{ "type": "genome", "identifier": "GCF_000614545.1", "organism": "Asaia platycodi JCM 25414", "title": "Asaia platycodi JCM 25414", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000614545.1", "bioproject": "PRJNA224116", "biosample": "SAMD00002827", "wgs_master": "BAKW00000000.1", "refseq_category": "reference genome", "taxid": "1236525", "species_taxid": "610243", "organism_name": "Asaia platycodi JCM 25414", "infraspecific_name": "strain=JCM 25414", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/03/31", "asm_name": "ASM61454v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_000614545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/614/545/GCF_000614545.1_ASM61454v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3150973", "genome_size_ungapped": "3150973", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000614545.1-RS_2024_12_15", "annotation_date": "2024-12-15", "total_gene_count": "3273", "protein_coding_gene_count": "2623", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-03-31", "dateModified": "2014-03-31", "datePublished": "2014-03-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Asaia platycodi JCM 25414" ], "sample_taxid": [ "1236525" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.891 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 93.92, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3150973", "Number of Sequences": "35", "Longest Sequences (bp)": "452832", "N50 (bp)": "117874", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.3", "Number of CDSs": "3682", "Average Protein Length": "245.7", "Coding Ratio (%)": "86.1", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Asaia platycodi", "strain": "strain=JCM 25414", "accession": "GCA_000614545.1", "taxid": 610243, "species_taxid": 610243, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1029, "total_fragments": 1031, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Asaia siamensis", "strain": "strain=CCM 7132", "accession": "GCA_014635085.1", "taxid": 110479, "species_taxid": 110479, "relation_to_type": "type", "validated": true, "ani": 85.6047, "matched_fragments": 848, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Asaia prunellae", "strain": "strain=JCM 25354", "accession": "GCA_000613885.1", "taxid": 610245, "species_taxid": 610245, "relation_to_type": "type", "validated": true, "ani": 82.3494, "matched_fragments": 644, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Asaia lannensis", "strain": "strain=NBRC 102526", "accession": "GCA_024054035.1", "taxid": 415421, "species_taxid": 415421, "relation_to_type": "type", "validated": true, "ani": 81.693, "matched_fragments": 638, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Asaia bogorensis", "strain": "strain=NBRC 16594", "accession": "GCA_007989265.1", "taxid": 91915, "species_taxid": 91915, "relation_to_type": "suspected-type", "validated": true, "ani": 81.6048, "matched_fragments": 633, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Asaia bogorensis", "strain": "strain=NBRC 16594", "accession": "GCA_001547995.1", "taxid": 91915, "species_taxid": 91915, "relation_to_type": "suspected-type", "validated": true, "ani": 81.5177, "matched_fragments": 653, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Asaia astilbis", "strain": "strain=JCM 15831", "accession": "GCA_000613845.1", "taxid": 610244, "species_taxid": 610244, "relation_to_type": "type", "validated": true, "ani": 81.206, "matched_fragments": 607, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter liquefaciens", "strain": "strain=NBRC 12388", "accession": "GCA_006539085.1", "taxid": 89584, "species_taxid": 89584, "relation_to_type": "type", "validated": true, "ani": 77.5428, "matched_fragments": 178, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter liquefaciens", "strain": "strain=LMG 1382", "accession": "GCA_014174285.1", "taxid": 89584, "species_taxid": 89584, "relation_to_type": "type", "validated": true, "ani": 77.5416, "matched_fragments": 182, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acetobacter garciniae", "strain": "strain=TBRC 12339", "accession": "GCA_017377735.1", "taxid": 2817435, "species_taxid": 2817435, "relation_to_type": "type", "validated": true, "ani": 77.2524, "matched_fragments": 121, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovastum atsumiense", "strain": "strain=G2-11", "accession": "GCA_937425535.1", "taxid": 504468, "species_taxid": 504468, "relation_to_type": "type", "validated": true, "ani": 76.7361, "matched_fragments": 100, "total_fragments": 1031, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 93.92, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000614545.1", "gtdb_species": "s__Asaia platycodi", "ani": 100.0, "matched_fragments": 1029, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "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_014635085.1", "gtdb_species": "s__Asaia siamensis", "ani": 85.6047, "matched_fragments": 848, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "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_000613885.1", "gtdb_species": "s__Asaia prunellae", "ani": 82.3494, "matched_fragments": 644, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "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_003994335.1", "gtdb_species": "s__Asaia sp003994335", "ani": 81.7674, "matched_fragments": 662, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "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_001547995.1", "gtdb_species": "s__Asaia bogorensis", "ani": 81.5177, "matched_fragments": 653, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.55", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900465345.1", "gtdb_species": "s__Asaia bogorensis_A", "ani": 81.4489, "matched_fragments": 615, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "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_000613845.1", "gtdb_species": "s__Asaia astilbis", "ani": 81.206, "matched_fragments": 607, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia", "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_007988945.1", "gtdb_species": "s__Swaminathania salitolerans", "ani": 80.1639, "matched_fragments": 477, "total_fragments": 1031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania", "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": -0.239, "cell_length": 0.048, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": 3.25, "genome_size": 3339939.5, "gc_content": 59.8, "coding_genes": 2718.333, "rRNA16S_genes": 5.0, "tRNA_genes": 57.0, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "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": [ "Asaia", "platycodi", "JCM", "25414" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }