{ "type": "genome", "identifier": "GCA_900756015.1", "organism": "uncultured Collinsella sp.", "title": "uncultured Collinsella sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "DOE JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCA_900756015.1", "bioproject": "PRJEB31003", "biosample": "SAMEA5280024", "wgs_master": "CAAEIP000000000.1", "refseq_category": "na", "taxid": "165190", "species_taxid": "165190", "organism_name": "uncultured Collinsella sp.", "infraspecific_name": "", "isolate": "HGM04228", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/26", "asm_name": "ERS473306_16", "submitter": "DOE JGI", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/756/015/GCA_900756015.1_ERS473306_16", "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": "2020-06-26", "dateModified": "2020-06-26", "datePublished": "2020-06-26", "_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": [ "Sweden" ], "sample_host_location_id": [], "data_size": "0.458 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 68.66, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1602673", "Number of Sequences": "246", "Longest Sequences (bp)": "27437", "N50 (bp)": "7573", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.9", "Number of CDSs": "1258", "Average Protein Length": "310.4", "Coding Ratio (%)": "73.1", "Number of rRNAs": "0", "Number of tRNAs": "41", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Collinsella aerofaciens", "strain": "strain=NCTC11838", "accession": "GCA_900461335.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 93.4832, "matched_fragments": 360, "total_fragments": 405, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella aerofaciens", "strain": "strain=ATCC 25986", "accession": "GCA_000169035.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 93.4557, "matched_fragments": 356, "total_fragments": 405, "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": 93.3792, "matched_fragments": 363, "total_fragments": 405, "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": 80.4617, "matched_fragments": 152, "total_fragments": 405, "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": 79.6928, "matched_fragments": 165, "total_fragments": 405, "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": 79.6652, "matched_fragments": 144, "total_fragments": 405, "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": 79.6573, "matched_fragments": 167, "total_fragments": 405, "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": 79.6065, "matched_fragments": 140, "total_fragments": 405, "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": 79.5802, "matched_fragments": 145, "total_fragments": 405, "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": 79.0124, "matched_fragments": 133, "total_fragments": 405, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 68.66, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900552995.1", "gtdb_species": "s__Collinsella sp900552995", "ani": 95.7392, "matched_fragments": 229, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.58", "min_intra_species_ani": "95.21", "mean_intra_species_af": "0.80", 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"min_intra_species_af": "0.82", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_900768435.1", "gtdb_species": "s__Collinsella sp900768435", "ani": 94.5988, "matched_fragments": 366, "total_fragments": 405, "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_905215385.1", "gtdb_species": "s__Collinsella sp905215385", "ani": 94.5938, "matched_fragments": 358, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.2035, "mean_intra_species_ani": "95.42", "min_intra_species_ani": "95.23", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCA_900542275.1", "gtdb_species": "s__Collinsella sp900542275", "ani": 94.4932, "matched_fragments": 361, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.02", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900762345.1", "gtdb_species": "s__Collinsella sp900762345", "ani": 94.4835, "matched_fragments": 353, "total_fragments": 405, "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": "GCF_003436275.1", "gtdb_species": "s__Collinsella sp003436275", "ani": 94.4832, "matched_fragments": 368, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.89", "min_intra_species_ani": "95.08", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.83", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCA_905208635.1", "gtdb_species": "s__Collinsella sp905208635", "ani": 94.4264, "matched_fragments": 358, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.1948, "mean_intra_species_ani": "95.37", "min_intra_species_ani": "95.30", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", 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"status": "-" }, { "accession": "GCF_003471585.1", "gtdb_species": "s__Collinsella sp003471585", "ani": 94.2202, "matched_fragments": 361, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.1851, "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": "GCF_003459505.1", "gtdb_species": "s__Collinsella sp003459505", "ani": 94.1608, "matched_fragments": 361, "total_fragments": 405, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.69", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { 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