{ "type": "genome", "identifier": "GCF_025273675.1", "organism": "Gordonia pseudamarae", "title": "Gordonia pseudamarae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "La Trobe University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025273675.1", "bioproject": "PRJNA224116", "biosample": "SAMN13182582", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2831662", "species_taxid": "2831662", "organism_name": "Gordonia pseudamarae", "infraspecific_name": "strain=CON9", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/22", "asm_name": "ASM2527367v1", "asm_submitter": "La Trobe University", "gbrs_paired_asm": "GCA_025273675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/273/675/GCF_025273675.1_ASM2527367v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5147008", "genome_size_ungapped": "5147008", "gc_percent": "67.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025273675.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4508", "protein_coding_gene_count": "4351", "non_coding_gene_count": "69", "pubmed_id": "33927381" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-01-22", "dateModified": "2020-01-22", "datePublished": "2020-01-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Gordonia pseudamarae" ], "sample_taxid": [ "2831662" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Dachau" ], "sample_host_location_id": [], "data_size": "1.403 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5147008", "Number of Sequences": "1", "Longest Sequences (bp)": "5147008", "N50 (bp)": "5147008", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "4537", "Average Protein Length": "339.7", "Coding Ratio (%)": "89.8", "Number of rRNAs": "12", "Number of tRNAs": "58", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gordonia pseudamarae", "strain": "strain=CON9", "accession": "GCA_025273675.1", "taxid": 2831662, "species_taxid": 2831662, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1713, "total_fragments": 1715, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gordonia amarae", "strain": "strain=NBRC 15530", "accession": "GCA_000241345.2", "taxid": 36821, "species_taxid": 36821, "relation_to_type": "type", "validated": true, "ani": 85.0588, "matched_fragments": 1210, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia namibiensis", "strain": "strain=NBRC 108229", "accession": "GCA_000298235.1", "taxid": 168480, "species_taxid": 168480, "relation_to_type": "type", "validated": true, "ani": 79.4309, "matched_fragments": 660, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia rubripertincta", "strain": "strain=NBRC 101908", "accession": "GCA_000327325.1", "taxid": 36822, "species_taxid": 36822, "relation_to_type": "type", "validated": true, "ani": 79.4203, "matched_fragments": 662, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia alkanivorans", "strain": "strain=NBRC 16433", "accession": "GCA_000225505.1", "taxid": 84096, "species_taxid": 84096, "relation_to_type": "type", "validated": true, "ani": 79.3848, "matched_fragments": 658, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia westfalica", "strain": "strain=DSM 44215", "accession": "GCA_900105725.1", "taxid": 158898, "species_taxid": 158898, "relation_to_type": "type", "validated": true, "ani": 79.3657, "matched_fragments": 699, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia rubripertincta", "strain": "strain=ATCC 14352", "accession": "GCA_012396225.1", "taxid": 36822, "species_taxid": 36822, "relation_to_type": "type", "validated": true, "ani": 79.3639, "matched_fragments": 662, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia mangrovi", "strain": "strain=HNM0687", "accession": "GCA_024734075.1", "taxid": 2665643, "species_taxid": 2665643, "relation_to_type": "type", "validated": true, "ani": 79.1675, "matched_fragments": 657, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia rhizosphera", "strain": "strain=NBRC 16068", "accession": "GCA_000298195.1", "taxid": 83341, "species_taxid": 83341, "relation_to_type": "type", "validated": true, "ani": 79.1284, "matched_fragments": 633, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia mangrovi", "strain": "strain=HNM0687", "accession": "GCA_009828195.1", "taxid": 2665643, "species_taxid": 2665643, "relation_to_type": "type", "validated": true, "ani": 79.0087, "matched_fragments": 648, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia terrae", "strain": "strain=3612", "accession": "GCA_001698225.1", "taxid": 2055, "species_taxid": 2055, "relation_to_type": "suspected-type", "validated": true, "ani": 78.9708, "matched_fragments": 661, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia terrae", "strain": "strain=NRRL B-16283", "accession": "GCA_003183825.1", "taxid": 2055, "species_taxid": 2055, "relation_to_type": "suspected-type", "validated": true, "ani": 78.9291, "matched_fragments": 680, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia terrae", "strain": "strain=NBRC 100016", "accession": "GCA_000248035.2", "taxid": 2055, "species_taxid": 2055, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8786, "matched_fragments": 647, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia sputi", "strain": "strain=ATCC 29627", "accession": "GCA_012396255.1", "taxid": 36823, "species_taxid": 36823, "relation_to_type": "type", "validated": true, "ani": 78.6633, "matched_fragments": 520, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia sputi", "strain": "strain=NBRC 100414", "accession": "GCA_000248055.2", "taxid": 36823, "species_taxid": 36823, "relation_to_type": "type", "validated": true, "ani": 78.6358, "matched_fragments": 513, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia asplenii", "strain": "strain=TBRC 11910", "accession": "GCA_012933505.1", "taxid": 2725283, "species_taxid": 2725283, "relation_to_type": "type", "validated": true, "ani": 78.581, "matched_fragments": 587, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia araii", "strain": "strain=NBRC 100433", "accession": "GCA_000241265.2", "taxid": 263909, "species_taxid": 263909, "relation_to_type": "type", "validated": true, "ani": 78.5503, "matched_fragments": 471, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia araii", "strain": "strain=IFM 10211", "accession": "GCA_013004535.1", "taxid": 263909, "species_taxid": 263909, "relation_to_type": "type", "validated": true, "ani": 78.5382, "matched_fragments": 471, "total_fragments": 1715, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_009914535.1", "gtdb_species": "s__Gordonia pseudoamarae", "ani": 99.9419, "matched_fragments": 1699, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000241345.1", "gtdb_species": "s__Gordonia amarae", "ani": 85.0704, "matched_fragments": 1208, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000344155.1", "gtdb_species": "s__Gordonia paraffinivorans", "ani": 79.6042, "matched_fragments": 644, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_000327325.1", "gtdb_species": "s__Gordonia rubripertincta", "ani": 79.4358, "matched_fragments": 659, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.07", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000298235.1", "gtdb_species": "s__Gordonia namibiensis", "ani": 79.4318, "matched_fragments": 660, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.13", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000225505.1", "gtdb_species": "s__Gordonia alkanivorans", "ani": 79.4179, "matched_fragments": 654, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.26", "min_intra_species_ani": "97.87", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900105725.1", "gtdb_species": "s__Gordonia westfalica", "ani": 79.3654, "matched_fragments": 698, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_011290605.1", "gtdb_species": "s__Gordonia sp002009645", "ani": 79.2047, "matched_fragments": 630, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "97.37", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_004193205.1", "gtdb_species": "s__Gordonia sediminis", "ani": 78.9978, "matched_fragments": 679, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_009828195.1", "gtdb_species": "s__Gordonia sp009828195", "ani": 78.9967, "matched_fragments": 652, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_003797825.1", "gtdb_species": "s__Gordonia sp003797825", "ani": 78.962, "matched_fragments": 628, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_001698225.1", "gtdb_species": "s__Gordonia terrae", "ani": 78.953, "matched_fragments": 662, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.37", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002149015.1", "gtdb_species": "s__Gordonia lacunae", "ani": 78.9284, "matched_fragments": 645, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_009862785.1", "gtdb_species": "s__Gordonia sp009862785", "ani": 78.7111, "matched_fragments": 568, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_013348785.1", "gtdb_species": "s__Gordonia sp013348785", "ani": 78.6733, "matched_fragments": 476, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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_000248055.1", "gtdb_species": "s__Gordonia sputi", "ani": 78.6433, "matched_fragments": 512, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "96.52", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000241265.1", "gtdb_species": "s__Gordonia araii", "ani": 78.5332, "matched_fragments": 472, "total_fragments": 1715, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.29, "cell_length": -0.067, "doubling_h": null, "growth_tmp": 28.984, "optimum_tmp": 29.25, "optimum_ph": 7.479, "genome_size": 4870429.978, "gc_content": 67.579, "coding_genes": 4526.729, "rRNA16S_genes": 2.666, "tRNA_genes": 48.25, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": 0.8, "coccus_cell_shape": 0.15, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.05, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Gordonia", "pseudamarae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }