{ "type": "genome", "identifier": "GCA_028708865.1", "organism": "Desulfovibrio sp.", "title": "Desulfovibrio sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Waterloo", "publication": [ {} ], "properties": { "assembly_accession": "GCA_028708865.1", "bioproject": "PRJNA900590", "biosample": "SAMN32737529", "wgs_master": "JAQVYA000000000.1", "refseq_category": "na", "taxid": "885", "species_taxid": "885", "organism_name": "Desulfovibrio sp.", "infraspecific_name": "", "isolate": "STF2_139", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/02/18", "asm_name": "ASM2870886v1", "submitter": "University of Waterloo", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/708/865/GCA_028708865.1_ASM2870886v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-02-18", "dateModified": "2023-02-18", "datePublished": "2023-02-18", "_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": [ "USA" ], "sample_host_location_id": [], "data_size": "0.890 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3131501", "Number of Sequences": "226", "Longest Sequences (bp)": "82792", "N50 (bp)": "18536", "Gap Ratio (%)": "0.000639", "GCcontent (%)": "60.3", "Number of CDSs": "2670", "Average Protein Length": "314.4", "Coding Ratio (%)": "80.4", "Number of rRNAs": "0", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paucidesulfovibrio gracilis", "strain": "strain=DSM 16080", "accession": "GCA_900167125.1", "taxid": 47158, "species_taxid": 47158, "relation_to_type": "type", "validated": true, "ani": 81.4725, "matched_fragments": 556, "total_fragments": 924, "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": 80.3509, "matched_fragments": 544, "total_fragments": 924, "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": 77.6072, "matched_fragments": 202, "total_fragments": 924, "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": 77.4703, "matched_fragments": 202, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio tunisiensis", "strain": "strain=RB22", "accession": "GCA_022809775.1", "taxid": 463192, "species_taxid": 463192, "relation_to_type": "type", "validated": true, "ani": 77.124, "matched_fragments": 191, "total_fragments": 924, "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": 77.0526, "matched_fragments": 165, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonatronum thiodismutans", "strain": "strain=MLF-1", "accession": "GCA_000717475.2", "taxid": 159290, "species_taxid": 159290, "relation_to_type": "type", "validated": true, "ani": 76.416, "matched_fragments": 80, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio sulfodismutans", "strain": "strain=DSM 3696", "accession": "GCA_013376455.1", "taxid": 63561, "species_taxid": 63561, "relation_to_type": "type", "validated": true, "ani": 76.3716, "matched_fragments": 122, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio sulfodismutans", "strain": "strain=DSM 3696", "accession": "GCA_010499425.1", "taxid": 63561, "species_taxid": 63561, "relation_to_type": "type", "validated": true, "ani": 76.3462, "matched_fragments": 120, "total_fragments": 924, "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": 76.3129, "matched_fragments": 106, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonatronum lacustre", "strain": "strain=DSM 10312", "accession": "GCA_000519265.1", "taxid": 66849, "species_taxid": 66849, "relation_to_type": "type", "validated": true, "ani": 76.2812, "matched_fragments": 80, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonatronum thiosulfatophilum", "strain": "strain=ASO4-2", "accession": "GCA_900104215.1", "taxid": 617002, "species_taxid": 617002, "relation_to_type": "type", "validated": true, "ani": 75.5243, "matched_fragments": 54, "total_fragments": 924, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_900167125.1", "gtdb_species": "s__Paucidesulfovibrio gracilis", "ani": 81.4762, "matched_fragments": 556, "total_fragments": 924, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio", "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_000420485.1", "gtdb_species": "s__Paucidesulfovibrio longus", "ani": 80.3753, "matched_fragments": 543, "total_fragments": 924, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio", "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_008001235.1", "gtdb_species": "s__Pseudodesulfovibrio sp008001235", "ani": 77.6332, "matched_fragments": 214, "total_fragments": 924, "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": "-" }, { "accession": "GCF_001874525.1", "gtdb_species": "s__Pseudodesulfovibrio hydrargyri", "ani": 77.607, "matched_fragments": 202, "total_fragments": 924, "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": "-" }, { "accession": "GCF_008830225.1", "gtdb_species": "s__Pseudodesulfovibrio senegalensis", "ani": 77.5461, "matched_fragments": 184, "total_fragments": 924, "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": "-" }, { "accession": "GCF_000189295.2", "gtdb_species": "s__Pseudodesulfovibrio mercurii", "ani": 77.4555, "matched_fragments": 203, "total_fragments": 924, "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": "-" }, { "accession": "GCF_000176915.2", "gtdb_species": "s__Pseudodesulfovibrio aespoeensis", "ani": 77.4005, "matched_fragments": 180, "total_fragments": 924, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.94", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.98", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_002840405.1", "gtdb_species": "s__Humidesulfovibrio sp002840405", "ani": 77.3812, "matched_fragments": 143, "total_fragments": 924, "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_002382645.1", "gtdb_species": "s__Aminidesulfovibrio sp002382645", "ani": 77.341, "matched_fragments": 185, "total_fragments": 924, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Aminidesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000422565.1", "gtdb_species": "s__Aminidesulfovibrio aminophilus", "ani": 77.2711, "matched_fragments": 204, 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