{ "type": "genome", "identifier": "GCF_013166575.1", "organism": "Xylanibacter rodentium", "title": "Xylanibacter rodentium", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Helmholtz Centre for Infection Research - HZI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013166575.1", "bioproject": "PRJNA224116", "biosample": "SAMN14906827", "wgs_master": "JABKKE000000000.1", "refseq_category": "reference genome", "taxid": "2736289", "species_taxid": "2736289", "organism_name": "Xylanibacter rodentium", "infraspecific_name": "strain=PROD", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/25", "asm_name": "ASM1316657v1", "asm_submitter": "Helmholtz Centre for Infection Research - HZI", "gbrs_paired_asm": "GCA_013166575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/166/575/GCF_013166575.1_ASM1316657v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3532990", "genome_size_ungapped": "3532990", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "67", "contig_count": "67", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013166575.1-RS_2025_01_08", "annotation_date": "2025-01-08", "total_gene_count": "2824", "protein_coding_gene_count": "2721", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-25", "dateModified": "2020-05-25", "datePublished": "2020-05-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Xylanibacter rodentium" ], "sample_taxid": [ "2736289" ], "sample_host_organism": [ "Mus musculus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany:Braunschweig" ], "sample_host_location_id": [], "data_size": "1.007 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)": "3532990", "Number of Sequences": "67", "Longest Sequences (bp)": "407768", "N50 (bp)": "140305", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.7", "Number of CDSs": "2699", "Average Protein Length": "371.9", "Coding Ratio (%)": "85.2", "Number of rRNAs": "2", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xylanibacter rodentium", "strain": "strain=PROD", "accession": "GCA_013166575.1", "taxid": 2736289, "species_taxid": 2736289, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1137, "total_fragments": 1139, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Phocaeicola barnesiae", "strain": "strain=DSM 18169", "accession": "GCA_000374585.1", "taxid": 376804, "species_taxid": 376804, "relation_to_type": "type", "validated": true, "ani": 83.3975, "matched_fragments": 56, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella multiformis", "strain": "strain=DSM 16608", "accession": "GCA_000191065.1", "taxid": 282402, "species_taxid": 282402, "relation_to_type": "type", "validated": true, "ani": 79.8061, "matched_fragments": 78, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella koreensis", "strain": "strain=KCOM 3155", "accession": "GCA_003977605.1", "taxid": 2490854, "species_taxid": 2490854, "relation_to_type": "type", "validated": true, "ani": 79.774, "matched_fragments": 87, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylanibacter muris", "strain": "strain=PMUR", "accession": "GCA_013166605.1", "taxid": 2736290, "species_taxid": 2736290, "relation_to_type": "type", "validated": true, "ani": 78.5018, "matched_fragments": 174, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella ruminicola", "strain": "strain=Bryant 23", "accession": "GCA_000025925.1", "taxid": 839, "species_taxid": 839, "relation_to_type": "type", "validated": true, "ani": 77.5062, "matched_fragments": 65, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella denticola", "strain": "strain=NCTC13067", "accession": "GCA_900454835.1", "taxid": 28129, "species_taxid": 28129, "relation_to_type": "type", "validated": true, "ani": 77.4276, "matched_fragments": 59, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella pectinovora", "strain": "strain=P4-76", "accession": "GCA_000834015.1", "taxid": 1602169, "species_taxid": 1602169, "relation_to_type": "type", "validated": true, "ani": 77.2023, "matched_fragments": 112, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella ruminicola", "strain": "strain=ATCC 19189", "accession": "GCA_900108375.1", "taxid": 839, "species_taxid": 839, "relation_to_type": "type", "validated": true, "ani": 77.0348, "matched_fragments": 63, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hallella faecis", "strain": "strain=CLA-AA-H145", "accession": "GCA_018789675.1", "taxid": 2841596, "species_taxid": 2841596, "relation_to_type": "type", "validated": true, "ani": 76.9841, "matched_fragments": 80, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella denticola", "strain": "strain=DSM 20614", "accession": "GCA_000421205.1", "taxid": 28129, "species_taxid": 28129, "relation_to_type": "type", "validated": true, "ani": 76.8464, "matched_fragments": 59, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella dentasini", "strain": "strain=JCM 15908", "accession": "GCA_000614065.1", "taxid": 589537, "species_taxid": 589537, "relation_to_type": "type", "validated": true, "ani": 76.8221, "matched_fragments": 66, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella buccae", "strain": "strain=ATCC 33574", "accession": "GCA_000184945.1", "taxid": 28126, "species_taxid": 28126, "relation_to_type": "type", "validated": true, "ani": 76.7254, "matched_fragments": 109, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella brevis", "strain": "strain=ATCC 19188", "accession": "GCA_000621725.1", "taxid": 83231, "species_taxid": 83231, "relation_to_type": "type", "validated": true, "ani": 76.6287, "matched_fragments": 78, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013166545.1", "gtdb_species": "s__Prevotella sp013166545", "ani": 99.8777, "matched_fragments": 1102, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCA_900549175.1", "gtdb_species": "s__Prevotella sp900549175", "ani": 81.1784, "matched_fragments": 550, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017483185.1", "gtdb_species": "s__Prevotella sp017483185", "ani": 79.1383, "matched_fragments": 273, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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_900553965.1", "gtdb_species": "s__Prevotella sp900553965", "ani": 78.5055, "matched_fragments": 253, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "97.60", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_905216025.1", "gtdb_species": "s__Prevotella sp905216025", "ani": 78.3767, "matched_fragments": 311, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.83", "min_intra_species_ani": "95.83", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017623155.1", "gtdb_species": "s__Prevotella sp017623155", "ani": 78.1367, "matched_fragments": 224, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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_002933775.1", "gtdb_species": "s__Prevotella sp002933775", "ani": 78.1335, "matched_fragments": 211, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "97.52", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.83", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_900545525.1", "gtdb_species": "s__Prevotella sp900545525", "ani": 78.0998, "matched_fragments": 132, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.76", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_016899955.1", "gtdb_species": "s__Prevotella sp900540415", "ani": 77.2344, "matched_fragments": 197, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "98.08", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_017410365.1", "gtdb_species": "s__Prevotella sp017410365", "ani": 77.0655, "matched_fragments": 128, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.93", "min_intra_species_ani": "96.60", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.74", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_002394385.1", "gtdb_species": "s__Prevotella sp002394385", "ani": 76.8221, "matched_fragments": 120, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.28", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_900772835.1", "gtdb_species": "s__Prevotella sp900772835", "ani": 76.4764, "matched_fragments": 88, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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_900315835.1", "gtdb_species": "s__Prevotella sp900315835", "ani": 76.2408, "matched_fragments": 69, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.59", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_905198745.1", "gtdb_species": "s__Prevotella sp905198745", "ani": 76.2121, "matched_fragments": 92, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "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, "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 }, "_genome_taxon": [ "Xylanibacter", "rodentium" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }