{ "type": "genome", "identifier": "GCF_900101365.1", "organism": "Thiohalorhabdus denitrificans", "title": "Thiohalorhabdus denitrificans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900101365.1", "bioproject": "PRJNA224116", "biosample": "SAMN05661077", "wgs_master": "FMUN00000000.1", "refseq_category": "na", "taxid": "381306", "species_taxid": "381306", "organism_name": "Thiohalorhabdus denitrificans", "infraspecific_name": "strain=HL 19", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/17", "asm_name": "IMG-taxon 2596583511 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900101365.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/101/365/GCF_900101365.1_IMG-taxon_2596583511_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2876643", "genome_size_ungapped": "2876643", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900101365.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "2777", "protein_coding_gene_count": "2707", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-17", "dateModified": "2016-10-17", "datePublished": "2016-10-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Thiohalorhabdus denitrificans" ], "sample_taxid": [ "381306" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia:South-west Siberia" ], "sample_host_location_id": [], "data_size": "0.785 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)": "2876643", "Number of Sequences": "18", "Longest Sequences (bp)": "543608", "N50 (bp)": "344576", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.9", "Number of CDSs": "2744", "Average Protein Length": "310.2", "Coding Ratio (%)": "88.8", "Number of rRNAs": "1", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thiohalorhabdus denitrificans", "strain": "strain=HL 19", "accession": "GCA_900101365.1", "taxid": 381306, "species_taxid": 381306, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 950, "total_fragments": 951, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thiohalorhabdus denitrificans", "strain": "strain=HL 19", "accession": "GCA_001399755.1", "taxid": 381306, "species_taxid": 381306, "relation_to_type": "type", "validated": true, "ani": 99.9915, "matched_fragments": 943, "total_fragments": 951, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thiohalospira halophila", "strain": "strain=HL 3", "accession": "GCA_900112605.1", "taxid": 381300, "species_taxid": 381300, "relation_to_type": "type", "validated": true, "ani": 78.1339, "matched_fragments": 221, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalbus denitrificans", "strain": "strain=DSM 26407", "accession": "GCA_003337735.1", "taxid": 547122, "species_taxid": 547122, "relation_to_type": "type", "validated": true, "ani": 77.4568, "matched_fragments": 226, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermithiobacillus tepidarius", "strain": "strain=DSM 3134", "accession": "GCA_000423825.1", "taxid": 929, "species_taxid": 929, "relation_to_type": "type", "validated": true, "ani": 77.4527, "matched_fragments": 185, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arhodomonas aquaeolei", "strain": "strain=DSM 8974", "accession": "GCA_000374645.1", "taxid": 2369, "species_taxid": 2369, "relation_to_type": "type", "validated": true, "ani": 77.1045, "matched_fragments": 156, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas denitrificans", "strain": "strain=DSM 18045", "accession": "GCA_003056305.1", "taxid": 370769, "species_taxid": 370769, "relation_to_type": "type", "validated": true, "ani": 77.0528, "matched_fragments": 168, "total_fragments": 951, "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": 77.0173, "matched_fragments": 184, "total_fragments": 951, "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": 76.9696, "matched_fragments": 165, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio thiocyanodenitrificans", "strain": "strain=ARhD 1", "accession": "GCA_000378965.1", "taxid": 243063, "species_taxid": 243063, "relation_to_type": "type", "validated": true, "ani": 76.8943, "matched_fragments": 131, "total_fragments": 951, "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": 76.8417, "matched_fragments": 116, "total_fragments": 951, "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": 76.7994, "matched_fragments": 117, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas ventosae", "strain": "strain=CECT 5797", "accession": "GCA_004363555.1", "taxid": 229007, "species_taxid": 229007, "relation_to_type": "type", "validated": true, "ani": 76.7436, "matched_fragments": 163, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aestuarii", "strain": "strain=Hb3", "accession": "GCA_001886615.1", "taxid": 1897729, "species_taxid": 1897729, "relation_to_type": "type", "validated": true, "ani": 76.6836, "matched_fragments": 146, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorhodospira halophila", "strain": "strain=SL1", "accession": "GCA_000015585.1", "taxid": 1053, "species_taxid": 1053, "relation_to_type": "suspected-type", "validated": true, "ani": 76.673, "matched_fragments": 109, "total_fragments": 951, "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": 76.6589, "matched_fragments": 134, "total_fragments": 951, "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": 76.6215, "matched_fragments": 156, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio versutus", "strain": "strain=AL 2", "accession": "GCA_001999325.1", "taxid": 106634, "species_taxid": 106634, "relation_to_type": "type", "validated": true, "ani": 76.5827, "matched_fragments": 106, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 76.1376, "matched_fragments": 123, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ottowia beijingensis", "strain": "strain=GCS-AN-3", "accession": "GCA_013423955.1", "taxid": 1207057, "species_taxid": 1207057, "relation_to_type": "type", "validated": true, "ani": 75.9611, "matched_fragments": 105, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mitsuaria chitinivorans", "strain": "strain=HWN-4", "accession": "GCA_002761755.1", "taxid": 2917965, "species_taxid": 2917965, "relation_to_type": "type", "validated": true, "ani": 75.6819, "matched_fragments": 110, "total_fragments": 951, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001399755.1", "gtdb_species": "s__Thiohalorhabdus denitrificans", "ani": 99.9915, "matched_fragments": 943, "total_fragments": 951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalorhabdales;f__Thiohalorhabdaceae;g__Thiohalorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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76.6959, "matched_fragments": 112, "total_fragments": 951, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048", "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_004337445.1", "gtdb_species": "s__Parasulfuritortus cantonensis", "ani": 76.6913, "matched_fragments": 117, "total_fragments": 951, "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_010983895.1", "gtdb_species": "s__Denitromonas sp010983895", "ani": 76.6749, "matched_fragments": 133, "total_fragments": 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