{ "type": "genome", "identifier": "GCF_000420465.1", "organism": "Desulfovibrio desulfuricans DSM 642", "title": "Desulfovibrio desulfuricans DSM 642", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000420465.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440572", "wgs_master": "ATUZ00000000.1", "refseq_category": "na", "taxid": "1121445", "species_taxid": "876", "organism_name": "Desulfovibrio desulfuricans DSM 642", "infraspecific_name": "strain=DSM 642", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/09", "asm_name": "ASM42046v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000420465.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/420/465/GCF_000420465.1_ASM42046v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3391683", "genome_size_ungapped": "3391683", "gc_percent": "57.500000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000420465.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "2916", "protein_coding_gene_count": "2839", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-09", "dateModified": "2013-07-09", "datePublished": "2013-07-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfovibrio desulfuricans DSM 642" ], "sample_taxid": [ "1121445" ], "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": "0.955 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)": "3391683", "Number of Sequences": "20", "Longest Sequences (bp)": "835434", "N50 (bp)": "378826", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.4", "Number of CDSs": "2894", "Average Protein Length": "337.7", "Coding Ratio (%)": "86.4", "Number of rRNAs": "4", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfovibrio intestinalis", "strain": "strain=DSM 11275", "accession": "GCA_014202345.1", "taxid": 58621, "species_taxid": 58621, "relation_to_type": "type", "validated": true, "ani": 79.6295, "matched_fragments": 443, "total_fragments": 1120, "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": 79.296, "matched_fragments": 423, "total_fragments": 1120, "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": 79.1831, "matched_fragments": 433, "total_fragments": 1120, "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": 78.8799, "matched_fragments": 292, "total_fragments": 1120, "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": 77.8774, "matched_fragments": 159, "total_fragments": 1120, "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": 77.331, "matched_fragments": 184, "total_fragments": 1120, "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": 77.0695, "matched_fragments": 103, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio subterraneus", "strain": "strain=HN2", "accession": "GCA_013340285.1", "taxid": 2718620, "species_taxid": 2718620, "relation_to_type": "type", "validated": true, "ani": 76.6703, "matched_fragments": 104, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000420465.1", "gtdb_species": "s__Desulfovibrio desulfuricans", "ani": 100.0, "matched_fragments": 1120, "total_fragments": 1120, "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": "conclusive" }, { "accession": "GCA_003251995.1", "gtdb_species": "s__Desulfovibrio desulfuricans_B", "ani": 86.0563, "matched_fragments": 422, "total_fragments": 1120, "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": "GCA_009929215.1", "gtdb_species": "s__Desulfovibrio sp009929215", "ani": 85.0625, "matched_fragments": 768, "total_fragments": 1120, "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": 85.0559, "matched_fragments": 828, "total_fragments": 1120, "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": "GCA_009712225.1", "gtdb_species": "s__Desulfovibrio sp009712225", "ani": 84.8912, "matched_fragments": 859, "total_fragments": 1120, "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": "GCA_002237645.1", "gtdb_species": "s__Desulfovibrio sp002237645", "ani": 79.9113, "matched_fragments": 500, "total_fragments": 1120, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.259, "cell_length": 0.375, "doubling_h": 1.142, "growth_tmp": 31.0, "optimum_tmp": 32.333, "optimum_ph": 7.283, "genome_size": 3335420.308, "gc_content": 60.8, "coding_genes": 2902.167, "rRNA16S_genes": 2.5, "tRNA_genes": 53.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.5, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Desulfovibrio", "desulfuricans", "DSM", "642" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }