{ "type": "genome", "identifier": "GCF_002895925.1", "organism": "Mixta theicola", "title": "Mixta theicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Pretoria", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002895925.1", "bioproject": "PRJNA224116", "biosample": "SAMN07663080", "wgs_master": "NWUO00000000.1", "refseq_category": "reference genome", "taxid": "1458355", "species_taxid": "1458355", "organism_name": "Mixta theicola", "infraspecific_name": "strain=QC88-366", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/23", "asm_name": "ASM289592v1", "asm_submitter": "University of Pretoria", "gbrs_paired_asm": "GCA_002895925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/895/925/GCF_002895925.1_ASM289592v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4291231", "genome_size_ungapped": "4291231", "gc_percent": "54.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002895925.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4123", "protein_coding_gene_count": "3868", "non_coding_gene_count": "96", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-23", "dateModified": "2018-01-23", "datePublished": "2018-01-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Mixta theicola" ], "sample_taxid": [ "1458355" ], "sample_host_organism": [ "black tea" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.210 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)": "4291231", "Number of Sequences": "72", "Longest Sequences (bp)": "526330", "N50 (bp)": "278310", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.0", "Number of CDSs": "3977", "Average Protein Length": "307.6", "Coding Ratio (%)": "85.5", "Number of rRNAs": "6", "Number of tRNAs": "72", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mixta calida", "strain": "strain=LMG 25383", "accession": "GCA_002095355.1", "taxid": 665913, "species_taxid": 665913, "relation_to_type": "type", "validated": true, "ani": 84.8715, "matched_fragments": 973, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mixta calida", "strain": "strain=DSM 22759", "accession": "GCA_002953215.1", "taxid": 665913, "species_taxid": 665913, "relation_to_type": "type", "validated": true, "ani": 84.8557, "matched_fragments": 1078, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mixta gaviniae", "strain": "strain=DSM 22758", "accession": "GCA_002953195.1", "taxid": 665914, "species_taxid": 665914, "relation_to_type": "type", "validated": true, "ani": 84.802, "matched_fragments": 1066, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mixta tenebrionis", "strain": "strain=BIT-26", "accession": "GCA_006517625.1", "taxid": 2562439, "species_taxid": 2562439, "relation_to_type": "type", "validated": true, "ani": 84.0831, "matched_fragments": 1008, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea septica", "strain": "strain=LMG 5345", "accession": "GCA_002095575.1", "taxid": 472695, "species_taxid": 472695, "relation_to_type": "type", "validated": true, "ani": 80.3174, "matched_fragments": 720, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia iniecta", "strain": "strain=B120", "accession": "GCA_001267535.1", "taxid": 1560201, "species_taxid": 1560201, "relation_to_type": "type", "validated": true, "ani": 80.1069, "matched_fragments": 699, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia phyllosphaerae", "strain": "strain=CMYE1", "accession": "GCA_019132875.1", "taxid": 2853256, "species_taxid": 2853256, "relation_to_type": "type", "validated": true, "ani": 79.8826, "matched_fragments": 637, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=X001", "accession": "GCA_024169515.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 79.6731, "matched_fragments": 691, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=JCM 21238", "accession": "GCA_014773485.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 79.639, "matched_fragments": 674, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_001971035.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 78.9538, "matched_fragments": 518, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siccibacter turicensis", "strain": "strain=LMG 23730", "accession": "GCA_000463155.2", "taxid": 357233, "species_taxid": 357233, "relation_to_type": "type", "validated": true, "ani": 78.7863, "matched_fragments": 520, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 78.7294, "matched_fragments": 469, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 78.65, "matched_fragments": 483, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia thailandensis", "strain": "strain=KCTC 23281", "accession": "GCA_014652175.1", "taxid": 990144, "species_taxid": 990144, "relation_to_type": "type", "validated": true, "ani": 77.8423, "matched_fragments": 82, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002895925.1", "gtdb_species": "s__Mixta theicola", "ani": 100.0, "matched_fragments": 1400, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta", "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_002101395.1", "gtdb_species": "s__Mixta alhagi", "ani": 89.5439, "matched_fragments": 1106, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta", "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_002953215.1", "gtdb_species": "s__Mixta calida", "ani": 84.8583, "matched_fragments": 1077, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_002953195.1", "gtdb_species": "s__Mixta gaviniae", "ani": 84.7925, "matched_fragments": 1067, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006517625.1", "gtdb_species": "s__Mixta tenebrionis", "ani": 84.0986, "matched_fragments": 1005, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009914055.1", "gtdb_species": "s__Mixta intestinalis", "ani": 83.5918, "matched_fragments": 993, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta", "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_002920175.1", "gtdb_species": "s__Pantoea sp002920175", "ani": 80.7523, "matched_fragments": 766, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002095465.1", "gtdb_species": "s__Pantoea rodasii", "ani": 79.5155, "matched_fragments": 588, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018842675.1", "gtdb_species": "s__Pantoea sp018842675", "ani": 79.3439, "matched_fragments": 588, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "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_002858715.1", "gtdb_species": "s__Chimaeribacter coloradensis", "ani": 78.8337, "matched_fragments": 516, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "98.66", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "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": [ "Mixta", "theicola" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }