{ "type": "genome", "identifier": "GCA_902782015.1", "organism": "uncultured Desulfovibrio sp.", "title": "uncultured Desulfovibrio sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902782015.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6150867", "wgs_master": "CACZLO000000000.1", "refseq_category": "na", "taxid": "167968", "species_taxid": "167968", "organism_name": "uncultured Desulfovibrio sp.", "infraspecific_name": "", "isolate": "RUG12731", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/15", "asm_name": "Rumen uncultured genome RUG12731", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/782/015/GCA_902782015.1_Rumen_uncultured_genome_RUG12731", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-15", "dateModified": "2020-02-15", "datePublished": "2020-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Desulfovibrio sp." ], "sample_taxid": [ "167968" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "0.599 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 79.17, "contamination": 0.52, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2106514", "Number of Sequences": "253", "Longest Sequences (bp)": "96573", "N50 (bp)": "11727", "Gap Ratio (%)": "0.039639", "GCcontent (%)": "59.0", "Number of CDSs": "1720", "Average Protein Length": "305.4", "Coding Ratio (%)": "74.8", "Number of rRNAs": "1", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 77.7264, "matched_fragments": 128, "total_fragments": 577, "ani_threshold": 95, "status": "below_threshold" }, { "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": 76.9647, "matched_fragments": 111, "total_fragments": 577, "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": 76.7893, "matched_fragments": 55, "total_fragments": 577, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio legallii", "strain": "strain=H1T", "accession": "GCA_004309735.1", "taxid": 571438, "species_taxid": 571438, "relation_to_type": "type", "validated": true, "ani": 76.7364, "matched_fragments": 88, "total_fragments": 577, "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": 76.5193, "matched_fragments": 58, "total_fragments": 577, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.17, "contamination": 0.52, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900319575.1", "gtdb_species": "s__Desulfovibrio sp900319575", "ani": 98.1549, "matched_fragments": 448, "total_fragments": 577, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.78", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCA_900546145.1", "gtdb_species": "s__Desulfovibrio sp900546145", "ani": 94.7231, "matched_fragments": 536, "total_fragments": 577, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002369295.1", "gtdb_species": "s__Desulfovibrio sp002369295", "ani": 78.9611, "matched_fragments": 196, "total_fragments": 577, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016284885.1", "gtdb_species": "s__Desulfovibrio sp016284885", "ani": 78.7544, "matched_fragments": 203, "total_fragments": 577, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.92", 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"min_intra_species_ani": "98.09", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_900116045.1", "gtdb_species": "s__Desulfovibrio piger_A", "ani": 77.5099, "matched_fragments": 139, "total_fragments": 577, "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": "GCA_019118745.1", "gtdb_species": "s__Desulfovibrio gallistercoris", "ani": 77.3382, "matched_fragments": 106, "total_fragments": 577, "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", 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"min_intra_species_ani": "95.23", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "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", 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