{ "type": "genome", "identifier": "GCF_900269665.1", "organism": "Nocardia suismassiliense", "title": "Nocardia suismassiliense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900269665.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104566999", "wgs_master": "OIFR00000000.1", "refseq_category": "reference genome", "taxid": "2077092", "species_taxid": "2077092", "organism_name": "Nocardia suismassiliense", "infraspecific_name": "strain=S-137", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/02/21", "asm_name": "PRJEB24498", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900269665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/269/665/GCF_900269665.1_PRJEB24498", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9465194", "genome_size_ungapped": "9464996", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900269665.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "8560", "protein_coding_gene_count": "8397", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-02-21", "dateModified": "2018-02-21", "datePublished": "2018-02-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardia suismassiliense" ], "sample_taxid": [ "2077092" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "2.591 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 6.48, "strain_heterogeneity": 33.33, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9465194", "Number of Sequences": "25", "Longest Sequences (bp)": "9122433", "N50 (bp)": "9122433", "Gap Ratio (%)": "0.003138", "GCcontent (%)": "67.1", "Number of CDSs": "8643", "Average Protein Length": "320.7", "Coding Ratio (%)": "87.9", "Number of rRNAs": "9", "Number of tRNAs": "66", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardia suismassiliense", "strain": "strain=S-137", "accession": "GCA_900269665.1", "taxid": 2077092, "species_taxid": 2077092, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3141, "total_fragments": 3141, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardia ninae", "strain": "strain=NBRC 108245", "accession": "GCA_007990755.1", "taxid": 356145, "species_taxid": 356145, "relation_to_type": "type", "validated": true, "ani": 94.9074, "matched_fragments": 2594, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia colli", "strain": "strain=CICC 11023", "accession": "GCA_008704205.1", "taxid": 2545717, "species_taxid": 2545717, "relation_to_type": "type", "validated": true, "ani": 87.4244, "matched_fragments": 2264, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia iowensis", "strain": "strain=NRRL 5646", "accession": "GCA_019222765.1", "taxid": 204891, "species_taxid": 204891, "relation_to_type": "type", "validated": true, "ani": 87.1552, "matched_fragments": 2131, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia tenerifensis", "strain": "strain=DSM 44704", "accession": "GCA_003202065.1", "taxid": 228006, "species_taxid": 228006, "relation_to_type": "type", "validated": true, "ani": 86.7305, "matched_fragments": 2154, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia tenerifensis", "strain": "strain=NBRC 101015", "accession": "GCA_000308715.1", "taxid": 228006, "species_taxid": 228006, "relation_to_type": "type", "validated": true, "ani": 86.6549, "matched_fragments": 1938, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia altamirensis", "strain": "strain=NBRC 108246", "accession": "GCA_001612685.1", "taxid": 472158, "species_taxid": 472158, "relation_to_type": "type", "validated": true, "ani": 85.1319, "matched_fragments": 1989, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia vulneris", "strain": "strain=W9851", "accession": "GCA_000811985.1", "taxid": 1141657, "species_taxid": 1141657, "relation_to_type": "type", "validated": true, "ani": 85.0001, "matched_fragments": 2030, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia vulneris", "strain": "strain=NBRC 108936", "accession": "GCA_001613425.1", "taxid": 1141657, "species_taxid": 1141657, "relation_to_type": "type", "validated": true, "ani": 84.9945, "matched_fragments": 2043, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardia rhizosphaerihabitans", "strain": "strain=CGMCC 4.7329", "accession": "GCA_014646295.1", "taxid": 1691570, "species_taxid": 1691570, "relation_to_type": "type", "validated": true, "ani": 81.1237, "matched_fragments": 1274, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia zhaorongruii", "strain": "strain=HY186", "accession": "GCA_007559005.1", "taxid": 2597659, "species_taxid": 2597659, "relation_to_type": "type", "validated": true, "ani": 77.6172, "matched_fragments": 297, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia jinhuaensis", "strain": "strain=CGMCC 1.12827", "accession": "GCA_014639795.1", "taxid": 1517702, "species_taxid": 1517702, "relation_to_type": "type", "validated": true, "ani": 77.5302, "matched_fragments": 386, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia spumicola", "strain": "strain=NBRC 107696", "accession": "GCA_009932475.1", "taxid": 589161, "species_taxid": 589161, "relation_to_type": "type", "validated": true, "ani": 77.5177, "matched_fragments": 426, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gordonia hydrophobica", "strain": "strain=NBRC 16057", "accession": "GCA_001592365.1", "taxid": 40516, "species_taxid": 40516, "relation_to_type": "type", "validated": true, "ani": 77.2757, "matched_fragments": 399, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amycolatopsis albispora", "strain": "strain=WP1", "accession": "GCA_003312875.1", "taxid": 1804986, "species_taxid": 1804986, "relation_to_type": "type", "validated": true, "ani": 76.9111, "matched_fragments": 675, "total_fragments": 3141, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 6.48, "strain_heterogeneity": 33.33 }, "gtdb_result": [ { "accession": "GCF_900269665.1", "gtdb_species": "s__Nocardia suismassiliense", "ani": 100.0, "matched_fragments": 3141, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.20", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_007990755.1", "gtdb_species": "s__Nocardia ninae", "ani": 94.9074, "matched_fragments": 2594, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.51", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008704205.1", "gtdb_species": "s__Nocardia colli", "ani": 87.4325, "matched_fragments": 2262, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_019222765.1", "gtdb_species": "s__Nocardia iowensis", "ani": 87.1484, "matched_fragments": 2130, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_000308715.1", "gtdb_species": "s__Nocardia tenerifensis", "ani": 86.6741, "matched_fragments": 1935, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001612685.1", "gtdb_species": "s__Nocardia altamirensis", "ani": 85.0933, "matched_fragments": 1996, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_001613425.1", "gtdb_species": "s__Nocardia vulneris", "ani": 85.0224, "matched_fragments": 2038, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.8238, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000284035.1", "gtdb_species": "s__Nocardia cyriacigeorgica_B", "ani": 81.5192, "matched_fragments": 1196, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_014646295.1", "gtdb_species": "s__Nocardia rhizosphaerihabitans", "ani": 81.1204, "matched_fragments": 1273, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "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_010868145.1", "gtdb_species": "s__Nocardia cyriacigeorgica_D", "ani": 80.8913, "matched_fragments": 1107, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "99.66", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_011290605.1", "gtdb_species": "s__Gordonia sp002009645", "ani": 77.7531, "matched_fragments": 462, "total_fragments": 3141, "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": "GCF_009932475.1", "gtdb_species": "s__Gordonia spumicola", "ani": 77.4712, "matched_fragments": 426, "total_fragments": 3141, "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_001592365.1", "gtdb_species": "s__Gordonia hydrophobica", "ani": 77.2894, "matched_fragments": 397, "total_fragments": 3141, "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": "-" }, { "accession": "GCF_004362825.1", "gtdb_species": "s__Labedaea rhizosphaerae", "ani": 76.7327, "matched_fragments": 595, "total_fragments": 3141, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea", "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": -0.223, "cell_length": 0.046, "doubling_h": null, "growth_tmp": 29.192, "optimum_tmp": 30.56, "optimum_ph": 7.496, "genome_size": 7903167.49, "gc_content": 68.006, "coding_genes": 6908.619, "rRNA16S_genes": 3.166, "tRNA_genes": 53.5, "gram_stain": 1.0, "sporulation": 0.833, "motility": 0.0, "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": 0.098, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.882, "coccobacillus_cell_shape": 0.019, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardia", "suismassiliense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }