{ "type": "genome", "identifier": "GCF_004792655.1", "organism": "Palleniella muris", "title": "Palleniella muris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Toronto", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004792655.1", "bioproject": "PRJNA224116", "biosample": "SAMN10878314", "wgs_master": "SRZC00000000.1", "refseq_category": "reference genome", "taxid": "3038145", "species_taxid": "3038145", "organism_name": "Palleniella muris", "infraspecific_name": "strain=NM73_A23", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/14", "asm_name": "ASM479265v1", "asm_submitter": "University of Toronto", "gbrs_paired_asm": "GCA_004792655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/792/655/GCF_004792655.1_ASM479265v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3580472", "genome_size_ungapped": "3580472", "gc_percent": "47.000000", "replicon_count": "0", "scaffold_count": "59", "contig_count": "59", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004792655.1-RS_2024_04_04", "annotation_date": "2024-04-04", "total_gene_count": "3015", "protein_coding_gene_count": "2900", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-14", "dateModified": "2019-04-14", "datePublished": "2019-04-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Palleniella muris" ], "sample_taxid": [ "3038145" ], "sample_host_organism": [ "Mus musculus" ], "sample_host_organism_id": [], "sample_host_disease": [ "colon cancer, Lynch syndrome" ], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Toronto" ], "sample_host_location_id": [], "data_size": "1.022 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 37.0, "max": 37.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3580472", "Number of Sequences": "59", "Longest Sequences (bp)": "279969", "N50 (bp)": "130099", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.1", "Number of CDSs": "2909", "Average Protein Length": "349.1", "Coding Ratio (%)": "85.1", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Palleniella intestinalis", "strain": "strain=PINT", "accession": "GCA_013166595.1", "taxid": 2736291, "species_taxid": 2736291, "relation_to_type": "type", "validated": true, "ani": 92.0128, "matched_fragments": 863, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella ihumii", "strain": "strain=Marseille-P3385", "accession": "GCA_900155655.1", "taxid": 1917878, "species_taxid": 1917878, "relation_to_type": "type", "validated": true, "ani": 82.8613, "matched_fragments": 53, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella lascolaii", "strain": "strain=khD1", "accession": "GCA_900079775.1", "taxid": 1776379, "species_taxid": 1776379, "relation_to_type": "type", "validated": true, "ani": 81.5494, "matched_fragments": 90, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylanibacter rodentium", "strain": "strain=PROD", "accession": "GCA_013166575.1", "taxid": 2736289, "species_taxid": 2736289, "relation_to_type": "type", "validated": true, "ani": 81.2048, "matched_fragments": 84, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella baroniae", "strain": "strain=JCM 13447", "accession": "GCA_000613565.1", "taxid": 305719, "species_taxid": 305719, "relation_to_type": "type", "validated": true, "ani": 80.7401, "matched_fragments": 60, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella baroniae", "strain": "strain=DSM 16972", "accession": "GCA_000426585.1", "taxid": 305719, "species_taxid": 305719, "relation_to_type": "type", "validated": true, "ani": 80.4417, "matched_fragments": 58, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella stercorea", "strain": "strain=DSM 18206", "accession": "GCA_000235885.1", "taxid": 363265, "species_taxid": 363265, "relation_to_type": "suspected-type", "validated": true, "ani": 79.9788, "matched_fragments": 111, "total_fragments": 1165, "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": 78.6227, "matched_fragments": 69, "total_fragments": 1165, "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": 77.8917, "matched_fragments": 85, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella copri", "strain": "strain=DSM 18205", "accession": "GCA_000157935.1", "taxid": 165179, "species_taxid": 165179, "relation_to_type": "suspected-type", "validated": true, "ani": 77.4304, "matched_fragments": 70, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Prevotella copri", "strain": "strain=DSM 18205", "accession": "GCA_009495405.1", "taxid": 165179, "species_taxid": 165179, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1043, "matched_fragments": 70, "total_fragments": 1165, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004792655.1", "gtdb_species": "s__Prevotella sp004792655", "ani": 100.0, "matched_fragments": 1164, "total_fragments": 1165, "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": "conclusive" }, { "accession": "GCF_013166595.1", "gtdb_species": "s__Prevotella sp002298815", "ani": 92.0376, "matched_fragments": 861, "total_fragments": 1165, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.76", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_017462915.1", "gtdb_species": "s__Prevotella sp017462915", "ani": 81.0998, "matched_fragments": 500, "total_fragments": 1165, "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_004555245.1", "gtdb_species": "s__Prevotella sp004555245", "ani": 77.6647, "matched_fragments": 144, "total_fragments": 1165, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017424205.1", "gtdb_species": "s__Prevotella sp017424205", "ani": 77.3764, "matched_fragments": 71, "total_fragments": 1165, "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_905233245.1", "gtdb_species": "s__Prevotella sp905233245", "ani": 77.1595, "matched_fragments": 71, "total_fragments": 1165, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_905233165.1", "gtdb_species": "s__Prevotella sp905233165", "ani": 77.1022, "matched_fragments": 60, "total_fragments": 1165, "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_004556065.1", "gtdb_species": "s__Prevotella sp004556065", "ani": 77.0757, "matched_fragments": 113, "total_fragments": 1165, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "97.47", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.76", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_900545525.1", "gtdb_species": "s__Prevotella sp900545525", "ani": 76.7728, "matched_fragments": 81, "total_fragments": 1165, "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": "GCA_902799455.1", "gtdb_species": "s__Prevotella sp902799455", "ani": 76.6477, "matched_fragments": 57, "total_fragments": 1165, "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_017476785.1", "gtdb_species": "s__Prevotella sp017476785", "ani": 75.9859, "matched_fragments": 50, "total_fragments": 1165, "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": [ "Palleniella", "muris" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }