{ "type": "genome", "identifier": "GCF_021343995.1", "organism": "Pseudonocardia terrae", "title": "Pseudonocardia terrae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kasetsart University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021343995.1", "bioproject": "PRJNA224116", "biosample": "SAMN24220458", "wgs_master": "JAJTTE000000000.1", "refseq_category": "reference genome", "taxid": "2905831", "species_taxid": "2905831", "organism_name": "Pseudonocardia terrae", "infraspecific_name": "strain=RS11V-5", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/01/01", "asm_name": "ASM2134399v1", "asm_submitter": "Kasetsart University", "gbrs_paired_asm": "GCA_021343995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/343/995/GCF_021343995.1_ASM2134399v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7464355", "genome_size_ungapped": "7464355", "gc_percent": "73.500000", "replicon_count": "0", "scaffold_count": "156", "contig_count": "156", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021343995.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "6983", "protein_coding_gene_count": "6788", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-01-01", "dateModified": "2022-01-01", "datePublished": "2022-01-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudonocardia terrae" ], "sample_taxid": [ "2905831" ], "sample_host_organism": [ "Oryza sativa L." ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "1.981 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7464355", "Number of Sequences": "156", "Longest Sequences (bp)": "288517", "N50 (bp)": "108261", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.3", "Number of CDSs": "6929", "Average Protein Length": "318.7", "Coding Ratio (%)": "88.7", "Number of rRNAs": "3", "Number of tRNAs": "66", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudonocardia terrae", "strain": "strain=RS11V-5", "accession": "GCA_021343995.1", "taxid": 2905831, "species_taxid": 2905831, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2401, "total_fragments": 2412, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudonocardia kujensis", "strain": "strain=KCTC 29062", "accession": "GCA_021283305.1", "taxid": 1128675, "species_taxid": 1128675, "relation_to_type": "type", "validated": true, "ani": 92.3434, "matched_fragments": 1781, "total_fragments": 2412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia pini", "strain": "strain=CAP47R", "accession": "GCA_013870575.1", "taxid": 2758030, "species_taxid": 2758030, "relation_to_type": "type", "validated": true, "ani": 83.7514, "matched_fragments": 870, "total_fragments": 2412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia oroxyli", "strain": "strain=CGMCC 4.3143", "accession": "GCA_900102195.1", "taxid": 366584, "species_taxid": 366584, "relation_to_type": "type", "validated": true, "ani": 83.0202, "matched_fragments": 1274, "total_fragments": 2412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia dioxanivorans", "strain": "strain=CB1190", "accession": "GCA_000196675.2", "taxid": 240495, "species_taxid": 240495, "relation_to_type": "type", "validated": true, "ani": 80.1301, "matched_fragments": 1208, "total_fragments": 2412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia ammonioxydans", "strain": "strain=CGMCC 4.1877", "accession": "GCA_900115005.1", "taxid": 260086, "species_taxid": 260086, "relation_to_type": "type", "validated": true, "ani": 79.711, "matched_fragments": 1144, "total_fragments": 2412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia nigra", "strain": "strain=DSM 104088", "accession": "GCA_019396355.1", "taxid": 1921578, "species_taxid": 1921578, "relation_to_type": "type", "validated": true, "ani": 79.6113, "matched_fragments": 1072, "total_fragments": 2412, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000717175.1", "gtdb_species": "s__Pseudonocardia autotrophica_A", "ani": 90.8231, "matched_fragments": 1901, "total_fragments": 2412, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_900102195.1", "gtdb_species": "s__Pseudonocardia oroxyli", "ani": 83.0153, "matched_fragments": 1277, "total_fragments": 2412, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_012911875.1", "gtdb_species": "s__Pseudonocardia bannensis", "ani": 80.5057, "matched_fragments": 1019, "total_fragments": 2412, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_007989085.1", "gtdb_species": "s__Pseudonocardia sulfidoxydans", "ani": 80.3028, "matched_fragments": 1084, "total_fragments": 2412, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_019263595.1", "gtdb_species": "s__Pseudonocardia sp019263595", "ani": 80.1526, "matched_fragments": 1027, "total_fragments": 2412, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "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_000196675.1", "gtdb_species": "s__Pseudonocardia dioxanivorans", "ani": 80.1521, "matched_fragments": 1202, "total_fragments": 2412, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" 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