{ "type": "genome", "identifier": "GCF_900496965.1", "organism": "Achromobacter agilis", "title": "Achromobacter agilis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "LM-UGent", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900496965.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4780388", "wgs_master": "UFQB00000000.1", "refseq_category": "reference genome", "taxid": "1353888", "species_taxid": "1353888", "organism_name": "Achromobacter agilis", "infraspecific_name": "strain=LMG 3411", "isolate": "LMG 3411", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/25", "asm_name": "LMG 3411T", "asm_submitter": "LM-UGent", "gbrs_paired_asm": "GCA_900496965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/496/965/GCF_900496965.1_LMG_3411T", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6376476", "genome_size_ungapped": "6376476", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "63", "contig_count": "63", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900496965.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "6024", "protein_coding_gene_count": "5887", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-25", "dateModified": "2019-01-25", "datePublished": "2019-01-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Achromobacter agilis" ], "sample_taxid": [ "1353888" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia" ], "sample_host_location_id": [], "data_size": "1.754 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)": "6376476", "Number of Sequences": "63", "Longest Sequences (bp)": "449474", "N50 (bp)": "181045", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.5", "Number of CDSs": "5943", "Average Protein Length": "322.6", "Coding Ratio (%)": "90.2", "Number of rRNAs": "2", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Achromobacter agilis", "strain": "strain=LMG 3411", "accession": "GCA_900496965.1", "taxid": 1353888, "species_taxid": 1353888, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2095, "total_fragments": 2100, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Achromobacter veterisilvae", "strain": "strain=LMG 30378", "accession": "GCA_900496975.1", "taxid": 2069367, "species_taxid": 2069367, "relation_to_type": "type", "validated": true, "ani": 90.9653, "matched_fragments": 1659, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter denitrificans", "strain": "strain=LMG 1231", "accession": "GCA_902859715.1", "taxid": 32002, "species_taxid": 32002, "relation_to_type": "type", "validated": true, "ani": 90.4164, "matched_fragments": 1696, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter denitrificans", "strain": "strain=NBRC 15125", "accession": "GCA_001571365.1", "taxid": 32002, "species_taxid": 32002, "relation_to_type": "type", "validated": true, "ani": 90.4088, "matched_fragments": 1703, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter 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"accession": "GCA_902859645.1", "taxid": 1287735, "species_taxid": 1287735, "relation_to_type": "type", "validated": true, "ani": 86.0355, "matched_fragments": 1405, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter xylosoxidans", "strain": "strain=PartM-Axylosoxidans-RM8376", "accession": "GCA_022870085.1", "taxid": 85698, "species_taxid": 85698, "relation_to_type": "type", "validated": true, "ani": 85.8433, "matched_fragments": 1448, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella bronchiseptica", "strain": "strain=CCUG 219", "accession": "GCA_021391275.1", "taxid": 518, "species_taxid": 518, "relation_to_type": "suspected-type", "validated": true, "ani": 82.0963, "matched_fragments": 906, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus numazuensis", "strain": "strain=LMG 26411", "accession": "GCA_905397435.1", "taxid": 221992, "species_taxid": 221992, "relation_to_type": "type", "validated": true, "ani": 77.4801, "matched_fragments": 484, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rugamonas brunnea", "strain": "strain=LX20W", "accession": "GCA_014042345.1", "taxid": 2758569, "species_taxid": 2758569, "relation_to_type": "type", "validated": true, "ani": 77.1954, "matched_fragments": 425, "total_fragments": 2100, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900496965.1", "gtdb_species": "s__Achromobacter agilis", "ani": 100.0, "matched_fragments": 2095, "total_fragments": 2100, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", 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"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_001571365.1", "gtdb_species": "s__Achromobacter denitrificans", "ani": 90.4088, "matched_fragments": 1703, "total_fragments": 2100, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_002885955.2", "gtdb_species": "s__Achromobacter pulmonis_A", "ani": 88.5075, "matched_fragments": 1535, "total_fragments": 2100, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", 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"min_intra_species_ani": "98.86", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_016127315.1", "gtdb_species": "s__Achromobacter insuavis_A", "ani": 85.9111, "matched_fragments": 1446, "total_fragments": 2100, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "ani_circumscription_radius": 95.6014, "mean_intra_species_ani": "97.14", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 30.807, "optimum_tmp": 29.833, "optimum_ph": null, "genome_size": 6480678.912, "gc_content": 65.825, "coding_genes": 5804.816, "rRNA16S_genes": 3.5, "tRNA_genes": 57.375, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.75, "range_salinity": 1.0, "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": [ "Achromobacter", "agilis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }