{ "type": "genome", "identifier": "GCF_004309735.1", "organism": "Desulfovibrio legallii", "title": "Desulfovibrio legallii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "LMBA", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004309735.1", "bioproject": "PRJNA224116", "biosample": "SAMN10320870", "wgs_master": "SIXC00000000.1", "refseq_category": "reference genome", "taxid": "571438", "species_taxid": "571438", "organism_name": "Desulfovibrio legallii", "infraspecific_name": "strain=H1T", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/27", "asm_name": "ASM430973v1", "asm_submitter": "LMBA", "gbrs_paired_asm": "GCA_004309735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/309/735/GCF_004309735.1_ASM430973v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2675015", "genome_size_ungapped": "2675015", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004309735.1-RS_2024_04_10", "annotation_date": "2024-04-10", "total_gene_count": "2325", "protein_coding_gene_count": "2256", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-27", "dateModified": "2019-02-27", "datePublished": "2019-02-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfovibrio legallii" ], "sample_taxid": [ "571438" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tunisia: Tunis" ], "sample_host_location_id": [], "data_size": "0.742 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)": "2675015", "Number of Sequences": "35", "Longest Sequences (bp)": "310558", "N50 (bp)": "220888", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.9", "Number of CDSs": "2251", "Average Protein Length": "340.0", "Coding Ratio (%)": "85.8", "Number of rRNAs": "6", "Number of tRNAs": "49", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfovibrio legallii", "strain": "strain=H1T", "accession": "GCA_004309735.1", "taxid": 571438, "species_taxid": 571438, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 875, "total_fragments": 875, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfovibrio porci", "strain": "strain=PG-178-WT-4", "accession": "GCA_009696265.1", "taxid": 2605782, "species_taxid": 2605782, "relation_to_type": "type", "validated": true, "ani": 80.2624, "matched_fragments": 473, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio piger", "strain": "strain=ATCC 29098", "accession": "GCA_000156375.1", "taxid": 901, "species_taxid": 901, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0409, "matched_fragments": 336, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio intestinalis", "strain": "strain=DSM 11275", "accession": "GCA_014202345.1", "taxid": 58621, "species_taxid": 58621, "relation_to_type": "type", "validated": true, "ani": 78.8152, "matched_fragments": 357, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupidesulfovibrio liaohensis", "strain": "strain=XJ01", "accession": "GCA_011682075.1", "taxid": 2604158, "species_taxid": 2604158, "relation_to_type": "type", "validated": true, "ani": 77.38, "matched_fragments": 185, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupidesulfovibrio termitidis", "strain": "strain=HI1", "accession": "GCA_000504305.1", "taxid": 42252, "species_taxid": 42252, "relation_to_type": "type", "validated": true, "ani": 77.1072, "matched_fragments": 222, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mailhella massiliensis", "strain": "strain=Marseille-P3199", "accession": "GCA_900155525.1", "taxid": 1903261, "species_taxid": 1903261, "relation_to_type": "type", "validated": true, "ani": 77.0877, "matched_fragments": 115, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Megalodesulfovibrio gigas", "strain": "strain=DSM 1382", "accession": "GCA_000429285.1", "taxid": 879, "species_taxid": 879, "relation_to_type": "type", "validated": true, "ani": 76.871, "matched_fragments": 126, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bilophila wadsworthia", "strain": "strain=ATCC 49260", "accession": "GCA_000701705.1", "taxid": 35833, "species_taxid": 35833, "relation_to_type": "type", "validated": true, "ani": 76.3442, "matched_fragments": 96, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004309735.1", "gtdb_species": "s__Desulfovibrio legallii", "ani": 100.0, "matched_fragments": 875, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_900102485.1", "gtdb_species": "s__Desulfovibrio legallii_A", "ani": 87.1657, "matched_fragments": 724, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.86", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009696265.1", "gtdb_species": "s__Desulfovibrio porci", "ani": 80.2701, "matched_fragments": 471, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.64", "min_intra_species_ani": "99.64", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_015062205.1", "gtdb_species": "s__Desulfovibrio desulfuricans_D", "ani": 80.0989, "matched_fragments": 415, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "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_001553605.1", "gtdb_species": "s__Desulfovibrio fairfieldensis", "ani": 80.0283, "matched_fragments": 493, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.09", "min_intra_species_ani": "95.23", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_910575755.1", "gtdb_species": "s__Desulfovibrio sp910575755", "ani": 79.6243, "matched_fragments": 417, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "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_004801255.1", "gtdb_species": "s__Desulfovibrio desulfuricans_C", "ani": 79.4866, "matched_fragments": 494, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "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_000420465.1", "gtdb_species": "s__Desulfovibrio desulfuricans", "ani": 79.2685, "matched_fragments": 452, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.33", "min_intra_species_ani": "95.61", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_009712225.1", "gtdb_species": "s__Desulfovibrio sp009712225", "ani": 79.262, "matched_fragments": 431, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "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_011039085.1", "gtdb_species": "s__Desulfovibrio sp011039085", "ani": 79.2252, "matched_fragments": 372, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900116045.1", "gtdb_species": "s__Desulfovibrio piger_A", "ani": 79.0905, "matched_fragments": 351, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.95", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000022125.1", "gtdb_species": "s__Desulfovibrio desulfuricans_A", "ani": 78.929, "matched_fragments": 379, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.36", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.259, "cell_length": 0.375, "doubling_h": 1.142, "growth_tmp": 35.0, "optimum_tmp": 33.065, "optimum_ph": 7.283, "genome_size": 2704428.0, "gc_content": 57.077, "coding_genes": 3187.904, "rRNA16S_genes": 3.788, "tRNA_genes": 62.766, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.947, "range_salinity": 0.5, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.937, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.062, "bacillus_cell_shape": 0.464, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.535, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Desulfovibrio", "legallii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }