{ "type": "genome", "identifier": "GCF_900461335.1", "organism": "Collinsella aerofaciens", "title": "Collinsella aerofaciens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900461335.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4364217", "wgs_master": "UFXC00000000.1", "refseq_category": "na", "taxid": "74426", "species_taxid": "74426", "organism_name": "Collinsella aerofaciens", "infraspecific_name": "strain=NCTC11838", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/07", "asm_name": "50279_E02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900461335.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/461/335/GCF_900461335.1_50279_E02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2463631", "genome_size_ungapped": "2463631", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900461335.1-RS_2024_08_16", "annotation_date": "2024-08-16", "total_gene_count": "2210", "protein_coding_gene_count": "2116", "non_coding_gene_count": "76", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-07", "dateModified": "2018-08-07", "datePublished": "2018-08-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Collinsella aerofaciens" ], "sample_taxid": [ "74426" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.690 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": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2463631", "Number of Sequences": "4", "Longest Sequences (bp)": "2425877", "N50 (bp)": "2425877", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.6", "Number of CDSs": "2160", "Average Protein Length": "327.7", "Coding Ratio (%)": "86.2", "Number of rRNAs": "15", "Number of tRNAs": "59", "Number of CRISPRs": "1" }, "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": 100.0, "matched_fragments": 815, "total_fragments": 819, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Collinsella aerofaciens", "strain": "strain=JCM 10188", "accession": "GCA_010509075.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 99.9941, "matched_fragments": 811, "total_fragments": 819, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Collinsella aerofaciens", "strain": "strain=ATCC 25986", "accession": "GCA_000169035.1", "taxid": 74426, "species_taxid": 74426, "relation_to_type": "type", "validated": true, "ani": 99.9781, "matched_fragments": 793, "total_fragments": 819, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Collinsella bouchesdurhonensis", "strain": "strain=Marseille-P3296", "accession": "GCA_900155365.1", "taxid": 1907654, "species_taxid": 1907654, "relation_to_type": "type", "validated": true, "ani": 80.8198, "matched_fragments": 248, "total_fragments": 819, "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": 80.3871, "matched_fragments": 294, "total_fragments": 819, "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": 80.1592, "matched_fragments": 291, "total_fragments": 819, "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": 79.971, "matched_fragments": 250, "total_fragments": 819, "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": 79.7742, "matched_fragments": 257, "total_fragments": 819, "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": 79.5103, "matched_fragments": 249, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collinsella provencensis", "strain": "strain=Marseille-P3740", "accession": "GCA_900199705.1", "taxid": 1937461, "species_taxid": 1937461, "relation_to_type": "type", "validated": true, "ani": 79.4093, "matched_fragments": 187, "total_fragments": 819, "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": 78.9996, "matched_fragments": 219, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010509075.1", "gtdb_species": "s__Collinsella aerofaciens", "ani": 99.994, "matched_fragments": 810, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_900543515.1", "gtdb_species": "s__Collinsella sp900543515", "ani": 94.6542, "matched_fragments": 572, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.1148, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900550825.1", "gtdb_species": "s__Collinsella sp900550825", "ani": 94.6298, "matched_fragments": 477, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900541795.1", "gtdb_species": "s__Collinsella sp900541795", "ani": 94.6177, "matched_fragments": 621, "total_fragments": 819, "gtdb_taxonomy": 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"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_900545165.1", "gtdb_species": "s__Collinsella sp900545165", "ani": 94.4376, "matched_fragments": 514, "total_fragments": 819, "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_900761155.1", "gtdb_species": "s__Collinsella sp900761155", "ani": 94.4127, "matched_fragments": 525, "total_fragments": 819, "gtdb_taxonomy": 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"d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900544845.1", "gtdb_species": "s__Collinsella sp900544845", "ani": 94.316, "matched_fragments": 560, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900757505.1", "gtdb_species": "s__Collinsella sp900757505", "ani": 94.1671, "matched_fragments": 559, "total_fragments": 819, "gtdb_taxonomy": 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