{ "type": "genome", "identifier": "GCF_025685655.1", "organism": "Acidicapsa ligni", "title": "Acidicapsa ligni", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Sun Yat-sen University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025685655.1", "bioproject": "PRJNA224116", "biosample": "SAMN18744430", "wgs_master": "JAGSYG000000000.1", "refseq_category": "reference genome", "taxid": "542300", "species_taxid": "542300", "organism_name": "Acidicapsa ligni", "infraspecific_name": "strain=WH120", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/13", "asm_name": "ASM2568565v1", "asm_submitter": "Sun Yat-sen University", "gbrs_paired_asm": "GCA_025685655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/685/655/GCF_025685655.1_ASM2568565v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5677642", "genome_size_ungapped": "5677642", "gc_percent": "55.500000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025685655.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "4631", "protein_coding_gene_count": "4557", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-10-13", "dateModified": "2022-10-13", "datePublished": "2022-10-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Acidicapsa ligni" ], "sample_taxid": [ "542300" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Netherlands" ], "sample_host_location_id": [], "data_size": "1.616 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)": "5677642", "Number of Sequences": "17", "Longest Sequences (bp)": "1557555", "N50 (bp)": "961249", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.4", "Number of CDSs": "4703", "Average Protein Length": "348.5", "Coding Ratio (%)": "86.6", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Acidisarcina polymorpha", "strain": "strain=SBC82", "accession": "GCA_003330725.1", "taxid": 2211140, "species_taxid": 2211140, "relation_to_type": "type", "validated": true, "ani": 77.6953, "matched_fragments": 123, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Edaphobacter lichenicola", "strain": "strain=DSM 104462", "accession": "GCA_025264645.1", "taxid": 2051959, "species_taxid": 2051959, "relation_to_type": "suspected-type", "validated": true, "ani": 77.3613, "matched_fragments": 112, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terriglobus roseus", "strain": "strain=DSM 18391", "accession": "GCA_000265425.1", "taxid": 392734, "species_taxid": 392734, "relation_to_type": "type", "validated": true, "ani": 77.2415, "matched_fragments": 83, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Silvibacterium bohemicum", "strain": "strain=DSM 103733", "accession": "GCA_014201455.1", "taxid": 1577686, "species_taxid": 1577686, "relation_to_type": "type", "validated": true, "ani": 77.1124, "matched_fragments": 165, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alloacidobacterium dinghuense", "strain": "strain=4Y35", "accession": "GCA_014274465.1", "taxid": 2763107, "species_taxid": 2763107, "relation_to_type": "type", "validated": true, "ani": 77.0851, "matched_fragments": 90, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidipila rosea", "strain": "strain=DSM 103428", "accession": "GCA_004339725.1", "taxid": 768535, "species_taxid": 768535, "relation_to_type": "type", "validated": true, "ani": 77.0838, "matched_fragments": 117, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occallatibacter riparius", "strain": "strain=DSM 25168", "accession": "GCA_025264625.1", "taxid": 1002689, "species_taxid": 1002689, "relation_to_type": "type", "validated": true, "ani": 77.039, "matched_fragments": 135, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidobacterium capsulatum", "strain": "strain=ATCC 51196", "accession": "GCA_000022565.1", "taxid": 33075, "species_taxid": 33075, "relation_to_type": "type", "validated": true, "ani": 77.013, "matched_fragments": 110, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Silvibacterium dinghuense", "strain": "strain=CGMCC 1.13007", "accession": "GCA_014640355.1", "taxid": 1560006, "species_taxid": 1560006, "relation_to_type": "type", "validated": true, "ani": 77.007, "matched_fragments": 144, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Silvibacterium dinghuense", "strain": "strain=DHOF10", "accession": "GCA_004123295.1", "taxid": 1560006, "species_taxid": 1560006, "relation_to_type": "type", "validated": true, "ani": 76.9326, "matched_fragments": 143, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terracidiphilus gabretensis", "strain": "strain=S55", "accession": "GCA_001449115.1", "taxid": 1577687, "species_taxid": 1577687, "relation_to_type": "type", "validated": true, "ani": 76.9285, "matched_fragments": 148, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Edaphobacter dinghuensis", "strain": "strain=CGMCC 1.12997", "accession": "GCA_014640335.1", "taxid": 1560005, "species_taxid": 1560005, "relation_to_type": "type", "validated": true, "ani": 76.8771, "matched_fragments": 112, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Edaphobacter aggregans", "strain": "strain=DSM 19364", "accession": "GCA_000745965.1", "taxid": 570835, "species_taxid": 570835, "relation_to_type": "type", "validated": true, "ani": 76.8542, "matched_fragments": 119, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Edaphobacter modestus", "strain": "strain=DSM 18101", "accession": "GCA_004217555.1", "taxid": 388466, "species_taxid": 388466, "relation_to_type": "type", "validated": true, "ani": 76.6563, "matched_fragments": 126, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracidobacterium acidisoli", "strain": "strain=4G-K13", "accession": "GCA_003428625.2", "taxid": 2303751, "species_taxid": 2303751, "relation_to_type": "type", "validated": true, "ani": 76.5028, "matched_fragments": 138, "total_fragments": 1885, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903832055.1", "gtdb_species": "s__CAIVDV01 sp903832055", "ani": 78.1829, "matched_fragments": 359, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_903832475.1", "gtdb_species": "s__CAIVDV01 sp903832475", "ani": 77.8839, "matched_fragments": 278, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "98.66", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903904755.1", "gtdb_species": "s__CAIVDV01 sp903904755", "ani": 77.8447, "matched_fragments": 223, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.89", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_903849645.1", "gtdb_species": "s__Terracidiphilus sp903849645", "ani": 77.3005, "matched_fragments": 190, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003131205.1", "gtdb_species": "s__Terracidiphilus savannae", "ani": 76.9852, "matched_fragments": 149, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "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_001449115.1", "gtdb_species": "s__Terracidiphilus gabretensis", "ani": 76.9285, "matched_fragments": 148, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "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_013410875.1", "gtdb_species": "s__Edaphobacter lichenicola_C", "ani": 76.8911, "matched_fragments": 117, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter", "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_015654835.1", "gtdb_species": "s__Terracidiphilus sp015654835", "ani": 76.7, "matched_fragments": 150, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "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_014201315.1", "gtdb_species": "s__Edaphobacter lichenicola_B", "ani": 76.65, "matched_fragments": 107, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter", "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_003151435.1", "gtdb_species": "s__Terracidiphilus sp003151435", "ani": 76.5565, "matched_fragments": 133, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.67", "min_intra_species_ani": "99.67", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003428625.2", "gtdb_species": "s__Palsa-343 sp003428625", "ani": 76.5028, "matched_fragments": 138, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343", "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_903828675.1", "gtdb_species": "s__Terracidiphilus sp903828675", "ani": 76.49, "matched_fragments": 132, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_013289875.1", "gtdb_species": "s__Silvibacterium sp013289875", "ani": 76.4734, "matched_fragments": 93, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium", "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_903842845.1", "gtdb_species": "s__CAIMNN01 sp903842845", "ani": 76.4617, "matched_fragments": 80, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIMNN01", "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_903873705.1", "gtdb_species": "s__CAIQPK01 sp903873705", "ani": 76.38, "matched_fragments": 83, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003140785.1", "gtdb_species": "s__Terracidiphilus sp003140785", "ani": 76.2367, "matched_fragments": 108, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.14", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.78", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003165935.1", "gtdb_species": "s__Terracidiphilus sp003165935", "ani": 76.1068, "matched_fragments": 115, "total_fragments": 1885, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus", "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": -0.241, "cell_length": 0.096, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 25.0, "optimum_ph": 4.25, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Acidicapsa", "ligni" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }