{ "type": "genome", "identifier": "GCF_008830225.1", "organism": "Pseudodesulfovibrio senegalensis", "title": "Pseudodesulfovibrio senegalensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea Institute of Ocean Science & Technology (KIOST)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008830225.1", "bioproject": "PRJNA224116", "biosample": "SAMN12871449", "wgs_master": "WAIE00000000.1", "refseq_category": "reference genome", "taxid": "1721087", "species_taxid": "1721087", "organism_name": "Pseudodesulfovibrio senegalensis", "infraspecific_name": "strain=DSM 101509", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/10/05", "asm_name": "ASM883022v1", "asm_submitter": "Korea Institute of Ocean Science & Technology (KIOST)", "gbrs_paired_asm": "GCA_008830225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/830/225/GCF_008830225.1_ASM883022v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3365778", "genome_size_ungapped": "3365778", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "16", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008830225.1-RS_2024_04_03", "annotation_date": "2024-04-03", "total_gene_count": "3164", "protein_coding_gene_count": "3097", "non_coding_gene_count": "62", "pubmed_id": "28867000" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-10-05", "dateModified": "2019-10-05", "datePublished": "2019-10-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudodesulfovibrio senegalensis" ], "sample_taxid": [ "1721087" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Senegal: Hann Bay" ], "sample_host_location_id": [], "data_size": "0.944 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)": "3365778", "Number of Sequences": "16", "Longest Sequences (bp)": "1320837", "N50 (bp)": "436221", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.1", "Number of CDSs": "3124", "Average Protein Length": "321.3", "Coding Ratio (%)": "89.5", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudodesulfovibrio tunisiensis", "strain": "strain=RB22", "accession": "GCA_022809775.1", "taxid": 463192, "species_taxid": 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"validated": true, "ani": 78.5179, "matched_fragments": 357, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio cashew", "strain": "strain=SRB007", "accession": "GCA_009762795.1", "taxid": 2678688, "species_taxid": 2678688, "relation_to_type": "type", "validated": true, "ani": 78.4406, "matched_fragments": 306, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio mercurii", "strain": "strain=ND132", "accession": "GCA_000189295.2", "taxid": 641491, "species_taxid": 641491, "relation_to_type": "type", "validated": true, "ani": 78.3386, "matched_fragments": 345, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio aespoeensis", "strain": "strain=Aspo-2", "accession": "GCA_000176915.2", "taxid": 182210, "species_taxid": 182210, "relation_to_type": "type", "validated": true, "ani": 78.2126, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio profundus", "strain": "strain=500-1", "accession": "GCA_900217235.1", "taxid": 57320, "species_taxid": 57320, "relation_to_type": "type", "validated": true, "ani": 77.2831, "matched_fragments": 170, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fundidesulfovibrio putealis", "strain": "strain=DSM 16056", "accession": "GCA_000429325.1", "taxid": 270496, "species_taxid": 270496, "relation_to_type": "type", "validated": true, "ani": 77.0201, "matched_fragments": 148, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio vulgaris", "strain": "strain=Hildenborough", "accession": "GCA_000195755.1", "taxid": 881, "species_taxid": 881, "relation_to_type": "type", "validated": true, "ani": 76.6499, "matched_fragments": 104, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio carbinoliphilus subsp. oakridgensis", "strain": "strain=FW-101-2B", "accession": "GCA_000177215.2", "taxid": 694327, "species_taxid": 345370, "relation_to_type": "type", "validated": true, "ani": 76.4244, "matched_fragments": 138, "total_fragments": 1114, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008830225.1", "gtdb_species": "s__Pseudodesulfovibrio senegalensis", "ani": 100.0, "matched_fragments": 1113, "total_fragments": 1114, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "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_008001235.1", 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"num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": -0.398, "growth_tmp": 29.75, "optimum_tmp": 29.167, "optimum_ph": 7.4, "genome_size": 3864922.362, "gc_content": 59.638, "coding_genes": 3485.083, "rRNA16S_genes": 1.5, "tRNA_genes": 54.333, "gram_stain": 0.0, "sporulation": 0.5, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Pseudodesulfovibrio", "senegalensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }