{ "type": "genome", "identifier": "GCF_008271345.1", "organism": "Selenomonas caprae", "title": "Selenomonas caprae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Faculty of Veterinary Science, Chulalongkorn University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008271345.1", "bioproject": "PRJNA224116", "biosample": "SAMN12650991", "wgs_master": "VTOZ00000000.1", "refseq_category": "reference genome", "taxid": "2606905", "species_taxid": "2606905", "organism_name": "Selenomonas caprae", "infraspecific_name": "strain=mPRGC8", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/03", "asm_name": "ASM827134v1", "asm_submitter": "Faculty of Veterinary Science, Chulalongkorn University", "gbrs_paired_asm": "GCA_008271345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/271/345/GCF_008271345.1_ASM827134v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3024613", "genome_size_ungapped": "3024613", "gc_percent": "53.000000", "replicon_count": "0", "scaffold_count": "78", "contig_count": "78", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008271345.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "2902", "protein_coding_gene_count": "2786", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-03", "dateModified": "2019-09-03", "datePublished": "2019-09-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Selenomonas caprae" ], "sample_taxid": [ "2606905" ], "sample_host_organism": [ "Capra hircus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand: Nakhon Pathom" ], "sample_host_location_id": [], "data_size": "0.859 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)": "3024613", "Number of Sequences": "78", "Longest Sequences (bp)": "222496", "N50 (bp)": "94052", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.0", "Number of CDSs": "2803", "Average Protein Length": "322.8", "Coding Ratio (%)": "89.7", "Number of rRNAs": "1", "Number of tRNAs": "70", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Selenomonas montiformis", "strain": "strain=WCA-380-WT-3B3", "accession": "GCA_009697385.1", "taxid": 2652285, 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76.7029, "matched_fragments": 75, "total_fragments": 977, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Selenomonas timonae", "strain": "strain=Marseille-Q3039", "accession": "GCA_014250475.1", "taxid": 2754044, "species_taxid": 2754044, "relation_to_type": "type", "validated": true, "ani": 76.5573, "matched_fragments": 103, "total_fragments": 977, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900113715.1", "gtdb_species": "s__Selenomonas_A ruminantium_F", "ani": 97.4056, "matched_fragments": 818, "total_fragments": 977, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "97.43", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", 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"GCF_008271295.1", "gtdb_species": "s__Selenomonas_A sp008271295", "ani": 82.2182, "matched_fragments": 539, "total_fragments": 977, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018052705.1", "gtdb_species": "s__Selenomonas_A sp018052705", "ani": 79.013, "matched_fragments": 253, "total_fragments": 977, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A", "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, 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