragments": 535, "total_fragments": 1908, "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": 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0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Thiorhodococcus", "minor" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }