{ "type": "genome", "identifier": "GCA_001871085.1", "organism": "Desulfovibrionaceae bacterium CG1_02_65_16", "title": "Desulfovibrionaceae bacterium CG1_02_65_16", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Banfield Lab, University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_001871085.1", "bioproject": "PRJNA297582", "biosample": "SAMN04328205", "wgs_master": "MNUQ00000000.1", "refseq_category": "na", "taxid": "1805130", "species_taxid": "1805130", "organism_name": "Desulfovibrionaceae bacterium CG1_02_65_16", "infraspecific_name": "", "isolate": "CG1_02_65_16", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/09", "asm_name": "ASM187108v1", "submitter": "Banfield Lab, University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/871/085/GCA_001871085.1_ASM187108v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-09", "dateModified": "2016-11-09", "datePublished": "2016-11-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfovibrionaceae bacterium CG1_02_65_16" ], "sample_taxid": [ "1805130" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Crystal Geyser near Green River, Utah" ], "sample_host_location_id": [], "data_size": "0.826 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2970163", "Number of Sequences": "185", "Longest Sequences (bp)": "96737", "N50 (bp)": "20006", "Gap Ratio (%)": "0.039392", "GCcontent (%)": "65.3", "Number of CDSs": "2622", "Average Protein Length": "316.1", "Coding Ratio (%)": "83.7", "Number of rRNAs": "2", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudodesulfovibrio mercurii", "strain": "strain=ND132", "accession": "GCA_000189295.2", "taxid": 641491, "species_taxid": 641491, "relation_to_type": "type", "validated": true, "ani": 78.1, "matched_fragments": 252, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio hydrargyri", "strain": "strain=BerOc1", "accession": "GCA_001874525.1", "taxid": 2125990, "species_taxid": 2125990, "relation_to_type": "type", "validated": true, "ani": 77.9959, "matched_fragments": 240, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paucidesulfovibrio longus", "strain": "strain=DSM 6739", "accession": "GCA_000420485.1", "taxid": 889, "species_taxid": 889, "relation_to_type": "type", "validated": true, "ani": 77.8139, "matched_fragments": 229, "total_fragments": 897, "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": 77.6688, "matched_fragments": 234, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio indicus", "strain": "strain=J2", "accession": "GCA_001563225.1", "taxid": 1716143, "species_taxid": 1716143, "relation_to_type": "type", "validated": true, "ani": 77.6603, "matched_fragments": 238, "total_fragments": 897, "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": 77.6463, "matched_fragments": 190, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fundidesulfovibrio magnetotacticus", "strain": "strain=FSS-1", "accession": "GCA_013019105.1", "taxid": 2730080, "species_taxid": 2730080, "relation_to_type": "type", "validated": true, "ani": 77.6252, "matched_fragments": 268, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio indicus", "strain": "strain=DSM 101483", "accession": "GCA_004365595.1", "taxid": 1716143, "species_taxid": 1716143, "relation_to_type": "type", "validated": true, "ani": 77.5932, "matched_fragments": 244, "total_fragments": 897, "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": 77.4434, "matched_fragments": 226, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Solidesulfovibrio magneticus", "strain": "strain=RS-1", "accession": "GCA_000010665.1", "taxid": 184917, "species_taxid": 184917, "relation_to_type": "type", "validated": true, "ani": 77.3071, "matched_fragments": 216, "total_fragments": 897, "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": 77.1778, "matched_fragments": 219, "total_fragments": 897, "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": 77.1393, "matched_fragments": 175, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio alkaliphilus", "strain": "strain=F-1", "accession": "GCA_009729555.1", "taxid": 2661613, "species_taxid": 2661613, "relation_to_type": "type", "validated": true, "ani": 77.0793, "matched_fragments": 183, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfocurvibacter africanus subsp. africanus", "strain": "strain=DSM 2603", "accession": "GCA_000422545.1", "taxid": 1511600, "species_taxid": 873, "relation_to_type": "type", "validated": true, "ani": 77.0309, "matched_fragments": 165, "total_fragments": 897, "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": 76.899, "matched_fragments": 199, "total_fragments": 897, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_001871085.1", "gtdb_species": "s__Humidesulfovibrio sp001871085", "ani": 100.0, "matched_fragments": 886, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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": "GCA_016218665.1", "gtdb_species": "s__Humidesulfovibrio sp016218665", "ani": 83.7016, "matched_fragments": 535, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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": "GCA_002422505.1", "gtdb_species": "s__Humidesulfovibrio sp002422505", "ani": 82.6758, "matched_fragments": 551, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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_900188225.1", "gtdb_species": "s__Humidesulfovibrio mexicanus", "ani": 82.3403, "matched_fragments": 598, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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": "GCA_903843965.1", "gtdb_species": "s__Humidesulfovibrio sp903843965", "ani": 81.8426, "matched_fragments": 575, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.89", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCA_018822105.1", "gtdb_species": "s__Humidesulfovibrio sp018822105", "ani": 81.6078, "matched_fragments": 539, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018817515.1", "gtdb_species": "s__Humidesulfovibrio sp018817515", "ani": 81.5811, "matched_fragments": 551, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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": "GCA_002840405.1", "gtdb_species": "s__Humidesulfovibrio sp002840405", "ani": 81.5292, "matched_fragments": 590, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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": "GCA_001799475.1", "gtdb_species": "s__Humidesulfovibrio sp001799475", "ani": 81.4834, "matched_fragments": 474, "total_fragments": 897, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.253, "cell_length": 0.376, "doubling_h": 0.949, "growth_tmp": 32.532, "optimum_tmp": 33.615, "optimum_ph": 7.266, "genome_size": 3707445.329, "gc_content": 56.489, "coding_genes": 3149.942, "rRNA16S_genes": 3.258, "tRNA_genes": 59.3, "gram_stain": 0.0, "sporulation": 0.023, "motility": 0.933, "range_salinity": 0.5, "facultative_respiration": 0.02, "anaerobic_respiration": 0.98, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.952, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.047, "bacillus_cell_shape": 0.529, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.47, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Desulfovibrionia", "o__Desulfovibrionales", "f__Desulfovibrionaceae", "g__Humidesulfovibrio", "s__Humidesulfovibrio sp001871085" ], "_genome_taxon": [ "Desulfovibrionaceae", "bacterium", "CG1_02_65_16", "d__Bacteria", "p__Desulfobacterota", "c__Desulfovibrionia", "o__Desulfovibrionales", "f__Desulfovibrionaceae", "g__Humidesulfovibrio", "s__Humidesulfovibrio sp001871085", "Bacteria", "Desulfobacterota", "Desulfovibrionia", "Desulfovibrionales", "Desulfovibrionaceae", "Humidesulfovibrio", "Humidesulfovibrio", "sp001871085" ], "_meo": [ { "id": "MEO_0000366", "label": "ground water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }