{ "type": "genome", "identifier": "GCF_001995255.1", "organism": "Thioalkalivibrio halophilus", "title": "Thioalkalivibrio halophilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Amsterdam", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001995255.1", "bioproject": "PRJNA224116", "biosample": "SAMN06317462", "wgs_master": "MUZR00000000.1", "refseq_category": "reference genome", "taxid": "252474", "species_taxid": "252474", "organism_name": "Thioalkalivibrio halophilus", "infraspecific_name": "strain=HL17", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/12", "asm_name": "Tv_HL17_v1", "asm_submitter": "University of Amsterdam", "gbrs_paired_asm": "GCA_001995255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/995/255/GCF_001995255.1_Tv_HL17_v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2871788", "genome_size_ungapped": "2870690", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "97", "contig_count": "97", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001995255.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "2806", "protein_coding_gene_count": "2680", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-12", "dateModified": "2017-02-12", "datePublished": "2017-02-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Thioalkalivibrio halophilus" ], "sample_taxid": [ "252474" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: Siberia" ], "sample_host_location_id": [], "data_size": "0.791 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)": "2871788", "Number of Sequences": "97", "Longest Sequences (bp)": "193845", "N50 (bp)": "70770", "Gap Ratio (%)": "0.039279", "GCcontent (%)": "67.5", "Number of CDSs": "2679", "Average Protein Length": "318.3", "Coding Ratio (%)": "89.1", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thioalkalivibrio halophilus", "strain": "strain=HL17", "accession": "GCA_001995255.1", "taxid": 252474, "species_taxid": 252474, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 907, "total_fragments": 909, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thioalkalivibrio thiocyanoxidans", "strain": "strain=ARh2", "accession": "GCA_000385215.1", "taxid": 152475, "species_taxid": 152475, "relation_to_type": "type", "validated": true, "ani": 81.7035, "matched_fragments": 483, "total_fragments": 909, "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": 81.5165, "matched_fragments": 524, "total_fragments": 909, "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": 78.8654, "matched_fragments": 297, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio nitratireducens", "strain": "strain=DSM 14787", "accession": "GCA_000321415.2", "taxid": 186931, "species_taxid": 186931, "relation_to_type": "type", "validated": true, "ani": 78.4658, "matched_fragments": 299, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio sulfidiphilus", "strain": "strain=HL-EbGR7", "accession": "GCA_000021985.1", "taxid": 1033854, "species_taxid": 1033854, "relation_to_type": "type", "validated": true, "ani": 78.411, "matched_fragments": 281, "total_fragments": 909, "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": 77.0167, "matched_fragments": 155, "total_fragments": 909, "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": 76.975, "matched_fragments": 161, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 76.889, "matched_fragments": 129, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiohalorhabdus denitrificans", "strain": "strain=HL 19", "accession": "GCA_900101365.1", "taxid": 381306, "species_taxid": 381306, "relation_to_type": "type", "validated": true, "ani": 76.8062, "matched_fragments": 104, "total_fragments": 909, "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": 76.7819, "matched_fragments": 145, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiohalorhabdus denitrificans", "strain": "strain=HL 19", "accession": "GCA_001399755.1", "taxid": 381306, "species_taxid": 381306, "relation_to_type": "type", "validated": true, "ani": 76.7665, "matched_fragments": 104, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mangiferae", "strain": "strain=DMKU BBB3-04", "accession": "GCA_007109405.1", "taxid": 2593654, "species_taxid": 2593654, "relation_to_type": "type", "validated": true, "ani": 76.6777, "matched_fragments": 142, "total_fragments": 909, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_024169805.1", 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio", "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_000377405.1", "gtdb_species": "s__Thioalkalivibrio sp000377405", "ani": 81.7798, "matched_fragments": 540, "total_fragments": 909, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.79", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_000385215.1", "gtdb_species": "s__Thioalkalivibrio thiocyanoxidans", "ani": 81.717, "matched_fragments": 481, "total_fragments": 909, 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"filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.25, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Thioalkalivibrio", "halophilus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }