{ "type": "genome", "identifier": "GCA_004562535.1", "organism": "bacterium", "title": "bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of Alberta", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004562535.1", "bioproject": "PRJNA494875", "biosample": "SAMN10183338", "wgs_master": "SFQN00000000.1", "refseq_category": "na", "taxid": "1869227", "species_taxid": "1869227", "organism_name": "bacterium", "infraspecific_name": "", "isolate": "W0P20.020", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/01", "asm_name": "ASM456253v1", "submitter": "University of Alberta", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/562/535/GCA_004562535.1_ASM456253v1", "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": "2019-04-01", "dateModified": "2019-04-01", "datePublished": "2019-04-01", "_annotation": { "sample_count": 1, "sample_organism": [ "bacterium" ], "sample_taxid": [ "1869227" ], "sample_host_organism": [ "Sus scrofa" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Edmonton" ], "sample_host_location_id": [], "data_size": "0.496 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 64.35, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1749183", "Number of Sequences": "196", "Longest Sequences (bp)": "53818", "N50 (bp)": "13581", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.3", "Number of CDSs": "1571", "Average Protein Length": "290.5", "Coding Ratio (%)": "78.3", "Number of rRNAs": "0", "Number of tRNAs": "30", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoflavonifractor gallinarum", "strain": "strain=DSM 107456", "accession": "GCA_014982855.1", "taxid": 2779352, "species_taxid": 2779352, "relation_to_type": "type", "validated": true, "ani": 79.3868, "matched_fragments": 65, "total_fragments": 478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dysosmobacter acutus", "strain": "strain=MSJ-2", "accession": "GCA_018919205.1", "taxid": 2841504, "species_taxid": 2841504, "relation_to_type": "type", "validated": true, "ani": 78.5225, "matched_fragments": 68, "total_fragments": 478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavonifractor plautii", "strain": "strain=JCM 32125", "accession": "GCA_010508875.1", "taxid": 292800, "species_taxid": 292800, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3001, "matched_fragments": 80, "total_fragments": 478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dysosmobacter welbionis", "strain": "strain=J115", "accession": "GCA_005121165.3", "taxid": 2093857, "species_taxid": 2093857, "relation_to_type": "type", "validated": true, "ani": 77.9429, "matched_fragments": 83, "total_fragments": 478, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 64.35, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_902778275.1", "gtdb_species": "s__Limivicinus sp902778275", "ani": 79.8401, "matched_fragments": 182, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_017470325.1", "gtdb_species": "s__Limivicinus sp017470325", "ani": 79.6666, "matched_fragments": 172, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_900316205.1", "gtdb_species": "s__Limivicinus sp900316205", "ani": 79.549, "matched_fragments": 164, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017428565.1", "gtdb_species": "s__Limivicinus sp017428565", "ani": 79.5359, "matched_fragments": 173, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902775985.1", "gtdb_species": "s__Limivicinus sp902775985", "ani": 79.4904, "matched_fragments": 171, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.76", "min_intra_species_af": "0.73", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_017545165.1", "gtdb_species": "s__Limivicinus sp017545165", "ani": 79.4745, "matched_fragments": 144, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902765595.1", "gtdb_species": "s__Limivicinus sp002350825", "ani": 79.4438, "matched_fragments": 180, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.80", "min_intra_species_ani": "99.80", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900316255.1", "gtdb_species": "s__Limivicinus sp900316255", "ani": 79.4413, "matched_fragments": 166, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.79", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_902786615.1", "gtdb_species": "s__Limivicinus sp902786615", "ani": 79.2643, "matched_fragments": 130, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_900319835.1", "gtdb_species": "s__Limivicinus sp900319835", "ani": 79.1368, "matched_fragments": 156, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902778285.1", "gtdb_species": "s__Limivicinus sp902778285", "ani": 79.029, "matched_fragments": 167, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.79", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902791215.1", "gtdb_species": "s__Limivicinus sp902791215", "ani": 79.0251, "matched_fragments": 134, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902793285.1", "gtdb_species": "s__Limivicinus sp902793285", "ani": 78.8381, "matched_fragments": 125, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.34", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017477695.1", "gtdb_species": "s__Limivicinus sp017477695", "ani": 78.8105, "matched_fragments": 134, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902785905.1", "gtdb_species": "s__Limivicinus sp902785905", "ani": 78.8, "matched_fragments": 127, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_902761635.1", "gtdb_species": "s__Limivicinus sp902761635", "ani": 78.683, "matched_fragments": 128, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_900549645.1", "gtdb_species": "s__Limivicinus sp900549645", "ani": 78.5138, "matched_fragments": 136, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.52", "min_intra_species_ani": "99.05", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_902789745.1", "gtdb_species": "s__Limivicinus sp902789745", "ani": 78.4155, "matched_fragments": 123, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "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_900547315.1", "gtdb_species": "s__Limivicinus sp900547315", "ani": 78.3599, "matched_fragments": 142, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003150355.1", "gtdb_species": "s__Limivicinus sp003150355", "ani": 78.3509, "matched_fragments": 114, "total_fragments": 478, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.34", "min_intra_species_ani": "96.94", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.68", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Oscillospiraceae", "g__Limivicinus", "s__" ], "_genome_taxon": [ "bacterium", "d__Bacteria", "p__Bacillota_A", "c__Clostridia", "o__Oscillospirales", "f__Oscillospiraceae", "g__Limivicinus", "s__", "Bacteria", "Bacillota", "A", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Limivicinus", "s", "", "" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }