{ "type": "genome", "identifier": "GCF_016722765.1", "organism": "Ramlibacter alkalitolerans", "title": "Ramlibacter alkalitolerans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Dongguk University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016722765.1", "bioproject": "PRJNA224116", "biosample": "SAMN17222283", "wgs_master": "JAEQND000000000.1", "refseq_category": "reference genome", "taxid": "2039631", "species_taxid": "2039631", "organism_name": "Ramlibacter alkalitolerans", "infraspecific_name": "strain=KACC 19305", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/01/19", "asm_name": "ASM1672276v1", "asm_submitter": "Dongguk University", "gbrs_paired_asm": "GCA_016722765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/722/765/GCF_016722765.1_ASM1672276v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5712197", "genome_size_ungapped": "5712197", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016722765.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "5521", "protein_coding_gene_count": "5421", "non_coding_gene_count": "64", "pubmed_id": "28920850" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-01-19", "dateModified": "2021-01-19", "datePublished": "2021-01-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Ramlibacter alkalitolerans" ], "sample_taxid": [ "2039631" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Anseong" ], "sample_host_location_id": [], "data_size": "1.538 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)": "5712197", "Number of Sequences": "33", "Longest Sequences (bp)": "623474", "N50 (bp)": "346469", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.2", "Number of CDSs": "5491", "Average Protein Length": "318.4", "Coding Ratio (%)": "91.8", "Number of rRNAs": "3", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ramlibacter alkalitolerans", "strain": "strain=KACC 19305", "accession": "GCA_016722765.1", "taxid": 2039631, "species_taxid": 2039631, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1886, "total_fragments": 1888, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ramlibacter monticola", "strain": "strain=KACC 19175", "accession": "GCA_016722785.1", "taxid": 1926872, "species_taxid": 1926872, "relation_to_type": "type", "validated": true, "ani": 86.6142, "matched_fragments": 1354, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter agri", "strain": "strain=G-1-2-2", "accession": "GCA_012927085.1", "taxid": 2728837, "species_taxid": 2728837, "relation_to_type": "type", "validated": true, "ani": 83.6535, "matched_fragments": 1124, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter tataouinensis", "strain": "strain=TTB310", "accession": "GCA_000215705.1", "taxid": 94132, "species_taxid": 94132, "relation_to_type": "type", "validated": true, "ani": 82.7129, "matched_fragments": 850, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter humi", "strain": "strain=18x22-1", "accession": "GCA_004681975.1", "taxid": 2530451, "species_taxid": 2530451, "relation_to_type": "type", "validated": true, "ani": 82.6301, "matched_fragments": 887, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter algicola", "strain": "strain=CrO1", "accession": "GCA_016641735.1", "taxid": 2795217, "species_taxid": 2795217, "relation_to_type": "type", "validated": true, "ani": 82.4979, "matched_fragments": 855, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter aquaticus", "strain": "strain=LMG 30558", "accession": "GCA_015159745.1", "taxid": 2780094, "species_taxid": 2780094, "relation_to_type": "type", "validated": true, "ani": 82.2858, "matched_fragments": 779, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter henchirensis", "strain": "strain=DSM 14656", "accession": "GCA_004682015.1", "taxid": 204072, "species_taxid": 204072, "relation_to_type": "type", "validated": true, "ani": 82.2803, "matched_fragments": 892, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter pinisoli", "strain": "strain=MAH-25", "accession": "GCA_009758015.1", "taxid": 2682844, "species_taxid": 2682844, "relation_to_type": "type", "validated": true, "ani": 82.1111, "matched_fragments": 978, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter lithotrophicus", "strain": "strain=RBP-1", "accession": "GCA_012184415.1", "taxid": 2606681, "species_taxid": 2606681, "relation_to_type": "type", "validated": true, "ani": 81.5476, "matched_fragments": 937, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter rhizophilus", "strain": "strain=CCTCC AB2015357", "accession": "GCA_004681965.1", "taxid": 1781167, "species_taxid": 1781167, "relation_to_type": "type", "validated": true, "ani": 81.4181, "matched_fragments": 787, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylophilus ampelinus", "strain": "strain=CFBP 1192", "accession": "GCA_024832295.1", "taxid": 54067, "species_taxid": 54067, "relation_to_type": "type", "validated": true, "ani": 80.1731, "matched_fragments": 587, "total_fragments": 1888, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016722765.1", "gtdb_species": "s__Ramlibacter alkalitolerans", "ani": 100.0, "matched_fragments": 1886, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_016722785.1", "gtdb_species": "s__Ramlibacter monticola", "ani": 86.6543, "matched_fragments": 1350, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_013087525.1", "gtdb_species": "s__Ramlibacter sp013087525", "ani": 85.2305, "matched_fragments": 1127, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_004144865.1", "gtdb_species": "s__Ramlibacter sp004144865", "ani": 84.5645, "matched_fragments": 930, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_014297465.1", "gtdb_species": "s__Ramlibacter sp014297465", "ani": 84.3479, "matched_fragments": 1161, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_015070875.1", "gtdb_species": "s__Ramlibacter sp015070875", "ani": 84.0098, "matched_fragments": 999, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_016654015.1", "gtdb_species": "s__Ramlibacter ginsenosidimutans", "ani": 83.8006, "matched_fragments": 1076, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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": "GCF_012927085.1", "gtdb_species": "s__Ramlibacter sp012927085", "ani": 83.5934, "matched_fragments": 1132, "total_fragments": 1888, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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": 29.333, "optimum_tmp": 30.0, "optimum_ph": 7.5, "genome_size": 4614330.857, "gc_content": 69.2, "coding_genes": 4012.5, "rRNA16S_genes": 1.333, "tRNA_genes": 44.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Ramlibacter", "alkalitolerans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }