{ "type": "genome", "identifier": "GCA_018433465.1", "organism": "Synergistaceae bacterium", "title": "Synergistaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018433465.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056170", "wgs_master": "JAHDRE000000000.1", "refseq_category": "na", "taxid": "2053624", "species_taxid": "2053624", "organism_name": "Synergistaceae bacterium", "infraspecific_name": "", "isolate": "SV1-B4.2", "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/018/433/465/GCA_018433465.1_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": [ "Synergistaceae bacterium" ], "sample_taxid": [ "2053624" ], "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": "0.980 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 2.6, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3462964", "Number of Sequences": "388", "Longest Sequences (bp)": "67893", "N50 (bp)": "13060", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.2", "Number of CDSs": "2792", "Average Protein Length": "321.5", "Coding Ratio (%)": "77.8", "Number of rRNAs": "1", "Number of tRNAs": "41", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Aminivibrio pyruvatiphilus", "strain": "strain=DSM 25964", "accession": "GCA_004366815.1", "taxid": 1005740, "species_taxid": 1005740, "relation_to_type": "type", "validated": true, "ani": 77.6392, "matched_fragments": 240, "total_fragments": 962, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 2.6, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_018436725.1", "gtdb_species": "s__JAAYLU01 sp018436725", "ani": 98.7626, "matched_fragments": 922, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_001604435.1", "gtdb_species": "s__JAAYLU01 sp001604435", "ani": 86.0617, "matched_fragments": 406, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01", "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_018436785.1", "gtdb_species": "s__JAAYLU01 sp018436785", "ani": 84.0828, "matched_fragments": 545, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01", "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_018436595.1", "gtdb_species": "s__Aminivibrio sp009929115", "ani": 78.0632, "matched_fragments": 205, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016756745.1", "gtdb_species": "s__Aminivibrio sp016756745", "ani": 77.9982, "matched_fragments": 189, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio", "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_002068355.1", "gtdb_species": "s__JAAYLU01 sp002068355", "ani": 77.8805, "matched_fragments": 158, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01", "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_004366815.1", "gtdb_species": "s__Aminivibrio pyruvatiphilus", "ani": 77.6348, "matched_fragments": 241, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012521675.1", "gtdb_species": "s__JAAYLU01 sp012521675", "ani": 77.1083, "matched_fragments": 149, "total_fragments": 962, "gtdb_taxonomy": "d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01", "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": -0.247, "cell_length": 0.407, "doubling_h": 0.859, "growth_tmp": 40.447, "optimum_tmp": 43.453, "optimum_ph": 6.983, "genome_size": 2474287.488, "gc_content": 54.082, "coding_genes": 2007.472, "rRNA16S_genes": 3.2, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.687, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.714, "thermophilic_range_tmp": 0.285, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.846, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.076, "vibrio_cell_shape": 0.076, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Synergistota", "c__Synergistia", "o__Synergistales", "f__Aminobacteriaceae", "g__JAAYLU01", "s__JAAYLU01 sp018436725" ], "_genome_taxon": [ "Synergistaceae", "bacterium", "d__Bacteria", "p__Synergistota", "c__Synergistia", "o__Synergistales", "f__Aminobacteriaceae", "g__JAAYLU01", "s__JAAYLU01 sp018436725", "Bacteria", "Synergistota", "Synergistia", "Synergistales", "Aminobacteriaceae", "JAAYLU01", "JAAYLU01", "sp018436725" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }