{ "type": "genome", "identifier": "GCF_900182975.1", "organism": "Epilithonimonas pallida", "title": "Epilithonimonas pallida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900182975.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421679", "wgs_master": "FXUO00000000.1", "refseq_category": "reference genome", "taxid": "373671", "species_taxid": "373671", "organism_name": "Epilithonimonas pallida", "infraspecific_name": "strain=DSM 18015", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/04/08", "asm_name": "IMG-taxon 2681813503 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900182975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/182/975/GCF_900182975.1_IMG-taxon_2681813503_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3831779", "genome_size_ungapped": "3831779", "gc_percent": "36.000000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "21", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900182975.1-RS_2024_05_22", "annotation_date": "2024-05-22", "total_gene_count": "3535", "protein_coding_gene_count": "3463", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-04-08", "dateModified": "2023-04-08", "datePublished": "2023-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Epilithonimonas pallida" ], "sample_taxid": [ "373671" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "1.072 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)": "3831779", "Number of Sequences": "21", "Longest Sequences (bp)": "721595", "N50 (bp)": "454914", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "36.1", "Number of CDSs": "3447", "Average Protein Length": "327.9", "Coding Ratio (%)": "88.5", "Number of rRNAs": "3", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Epilithonimonas arachidiradicis", "strain": "strain=DSM 27620", "accession": "GCA_003610695.1", "taxid": 1617282, "species_taxid": 1617282, "relation_to_type": "type", "validated": true, "ani": 88.3035, "matched_fragments": 860, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas arachidiradicis", "strain": "strain=CCM 8490", "accession": "GCA_014635405.1", "taxid": 1617282, "species_taxid": 1617282, "relation_to_type": "type", "validated": true, "ani": 88.2562, "matched_fragments": 864, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas zeae", "strain": "strain=DSM 27623", "accession": "GCA_900141765.1", "taxid": 1416779, "species_taxid": 1416779, "relation_to_type": "type", "validated": true, "ani": 83.9415, "matched_fragments": 864, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas caeni", "strain": "strain=DSM 17710", "accession": "GCA_000426465.1", "taxid": 365343, "species_taxid": 365343, "relation_to_type": "type", "validated": true, "ani": 83.5033, "matched_fragments": 804, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas hispanica", "strain": "strain=KCTC 22104", "accession": "GCA_003385395.1", "taxid": 358687, "species_taxid": 358687, "relation_to_type": "type", "validated": true, "ani": 83.3324, "matched_fragments": 709, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas vandammei", "strain": "strain=F5649", "accession": "GCA_003860525.1", "taxid": 2487072, "species_taxid": 2487072, "relation_to_type": "type", "validated": true, "ani": 83.2076, "matched_fragments": 697, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas hungarica", "strain": "strain=DSM 19684", "accession": "GCA_900102265.1", "taxid": 454006, "species_taxid": 454006, "relation_to_type": "type", "validated": true, "ani": 83.1504, "matched_fragments": 794, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas mollis", "strain": "strain=DSM 18016", "accession": "GCA_900142325.1", "taxid": 216903, "species_taxid": 216903, "relation_to_type": "type", "validated": true, "ani": 81.9769, "matched_fragments": 773, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas xixisoli", "strain": "strain=CGMCC 1.12802", "accession": "GCA_004365655.1", "taxid": 1476462, "species_taxid": 1476462, "relation_to_type": "type", "validated": true, "ani": 80.7431, "matched_fragments": 668, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas bovis", "strain": "strain=DSM 19482", "accession": "GCA_900108115.1", "taxid": 421530, "species_taxid": 421530, "relation_to_type": "type", "validated": true, "ani": 80.6981, "matched_fragments": 500, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Epilithonimonas tenax", "strain": "strain=DSM 16811", "accession": "GCA_000428485.1", "taxid": 191577, "species_taxid": 191577, "relation_to_type": "type", "validated": true, "ani": 80.0788, "matched_fragments": 609, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chryseobacterium geocarposphaerae", "strain": "strain=DSM 27617", "accession": "GCA_002797535.1", "taxid": 1416776, "species_taxid": 1416776, "relation_to_type": "type", "validated": true, "ani": 80.0158, "matched_fragments": 297, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chryseobacterium gwangjuense", "strain": "strain=THG-A18", "accession": "GCA_021311115.1", "taxid": 1069980, "species_taxid": 1069980, "relation_to_type": "type", "validated": true, "ani": 78.6853, "matched_fragments": 242, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chryseobacterium tagetis", "strain": "strain=RG1", "accession": "GCA_016735585.2", "taxid": 2801334, "species_taxid": 2801334, "relation_to_type": "type", "validated": true, "ani": 78.5456, "matched_fragments": 269, "total_fragments": 1267, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_001898785.1", "gtdb_species": "s__Epilithonimonas sp001898785", "ani": 97.6054, "matched_fragments": 978, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_003610695.1", "gtdb_species": "s__Epilithonimonas arachidiradicis", "ani": 88.2924, "matched_fragments": 861, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_003248755.1", "gtdb_species": "s__Epilithonimonas sp003248755", "ani": 84.1447, "matched_fragments": 780, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_900141765.1", "gtdb_species": "s__Epilithonimonas zeae", "ani": 83.9415, "matched_fragments": 864, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_003385395.1", "gtdb_species": "s__Epilithonimonas hispanica", "ani": 83.3402, "matched_fragments": 709, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_003860525.1", "gtdb_species": "s__Epilithonimonas vandammei", "ani": 83.2268, "matched_fragments": 695, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.28", "min_intra_species_ani": "95.86", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002383165.1", "gtdb_species": "s__Epilithonimonas sp002383165", "ani": 83.1552, "matched_fragments": 661, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_900102265.1", "gtdb_species": "s__Epilithonimonas hungarica", "ani": 83.1504, "matched_fragments": 794, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "97.55", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002345565.1", "gtdb_species": "s__Epilithonimonas sp002345565", "ani": 83.1312, "matched_fragments": 677, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_002476905.1", "gtdb_species": "s__Epilithonimonas sp002476905", "ani": 82.9795, "matched_fragments": 577, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_003730015.1", "gtdb_species": "s__Epilithonimonas hominis", "ani": 82.6499, "matched_fragments": 635, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.55", "min_intra_species_ani": "96.42", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900142325.1", "gtdb_species": "s__Epilithonimonas mollis", "ani": 81.9768, "matched_fragments": 773, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "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_900108115.1", "gtdb_species": "s__Epilithonimonas bovis", "ani": 80.6979, "matched_fragments": 500, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.92", "min_intra_species_ani": "96.69", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002797535.1", "gtdb_species": "s__Chryseobacterium geocarposphaerae", "ani": 80.0345, "matched_fragments": 296, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.65", "min_intra_species_ani": "95.65", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000799455.1", "gtdb_species": "s__Chryseobacterium sp000799455", "ani": 78.4699, "matched_fragments": 257, "total_fragments": 1267, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium", "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": [ "Epilithonimonas", "pallida" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }