{ "type": "genome", "identifier": "GCA_022841035.1", "organism": "Desulfovibrio sp.", "title": "Desulfovibrio sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "Colorado State University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022841035.1", "bioproject": "PRJNA818325", "biosample": "SAMN26856667", "wgs_master": "JALHCW000000000.1", "refseq_category": "na", "taxid": "885", "species_taxid": "885", "organism_name": "Desulfovibrio sp.", "infraspecific_name": "", "isolate": "1-no_shock_S1_016", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/08", "asm_name": "ASM2284103v1", "submitter": "Colorado State University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/841/035/GCA_022841035.1_ASM2284103v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-08", "dateModified": "2022-04-08", "datePublished": "2022-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfovibrio sp." ], "sample_taxid": [ "885" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.879 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 67.56, "contamination": 4.69, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3188319", "Number of Sequences": "950", "Longest Sequences (bp)": "26395", "N50 (bp)": "4286", "Gap Ratio (%)": "0.126117", "GCcontent (%)": "68.4", "Number of CDSs": "2018", "Average Protein Length": "285.0", "Coding Ratio (%)": "54.1", "Number of rRNAs": "5", "Number of tRNAs": "43", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cupidesulfovibrio termitidis", "strain": "strain=HI1", "accession": "GCA_000504305.1", "taxid": 42252, "species_taxid": 42252, "relation_to_type": "type", "validated": true, "ani": 90.8678, "matched_fragments": 508, "total_fragments": 567, "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": 90.0976, "matched_fragments": 427, "total_fragments": 567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupidesulfovibrio oxamicus", "strain": "strain=NCIMB 9442", "accession": "GCA_015731765.1", "taxid": 32016, "species_taxid": 32016, "relation_to_type": "type", "validated": true, "ani": 89.5963, "matched_fragments": 418, "total_fragments": 567, "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": 78.8189, "matched_fragments": 226, "total_fragments": 567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio vulgaris", "strain": "strain=Hildenborough", "accession": "GCA_902167245.1", "taxid": 881, "species_taxid": 881, "relation_to_type": "type", "validated": true, "ani": 78.6661, "matched_fragments": 227, "total_fragments": 567, "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": 77.9533, "matched_fragments": 111, "total_fragments": 567, "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": 76.8688, "matched_fragments": 128, "total_fragments": 567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Megalodesulfovibrio gigas", "strain": "strain=ATCC 19364", "accession": "GCA_000468495.1", "taxid": 879, "species_taxid": 879, "relation_to_type": "type", "validated": true, "ani": 76.8379, "matched_fragments": 131, "total_fragments": 567, "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": 76.8236, "matched_fragments": 75, "total_fragments": 567, "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": 76.7963, "matched_fragments": 113, "total_fragments": 567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Solidesulfovibrio carbinolicus", "strain": "strain=DSM 3852", "accession": "GCA_004135975.1", "taxid": 296842, "species_taxid": 296842, "relation_to_type": "type", "validated": true, "ani": 76.3665, "matched_fragments": 126, "total_fragments": 567, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 67.56, "contamination": 4.69, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_000021385.1", "gtdb_species": "s__Cupidesulfovibrio vulgaris_A", "ani": 90.9565, "matched_fragments": 496, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.08", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000226255.1", "gtdb_species": "s__Cupidesulfovibrio sp000226255", "ani": 90.9375, "matched_fragments": 502, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000504305.1", "gtdb_species": "s__Cupidesulfovibrio termitidis", "ani": 90.8948, "matched_fragments": 507, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "98.21", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011682075.1", "gtdb_species": "s__Cupidesulfovibrio liaohensis", "ani": 90.1284, "matched_fragments": 426, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio", "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_015731765.1", "gtdb_species": "s__Cupidesulfovibrio oxamicus", "ani": 89.5133, "matched_fragments": 422, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio", "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_000195755.1", "gtdb_species": "s__Nitratidesulfovibrio vulgaris", "ani": 78.7927, "matched_fragments": 226, "total_fragments": 567, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Nitratidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.25", "min_intra_species_ani": "98.85", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.259, "cell_length": 0.375, "doubling_h": 1.142, "growth_tmp": 32.446, "optimum_tmp": 33.065, "optimum_ph": 7.283, "genome_size": 3735623.274, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfovibrionia", "o__Desulfovibrionales", "f__Desulfovibrionaceae", "g__Cupidesulfovibrio", "s__Cupidesulfovibrio sp022837365" ], "_genome_taxon": [ "Desulfovibrio", "sp.", "d__Bacteria", "p__Desulfobacterota", "c__Desulfovibrionia", "o__Desulfovibrionales", "f__Desulfovibrionaceae", "g__Cupidesulfovibrio", "s__Cupidesulfovibrio sp022837365", "Bacteria", "Desulfobacterota", "Desulfovibrionia", "Desulfovibrionales", "Desulfovibrionaceae", "Cupidesulfovibrio", "Cupidesulfovibrio", "sp022837365" ], "_meo": [ { "id": "MEO_0001192", "label": "anaerobic digester" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }