{ "type": "genome", "identifier": "GCF_007747215.1", "organism": "Urbifossiella limnaea", "title": "Urbifossiella limnaea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Radboud Universiteit Nijmegen", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007747215.1", "bioproject": "PRJNA224116", "biosample": "SAMN10953902", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2528023", "species_taxid": "2528023", "organism_name": "Urbifossiella limnaea", "infraspecific_name": "strain=ETA_A1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/31", "asm_name": "ASM774721v1", "asm_submitter": "Radboud Universiteit Nijmegen", "gbrs_paired_asm": "GCA_007747215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/747/215/GCF_007747215.1_ASM774721v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7795793", "genome_size_ungapped": "7795793", "gc_percent": "71.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007747215.1-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "6371", "protein_coding_gene_count": "6215", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-31", "dateModified": "2019-07-31", "datePublished": "2019-07-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Urbifossiella limnaea" ], "sample_taxid": [ "2528023" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Wolfenbuettel" ], "sample_host_location_id": [], "data_size": "2.074 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7795793", "Number of Sequences": "1", "Longest Sequences (bp)": "7795793", "N50 (bp)": "7795793", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.3", "Number of CDSs": "6408", "Average Protein Length": "368.6", "Coding Ratio (%)": "90.9", "Number of rRNAs": "4", "Number of tRNAs": "98", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Urbifossiella limnaea", "strain": "strain=ETA_A1", "accession": "GCA_007747215.1", "taxid": 2528023, "species_taxid": 2528023, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2597, "total_fragments": 2598, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gemmata obscuriglobus", "strain": "strain=DSM 5831", "accession": "GCA_003149495.1", "taxid": 114, "species_taxid": 114, "relation_to_type": "type", "validated": true, "ani": 78.1319, "matched_fragments": 970, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmata obscuriglobus", "strain": "strain=DSM 5831", "accession": "GCA_008065095.1", "taxid": 114, "species_taxid": 114, "relation_to_type": "type", "validated": true, "ani": 78.0917, "matched_fragments": 957, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmata obscuriglobus", "strain": "", "accession": "GCA_901538385.1", "taxid": 114, "species_taxid": 114, "relation_to_type": "type", "validated": true, "ani": 78.0762, "matched_fragments": 978, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmata obscuriglobus", "strain": "strain=UQM 2246", "accession": "GCA_000171775.1", "taxid": 114, "species_taxid": 114, "relation_to_type": "type", "validated": true, "ani": 78.0493, "matched_fragments": 896, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania aurantiaca", "strain": "strain=1NDH13", "accession": "GCA_019711375.1", "taxid": 2867233, "species_taxid": 2867233, "relation_to_type": "type", "validated": true, "ani": 75.074, "matched_fragments": 57, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium nesterenkovii", "strain": "strain=CIP104813", "accession": "GCA_900163655.1", "taxid": 47847, "species_taxid": 47847, "relation_to_type": "type", "validated": true, "ani": 74.8753, "matched_fragments": 150, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=ATCC 700314", "accession": "GCA_003667445.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 74.8407, "matched_fragments": 266, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limimonas halophila", "strain": "strain=DSM 25584", "accession": "GCA_900100655.1", "taxid": 1082479, "species_taxid": 1082479, "relation_to_type": "type", "validated": true, "ani": 74.8347, "matched_fragments": 140, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=DSM 11105", "accession": "GCA_014206845.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 74.8217, "matched_fragments": 275, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corallococcus soli", "strain": "strain=ZKHCc1 1396", "accession": "GCA_014930455.1", "taxid": 2710757, "species_taxid": 2710757, "relation_to_type": "type", "validated": true, "ani": 74.8056, "matched_fragments": 279, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas fulva", "strain": "strain=DKR-3", "accession": "GCA_018531375.1", "taxid": 2835530, "species_taxid": 2835530, "relation_to_type": "type", "validated": true, "ani": 74.7896, "matched_fragments": 272, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodoferax soli", "strain": "strain=DSM 21634", "accession": "GCA_003337555.1", "taxid": 545864, "species_taxid": 545864, "relation_to_type": "type", "validated": true, "ani": 74.7849, "matched_fragments": 272, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter agilis", "strain": "strain=LMG 16336", "accession": "GCA_021730435.1", "taxid": 47492, "species_taxid": 47492, "relation_to_type": "type", "validated": true, "ani": 74.7805, "matched_fragments": 184, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter aminoxidans", "strain": "strain=ATCC BAA-299", "accession": "GCA_023571765.1", "taxid": 186280, "species_taxid": 186280, "relation_to_type": "type", "validated": true, "ani": 74.7705, "matched_fragments": 217, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfurifustis variabilis", "strain": "strain=skN76", "accession": "GCA_002355415.1", "taxid": 1675686, "species_taxid": 1675686, "relation_to_type": "type", "validated": true, "ani": 74.7588, "matched_fragments": 169, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium saimiriisciurei", "strain": "strain=SMA1", "accession": "GCA_010667655.1", "taxid": 2661627, "species_taxid": 2661627, "relation_to_type": "type", "validated": true, "ani": 74.7476, "matched_fragments": 70, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Beutenbergia cavernae", "strain": "strain=DSM 12333", "accession": "GCA_000023105.1", "taxid": 84757, "species_taxid": 84757, "relation_to_type": "type", "validated": true, "ani": 74.7047, "matched_fragments": 322, "total_fragments": 2598, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007747215.1", "gtdb_species": "s__Urbifossiella limnaea", "ani": 100.0, "matched_fragments": 2597, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella", "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": "GCA_017308215.1", "gtdb_species": "s__Urbifossiella sp017308215", "ani": 84.0806, "matched_fragments": 1520, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella", "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_013822345.1", "gtdb_species": "s__Gemmata sp013822345", "ani": 78.6845, "matched_fragments": 1206, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "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_901538445.1", "gtdb_species": "s__Gemmata sp901538445", "ani": 78.6523, "matched_fragments": 1177, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "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_013128195.2", "gtdb_species": "s__Gemmata tundricola", "ani": 78.135, "matched_fragments": 1045, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "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_008065095.1", "gtdb_species": "s__Gemmata obscuriglobus", "ani": 78.0972, "matched_fragments": 956, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_016872595.1", "gtdb_species": "s__Gemmata sp016872595", "ani": 78.0921, "matched_fragments": 948, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "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_017306025.1", "gtdb_species": "s__Gemmata sp017306025", "ani": 78.0309, "matched_fragments": 878, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "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_005773755.1", "gtdb_species": "s__Gemmata sp005773755", "ani": 77.5392, "matched_fragments": 676, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "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_000531095.1", "gtdb_species": "s__Gemmata massiliana", "ani": 77.4153, "matched_fragments": 772, "total_fragments": 2598, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "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": [ "Urbifossiella", "limnaea" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }