{ "type": "genome", "identifier": "GCA_018433535.1", "organism": "Syntrophaceae bacterium", "title": "Syntrophaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018433535.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056168", "wgs_master": "JAHDRC000000000.1", "refseq_category": "na", "taxid": "2052184", "species_taxid": "2052184", "organism_name": "Syntrophaceae bacterium", "infraspecific_name": "", "isolate": "SV1-B3.4", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/21", "asm_name": "SV1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/433/535/GCA_018433535.1_SV1", "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": "2021-05-21", "dateModified": "2021-05-21", "datePublished": "2021-05-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Syntrophaceae bacterium" ], "sample_taxid": [ "2052184" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Redwood City, CA" ], "sample_host_location_id": [], "data_size": "1.170 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "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)": "4145731", "Number of Sequences": "78", "Longest Sequences (bp)": "332941", "N50 (bp)": "115056", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.8", "Number of CDSs": "3734", "Average Protein Length": "329.0", "Coding Ratio (%)": "88.9", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002304995.1", "gtdb_species": "s__UBA8904 sp002304995", "ani": 98.9942, "matched_fragments": 1035, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCA_012729055.1", "gtdb_species": "s__UBA8904 sp012729055", "ani": 91.5952, "matched_fragments": 971, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012797505.1", "gtdb_species": "s__UBA8904 sp012797505", "ani": 80.4417, "matched_fragments": 387, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_012510495.1", "gtdb_species": "s__UBA8904 sp012510495", "ani": 79.6432, "matched_fragments": 363, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "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_003506745.1", "gtdb_species": "s__UBA8904 sp003506745", "ani": 79.0311, "matched_fragments": 227, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.70", "min_intra_species_af": "0.68", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018436925.1", "gtdb_species": "s__UBA8904 sp018436925", "ani": 78.8731, "matched_fragments": 368, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "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_009668925.1", "gtdb_species": "s__UBA8904 sp009668925", "ani": 78.485, "matched_fragments": 398, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "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_002840435.1", "gtdb_species": "s__UBA8904 sp002840435", "ani": 78.3573, "matched_fragments": 385, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "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_002382045.1", "gtdb_species": "s__UBA8904 sp002382045", "ani": 78.2067, "matched_fragments": 310, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "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_002070455.1", "gtdb_species": "s__UBA8904 sp002070455", "ani": 77.976, "matched_fragments": 213, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017860985.1", "gtdb_species": "s__UBA8904 sp017860985", "ani": 77.4007, "matched_fragments": 160, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904", "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_018056685.1", "gtdb_species": "s__Smithella sp018056685", "ani": 77.2235, "matched_fragments": 122, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella", "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_011046295.1", "gtdb_species": "s__UBA4810 sp011046295", "ani": 76.977, "matched_fragments": 86, "total_fragments": 1341, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA4810", "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": -0.094, "cell_length": 0.377, "doubling_h": 1.431, "growth_tmp": 35.0, "optimum_tmp": 34.722, "optimum_ph": 7.149, "genome_size": 4176389.15, "gc_content": 50.41, "coding_genes": 3784.666, "rRNA16S_genes": 1.0, "tRNA_genes": 48.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.333, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Desulfobacterota", "c__Syntrophia", "o__Syntrophales", "f__Smithellaceae", "g__UBA8904", "s__UBA8904 sp002304995" ], "_genome_taxon": [ "Syntrophaceae", "bacterium", "d__Bacteria", "p__Desulfobacterota", "c__Syntrophia", "o__Syntrophales", "f__Smithellaceae", "g__UBA8904", "s__UBA8904 sp002304995", "Bacteria", "Desulfobacterota", "Syntrophia", "Syntrophales", "Smithellaceae", "UBA8904", "UBA8904", "sp002304995" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }