{ "type": "genome", "identifier": "GCA_934643575.1", "organism": "uncultured Collinsella sp.", "title": "uncultured Collinsella sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "stanford university school of medicine", "publication": [ {} ], "properties": { "assembly_accession": "GCA_934643575.1", "bioproject": "PRJEB49206", "biosample": "SAMEA13491714", "wgs_master": "CAKUBX000000000.1", "refseq_category": "na", "taxid": "165190", "species_taxid": "165190", "organism_name": "uncultured Collinsella sp.", "infraspecific_name": "", "isolate": "REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_H_4_2261.30", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/16", "asm_name": "ERR7745561_bin.30", "submitter": "stanford university school of medicine", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/934/643/575/GCA_934643575.1_ERR7745561_bin.30", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-04-16", "dateModified": "2022-04-16", "datePublished": "2022-04-16", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Collinsella sp." ], "sample_taxid": [ "165190" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tanzania" ], "sample_host_location_id": [], "data_size": "0.669 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2339763", "Number of Sequences": "35", "Longest Sequences (bp)": "213146", "N50 (bp)": "105882", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.5", "Number of CDSs": "2082", "Average Protein Length": "322.5", "Coding Ratio (%)": "86.1", "Number of rRNAs": "0", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Collinsella aerofaciens", "strain": "strain=ATCC 25986", "accession": "GCA_000169035.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 91.4409, "matched_fragments": 557, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella aerofaciens", "strain": "strain=NCTC11838", "accession": "GCA_900461335.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 91.4335, "matched_fragments": 561, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella aerofaciens", "strain": "strain=JCM 10188", "accession": "GCA_010509075.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 91.4128, "matched_fragments": 558, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella bouchesdurhonensis", "strain": "strain=Marseille-P3296", "accession": "GCA_900155365.1", "taxid": 1907654, "species_taxid": 1907654, "relation_to_type": "type", "validated": true, "ani": 80.6638, "matched_fragments": 227, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella stercoris", "strain": "strain=DSM 13279", "accession": "GCA_000156215.1", "taxid": 147206, "species_taxid": 147206, "relation_to_type": "type", "validated": true, "ani": 79.7795, "matched_fragments": 266, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella stercoris", "strain": "strain=DSM 13279", "accession": "GCA_025149625.1", "taxid": 147206, "species_taxid": 147206, "relation_to_type": "type", "validated": true, "ani": 79.7362, "matched_fragments": 273, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella phocaeensis", "strain": "strain=Marseille-P3245", "accession": "GCA_900119895.1", "taxid": 1871016, "species_taxid": 1871016, "relation_to_type": "type", "validated": true, "ani": 79.6459, "matched_fragments": 242, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella intestinalis", "strain": "strain=DSM 13280", "accession": "GCA_000156175.1", "taxid": 147207, "species_taxid": 147207, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6123, "matched_fragments": 233, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella tanakaei", "strain": "strain=YIT 12063", "accession": "GCA_000225705.1", "taxid": 626935, "species_taxid": 626935, "relation_to_type": "suspected-type", "validated": true, "ani": 79.4593, "matched_fragments": 226, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enorma burkinafasonensis", "strain": "strain=Marseille-P9525", "accession": "GCA_902150035.1", "taxid": 2590867, "species_taxid": 2590867, "relation_to_type": "type", "validated": true, "ani": 79.2813, "matched_fragments": 238, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enorma timonensis", "strain": "strain=GD5", "accession": "GCA_000321165.1", "taxid": 1232436, "species_taxid": 1232436, "relation_to_type": "type", "validated": true, "ani": 78.903, "matched_fragments": 218, "total_fragments": 760, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_901212495.1", "gtdb_species": "s__Collinsella aerofaciens_H", "ani": 97.0569, "matched_fragments": 640, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.63", "min_intra_species_ani": "95.88", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 16, "status": "conclusive" }, { "accession": "GCA_900767675.1", "gtdb_species": "s__Collinsella sp900767675", "ani": 93.2393, "matched_fragments": 544, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900754075.1", "gtdb_species": "s__Collinsella sp900754075", "ani": 93.0897, "matched_fragments": 482, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900756765.1", "gtdb_species": "s__Collinsella sp900756765", "ani": 93.0081, "matched_fragments": 482, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_905209765.1", "gtdb_species": "s__Collinsella sp905209765", "ani": 92.8147, "matched_fragments": 458, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900557505.1", "gtdb_species": "s__Collinsella sp900557505", "ani": 92.2953, "matched_fragments": 289, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_905214105.1", "gtdb_species": "s__Collinsella sp905214105", "ani": 91.9737, "matched_fragments": 572, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900540095.1", "gtdb_species": "s__Collinsella sp900540095", "ani": 91.9582, "matched_fragments": 453, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.82", "min_intra_species_ani": "99.82", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900543615.1", "gtdb_species": "s__Collinsella sp900543615", "ani": 91.8128, "matched_fragments": 469, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900552685.1", "gtdb_species": "s__Collinsella sp900552685", "ani": 91.6684, "matched_fragments": 308, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0737, "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_900757465.1", "gtdb_species": "s__Collinsella sp900757465", "ani": 91.6467, "matched_fragments": 440, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900760905.1", "gtdb_species": "s__Collinsella sp900760905", "ani": 91.6415, "matched_fragments": 510, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.28", "min_intra_species_ani": "95.28", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900539035.1", "gtdb_species": "s__Collinsella sp900539035", "ani": 91.613, "matched_fragments": 527, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.92", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_008668235.1", "gtdb_species": "s__Collinsella aerofaciens_K", "ani": 91.5926, "matched_fragments": 503, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0357, "mean_intra_species_ani": "97.54", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.81", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900542125.1", "gtdb_species": "s__Collinsella sp900542125", "ani": 91.5608, "matched_fragments": 532, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900543605.1", "gtdb_species": "s__Collinsella sp900543605", "ani": 91.5346, "matched_fragments": 496, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900548495.1", "gtdb_species": "s__Collinsella sp900548495", "ani": 91.5126, "matched_fragments": 484, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0367, "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_900548515.1", "gtdb_species": "s__Collinsella sp900548515", "ani": 91.4906, "matched_fragments": 479, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900757505.1", "gtdb_species": "s__Collinsella sp900757505", "ani": 91.4842, "matched_fragments": 475, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900545905.1", "gtdb_species": "s__Collinsella sp900545905", "ani": 91.4285, "matched_fragments": 386, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900762015.1", "gtdb_species": "s__Collinsella sp900762015", "ani": 91.4259, "matched_fragments": 460, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.1172, "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_900549025.1", "gtdb_species": "s__Collinsella sp900549025", "ani": 91.4222, "matched_fragments": 468, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0692, "mean_intra_species_ani": "97.49", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.77", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900549085.1", "gtdb_species": "s__Collinsella sp900549085", "ani": 91.2169, "matched_fragments": 507, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900542825.1", "gtdb_species": "s__Collinsella sp900542825", "ani": 91.1344, "matched_fragments": 527, "total_fragments": 760, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "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_900550785.1", "gtdb_species": "s__Collinsella sp900550785", "ani": 91.1212, "matched_fragments": 448, "total_fragments": 760, "gtdb_taxonomy": 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