{ "type": "genome", "identifier": "GCF_004217185.1", "organism": "Pseudonocardia sediminis", "title": "Pseudonocardia sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004217185.1", "bioproject": "PRJNA224116", "biosample": "SAMN10865813", "wgs_master": "SHKL00000000.1", "refseq_category": "reference genome", "taxid": "1397368", "species_taxid": "1397368", "organism_name": "Pseudonocardia sediminis", "infraspecific_name": "strain=DSM 45779", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/20", "asm_name": "ASM421718v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004217185.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/217/185/GCF_004217185.1_ASM421718v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6612042", "genome_size_ungapped": "6612042", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004217185.1-RS_2024_04_10", "annotation_date": "2024-04-10", "total_gene_count": "6237", "protein_coding_gene_count": "6124", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-20", "dateModified": "2019-02-20", "datePublished": "2019-02-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudonocardia sediminis" ], "sample_taxid": [ "1397368" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.736 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)": "6612042", "Number of Sequences": "2", "Longest Sequences (bp)": "6501404", "N50 (bp)": "6501404", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.9", "Number of CDSs": "6281", "Average Protein Length": "316.6", "Coding Ratio (%)": "90.2", "Number of rRNAs": "9", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudonocardia sediminis", "strain": "strain=DSM 45779", "accession": "GCA_004217185.1", "taxid": 1397368, "species_taxid": 1397368, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2203, "total_fragments": 2203, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudonocardia endophytica", "strain": "strain=DSM 44969", "accession": "GCA_004339565.1", "taxid": 401976, "species_taxid": 401976, "relation_to_type": "type", "validated": true, "ani": 82.6452, "matched_fragments": 1395, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia antarctica", "strain": "strain=DSM 44749", "accession": "GCA_013408715.1", "taxid": 237656, "species_taxid": 237656, "relation_to_type": "type", "validated": true, "ani": 82.268, "matched_fragments": 1288, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia parietis", "strain": "strain=DSM 45256", "accession": "GCA_017876315.1", "taxid": 570936, "species_taxid": 570936, "relation_to_type": "type", "validated": true, "ani": 81.7708, "matched_fragments": 1286, "total_fragments": 2203, "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": 81.6761, "matched_fragments": 1315, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia autotrophica", "strain": "strain=NBRC 12743", "accession": "GCA_003945385.1", "taxid": 2074, "species_taxid": 2074, "relation_to_type": "suspected-type", "validated": true, "ani": 81.5177, "matched_fragments": 1260, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia autotrophica", "strain": "strain=DSM 535", "accession": "GCA_004361965.1", "taxid": 2074, "species_taxid": 2074, "relation_to_type": "suspected-type", "validated": true, "ani": 81.5012, "matched_fragments": 1254, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia autotrophica", "strain": "strain=DSM 535", "accession": "GCA_002119215.1", "taxid": 2074, "species_taxid": 2074, "relation_to_type": "suspected-type", "validated": true, "ani": 81.4192, "matched_fragments": 1234, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia terrae", "strain": "strain=RS11V-5", "accession": "GCA_021343995.1", "taxid": 2905831, "species_taxid": 2905831, "relation_to_type": "type", "validated": true, "ani": 80.1334, "matched_fragments": 1156, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia bannensis", "strain": "strain=DSM 45300", "accession": "GCA_012911875.1", "taxid": 630973, "species_taxid": 630973, "relation_to_type": "type", "validated": true, "ani": 80.1189, "matched_fragments": 981, "total_fragments": 2203, "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": 80.0943, "matched_fragments": 688, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudonocardia kujensis", "strain": "strain=KCTC 29062", "accession": "GCA_021283305.1", "taxid": 1128675, "species_taxid": 1128675, "relation_to_type": "type", "validated": true, "ani": 79.979, "matched_fragments": 1177, "total_fragments": 2203, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004217185.1", "gtdb_species": "s__Pseudonocardia sediminis", "ani": 100.0, "matched_fragments": 2203, "total_fragments": 2203, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia", 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