{ "type": "genome", "identifier": "GCF_019396355.1", "organism": "Pseudonocardia nigra", "title": "Pseudonocardia nigra", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chengdu University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019396355.1", "bioproject": "PRJNA224116", "biosample": "SAMN19373109", "wgs_master": "JAHKRK000000000.1", "refseq_category": "reference genome", "taxid": "1921578", "species_taxid": "1921578", "organism_name": "Pseudonocardia nigra", "infraspecific_name": "strain=DSM 104088", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/29", "asm_name": "ASM1939635v1", "asm_submitter": "Chengdu University", "gbrs_paired_asm": "GCA_019396355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/396/355/GCF_019396355.1_ASM1939635v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8494240", "genome_size_ungapped": "8493325", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "601", "contig_count": "601", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019396355.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "8688", "protein_coding_gene_count": "8123", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-29", "dateModified": "2021-07-29", "datePublished": "2021-07-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudonocardia nigra" ], "sample_taxid": [ "1921578" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "2.265 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8494240", "Number of Sequences": "601", "Longest Sequences (bp)": "150066", "N50 (bp)": "28177", "Gap Ratio (%)": "0.010949", "GCcontent (%)": "72.8", "Number of CDSs": "8253", "Average Protein Length": "292.1", "Coding Ratio (%)": "85.2", "Number of rRNAs": "2", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudonocardia nigra", "strain": "strain=DSM 104088", "accession": "GCA_019396355.1", "taxid": 1921578, "species_taxid": 1921578, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2526, "total_fragments": 2553, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudonocardia kunmingensis", "strain": "strain=DSM 45301", "accession": "GCA_006716445.1", "taxid": 630975, "species_taxid": 630975, "relation_to_type": "type", "validated": true, "ani": 82.5139, "matched_fragments": 1480, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia xinjiangensis", "strain": "strain=JCM 11839", "accession": "GCA_012911925.1", "taxid": 75289, "species_taxid": 75289, "relation_to_type": "type", "validated": true, "ani": 81.9432, "matched_fragments": 1174, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia cypriaca", "strain": "strain=DSM 45511", "accession": "GCA_006717045.1", "taxid": 882449, "species_taxid": 882449, "relation_to_type": "type", "validated": true, "ani": 81.7327, "matched_fragments": 1347, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia hierapolitana", "strain": "strain=DSM 45671", "accession": "GCA_007994075.1", "taxid": 1128676, "species_taxid": 1128676, "relation_to_type": "type", "validated": true, "ani": 81.7235, "matched_fragments": 1380, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia alaniniphila", "strain": "strain=Y-16303", "accession": "GCA_022524485.1", "taxid": 75291, "species_taxid": 75291, "relation_to_type": "type", "validated": true, "ani": 81.2732, "matched_fragments": 1223, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia oceani", "strain": "strain=KRD185", "accession": "GCA_019263585.2", "taxid": 2792013, "species_taxid": 2792013, "relation_to_type": "type", "validated": true, "ani": 80.8591, "matched_fragments": 1204, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia asaccharolytica", "strain": "strain=DSM 44247", "accession": "GCA_000423625.1", "taxid": 54010, "species_taxid": 54010, "relation_to_type": "type", "validated": true, "ani": 79.9293, "matched_fragments": 859, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia asaccharolytica", "strain": "strain=NBRC 16224", "accession": "GCA_007989065.1", "taxid": 54010, "species_taxid": 54010, "relation_to_type": "type", "validated": true, "ani": 79.916, "matched_fragments": 863, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia sulfidoxydans", "strain": "strain=NBRC 16205", "accession": "GCA_007989085.1", "taxid": 54011, "species_taxid": 54011, "relation_to_type": "type", "validated": true, "ani": 79.4545, "matched_fragments": 964, "total_fragments": 2553, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006716445.1", "gtdb_species": "s__Pseudonocardia kunmingensis", "ani": 82.5406, "matched_fragments": 1475, "total_fragments": 2553, "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_002262885.1", "gtdb_species": "s__Pseudonocardia sp002262885", "ani": 82.2424, "matched_fragments": 1468, "total_fragments": 2553, "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", 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1, "status": "-" }, { "accession": "GCF_007994075.1", "gtdb_species": "s__Pseudonocardia hierapolitana", "ani": 81.7481, "matched_fragments": 1376, "total_fragments": 2553, "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_001942185.1", "gtdb_species": "s__Pseudonocardia sp001942185", "ani": 81.4652, "matched_fragments": 1338, "total_fragments": 2553, "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": "-" }, { 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