{ "type": "genome", "identifier": "GCF_003751265.1", "organism": "Pseudokineococcus lusitanus", "title": "Pseudokineococcus lusitanus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003751265.1", "bioproject": "PRJNA224116", "biosample": "SAMN10363401", "wgs_master": "RJKN00000000.1", "refseq_category": "reference genome", "taxid": "763993", "species_taxid": "763993", "organism_name": "Pseudokineococcus lusitanus", "infraspecific_name": "strain=CECT 7306", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/11/15", "asm_name": "ASM375126v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003751265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/751/265/GCF_003751265.1_ASM375126v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3839029", "genome_size_ungapped": "3838681", "gc_percent": "77.000000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003751265.1-RS_2024_04_05", "annotation_date": "2024-04-05", "total_gene_count": "3463", "protein_coding_gene_count": "3395", "non_coding_gene_count": "54", "pubmed_id": "26203337" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-11-15", "dateModified": "2018-11-15", "datePublished": "2018-11-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudokineococcus lusitanus" ], "sample_taxid": [ "763993" ], "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": "0.971 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)": "3839029", "Number of Sequences": "19", "Longest Sequences (bp)": "711740", "N50 (bp)": "417836", "Gap Ratio (%)": "0.009065", "GCcontent (%)": "77.0", "Number of CDSs": "3421", "Average Protein Length": "339.5", "Coding Ratio (%)": "90.8", "Number of rRNAs": "3", "Number of tRNAs": "60", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudokineococcus lusitanus", "strain": "strain=CECT 7306", "accession": "GCA_003751265.1", "taxid": 763993, "species_taxid": 763993, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1269, "total_fragments": 1270, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudokineococcus marinus", "strain": "strain=JCM 14547", "accession": "GCA_013004605.1", "taxid": 351215, "species_taxid": 351215, "relation_to_type": "type", "validated": true, "ani": 83.2725, "matched_fragments": 653, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Quadrisphaera setariae", "strain": "strain=DD2A", "accession": "GCA_008041935.1", "taxid": 2593304, "species_taxid": 2593304, "relation_to_type": "type", "validated": true, "ani": 77.6352, "matched_fragments": 622, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus indalonis", "strain": "strain=T90", "accession": "GCA_009906395.1", "taxid": 2696566, "species_taxid": 2696566, "relation_to_type": "type", "validated": true, "ani": 77.6115, "matched_fragments": 461, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Quadrisphaera granulorum", "strain": "strain=DSM 44889", "accession": "GCA_003149145.1", "taxid": 317664, "species_taxid": 317664, "relation_to_type": "type", "validated": true, "ani": 77.4771, "matched_fragments": 519, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Quadrisphaera granulorum", "strain": "strain=DSM 44889", "accession": "GCA_900218025.1", "taxid": 317664, "species_taxid": 317664, "relation_to_type": "type", "validated": true, "ani": 77.4359, "matched_fragments": 526, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineococcus vitellinus", "strain": "strain=T13", "accession": "GCA_009906315.1", "taxid": 2696565, "species_taxid": 2696565, "relation_to_type": "type", "validated": true, "ani": 77.4002, "matched_fragments": 565, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Georgenia wutianyii", "strain": "strain=Z294", "accession": "GCA_006349365.1", "taxid": 2585135, "species_taxid": 2585135, "relation_to_type": "type", "validated": true, "ani": 77.3163, "matched_fragments": 492, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedococcus cremeus", "strain": "strain=CGMCC 1.6963", "accession": "GCA_900111375.1", "taxid": 587636, "species_taxid": 587636, "relation_to_type": "type", "validated": true, "ani": 77.288, "matched_fragments": 439, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus jejuensis", "strain": "strain=NRRL B-24460", "accession": "GCA_000720925.1", "taxid": 367299, "species_taxid": 367299, "relation_to_type": "type", "validated": true, "ani": 77.2636, "matched_fragments": 559, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotalea solisilvae", "strain": "strain=KACC 19191", "accession": "GCA_016464425.1", "taxid": 2072922, "species_taxid": 2072922, "relation_to_type": "type", "validated": true, "ani": 77.242, "matched_fragments": 597, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus mangrovi", "strain": "strain=KQZ13P-1", "accession": "GCA_018729305.1", "taxid": 2840470, "species_taxid": 2840470, "relation_to_type": "type", "validated": true, "ani": 77.2229, "matched_fragments": 561, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Georgenia faecalis", "strain": "strain=ZLJ0423", "accession": "GCA_003710105.1", "taxid": 2483799, "species_taxid": 2483799, "relation_to_type": "type", "validated": true, "ani": 77.1543, "matched_fragments": 527, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sanguibacter keddieii", "strain": "strain=DSM 10542", "accession": "GCA_000024925.1", "taxid": 60920, "species_taxid": 60920, "relation_to_type": "type", "validated": true, "ani": 76.9339, "matched_fragments": 486, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas palmilytica", "strain": "strain=EW123", "accession": "GCA_021590045.1", "taxid": 2608402, "species_taxid": 2608402, "relation_to_type": "type", "validated": true, "ani": 76.9014, "matched_fragments": 493, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotalea subterranea", "strain": "strain=HO-Ch2", "accession": "GCA_008364845.1", "taxid": 2607497, "species_taxid": 2607497, "relation_to_type": "type", "validated": true, "ani": 76.8659, "matched_fragments": 482, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Motilibacter rhizosphaerae", "strain": "strain=DSM 45622", "accession": "GCA_004216915.1", "taxid": 598652, "species_taxid": 598652, "relation_to_type": "type", "validated": true, "ani": 76.8414, "matched_fragments": 536, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Motilibacter aurantiacus", "strain": "strain=K478", "accession": "GCA_011250645.1", "taxid": 2714955, "species_taxid": 2714955, "relation_to_type": "type", "validated": true, "ani": 76.6723, "matched_fragments": 503, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium sediminis", "strain": "strain=EGI L100131", "accession": "GCA_021272345.1", "taxid": 2904603, "species_taxid": 2904603, "relation_to_type": "type", "validated": true, "ani": 76.6637, "matched_fragments": 338, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occultella gossypii", "strain": "strain=N2-46", "accession": "GCA_019947135.1", "taxid": 2800820, "species_taxid": 2800820, "relation_to_type": "type", "validated": true, 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"total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003751265.1", "gtdb_species": "s__Pseudokineococcus lusitanus", "ani": 100.0, "matched_fragments": 1269, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus", "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": "conclusive" }, { "accession": "GCF_013004605.1", "gtdb_species": "s__Pseudokineococcus marinus", "ani": 83.1128, "matched_fragments": 666, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus", "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_900101335.1", "gtdb_species": "s__Quadrisphaera sp900101335", "ani": 78.0702, "matched_fragments": 552, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera", "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_015390235.1", "gtdb_species": "s__Quadrisphaera sp015390235", "ani": 77.8561, "matched_fragments": 601, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera", "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_014270065.1", "gtdb_species": "s__Quadrisphaera sp014270065", "ani": 77.7444, "matched_fragments": 590, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera", "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_009906315.1", "gtdb_species": "s__Kineococcus vitellinus", "ani": 77.3824, "matched_fragments": 568, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_007991755.1", "gtdb_species": "s__Cellulomonas aerilata", "ani": 77.105, "matched_fragments": 494, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas", "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_000767215.1", "gtdb_species": "s__Actinotalea fermentans", "ani": 77.0959, "matched_fragments": 366, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea", "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", 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"filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudokineococcus", "lusitanus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }