{ "type": "genome", "identifier": "GCF_002000365.1", "organism": "Thioalkalivibrio denitrificans", "title": "Thioalkalivibrio denitrificans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Amsterdam", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002000365.1", "bioproject": "PRJNA224116", "biosample": "SAMN06319236", "wgs_master": "MVBK00000000.1", "refseq_category": "reference genome", "taxid": "108003", "species_taxid": "108003", "organism_name": "Thioalkalivibrio denitrificans", "infraspecific_name": "strain=ALJD", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/15", "asm_name": "ASM200036v1", "asm_submitter": "University of Amsterdam", "gbrs_paired_asm": "GCA_002000365.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/000/365/GCF_002000365.1_ASM200036v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3639353", "genome_size_ungapped": "3636700", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "167", "contig_count": "167", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002000365.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "3440", "protein_coding_gene_count": "3342", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-15", "dateModified": "2017-02-15", "datePublished": "2017-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Thioalkalivibrio denitrificans" ], "sample_taxid": [ "108003" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Kenya" ], "sample_host_location_id": [], "data_size": "1.021 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)": "3639353", "Number of Sequences": "167", "Longest Sequences (bp)": "143460", "N50 (bp)": "44353", "Gap Ratio (%)": "0.077157", "GCcontent (%)": "64.6", "Number of CDSs": "3370", "Average Protein Length": "302.9", "Coding Ratio (%)": "84.1", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thioalkalivibrio denitrificans", "strain": "strain=ALJD", "accession": "GCA_002000365.1", "taxid": 108003, "species_taxid": 108003, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1116, "total_fragments": 1123, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thioalkalivibrio sulfidiphilus", "strain": "strain=HL-EbGR7", "accession": "GCA_000021985.1", "taxid": 1033854, "species_taxid": 1033854, "relation_to_type": "type", "validated": true, "ani": 82.3426, "matched_fragments": 648, "total_fragments": 1123, "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": 82.2334, "matched_fragments": 666, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio thiocyanoxidans", "strain": "strain=ARh2", "accession": "GCA_000385215.1", "taxid": 152475, "species_taxid": 152475, "relation_to_type": "type", "validated": true, "ani": 78.1921, "matched_fragments": 221, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ectothiorhodospira magna", "strain": "strain=B7-7", "accession": "GCA_900110965.1", "taxid": 867345, "species_taxid": 867345, "relation_to_type": "type", "validated": true, "ani": 78.0192, "matched_fragments": 206, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ectothiorhodospira marina", "strain": "strain=DSM 241", "accession": "GCA_900109495.1", "taxid": 1396821, "species_taxid": 1396821, "relation_to_type": "type", "validated": true, "ani": 77.9597, "matched_fragments": 273, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio paradoxus", "strain": "strain=ARh 1", "accession": "GCA_000227685.3", "taxid": 108010, "species_taxid": 108010, "relation_to_type": "type", "validated": true, "ani": 77.8907, "matched_fragments": 210, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { 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"strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 76.8534, "matched_fragments": 148, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas shengliensis", "strain": "strain=CGMCC 1.6444", "accession": "GCA_900104135.1", "taxid": 419597, "species_taxid": 419597, "relation_to_type": "type", "validated": true, "ani": 76.8257, "matched_fragments": 144, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Natronocella acetinitrilica", "strain": "strain=ANL 6-2", "accession": "GCA_024170285.1", "taxid": 414046, "species_taxid": 414046, "relation_to_type": "type", "validated": true, "ani": 76.6562, "matched_fragments": 128, "total_fragments": 1123, "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": 76.6091, "matched_fragments": 106, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaliphila", "strain": "strain=JCM 10630", "accession": "GCA_900101755.1", "taxid": 101564, "species_taxid": 101564, "relation_to_type": "type", "validated": true, "ani": 76.1629, "matched_fragments": 99, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=DNSP21", "accession": "GCA_002890935.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 76.0021, "matched_fragments": 105, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002000365.1", "gtdb_species": "s__Thioalkalivibrio_A denitrificans", "ani": 100.0, "matched_fragments": 1116, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A", "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_000377945.1", "gtdb_species": "s__Thioalkalivibrio_A sulfidiphilus_A", "ani": 82.4016, "matched_fragments": 625, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A", "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, 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