{ "type": "genome", "identifier": "GCF_003687455.1", "organism": "Kocuria tytonicola", "title": "Kocuria tytonicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Pharmacy and Molecular Biotechnology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003687455.1", "bioproject": "PRJNA224116", "biosample": "SAMN08095948", "wgs_master": "PHOA00000000.1", "refseq_category": "na", "taxid": "2055946", "species_taxid": "2055946", "organism_name": "Kocuria tytonicola", "infraspecific_name": "strain=DSM 104133", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/24", "asm_name": "ASM368745v1", "asm_submitter": "Institute of Pharmacy and Molecular Biotechnology", "gbrs_paired_asm": "GCA_003687455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/687/455/GCF_003687455.1_ASM368745v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2614304", "genome_size_ungapped": "2614304", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "239", "contig_count": "239", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003687455.1-RS_2024_08_06", "annotation_date": "2024-08-06", "total_gene_count": "2411", "protein_coding_gene_count": "2291", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-24", "dateModified": "2018-10-24", "datePublished": "2018-10-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Kocuria tytonicola" ], "sample_taxid": [ "2055946" ], "sample_host_organism": [ "Tyto furcata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: RWTH Aachen University" ], "sample_host_location_id": [], "data_size": "0.712 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)": "2614304", "Number of Sequences": "239", "Longest Sequences (bp)": "83369", "N50 (bp)": "21669", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.0", "Number of CDSs": "2192", "Average Protein Length": "329.0", "Coding Ratio (%)": "82.8", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Kocuria tytonicola", "strain": "strain=DSM 104133", "accession": "GCA_003687455.1", "taxid": 2055946, "species_taxid": 2055946, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 756, "total_fragments": 762, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Kocuria tytonis", "strain": "strain=442", "accession": "GCA_003226895.2", "taxid": 2054280, "species_taxid": 2054280, "relation_to_type": "type", "validated": true, "ani": 87.8503, "matched_fragments": 672, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kocuria rhizophila", "strain": "strain=TA68", "accession": "GCA_003667225.1", "taxid": 72000, "species_taxid": 72000, "relation_to_type": "type", "validated": true, "ani": 87.7953, "matched_fragments": 630, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kocuria varians", "strain": "strain=NBRC 15358", "accession": "GCA_006539885.1", "taxid": 1272, "species_taxid": 1272, "relation_to_type": "type", "validated": true, "ani": 86.533, "matched_fragments": 635, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kocuria indica", "strain": "strain=DSM 25126", "accession": "GCA_002237805.1", "taxid": 1049583, "species_taxid": 1049583, "relation_to_type": "type", "validated": true, "ani": 84.6658, "matched_fragments": 595, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kocuria indica", "strain": "strain=NIO-1021", "accession": "GCA_003667205.1", "taxid": 1049583, "species_taxid": 1049583, "relation_to_type": "type", "validated": true, "ani": 84.6317, "matched_fragments": 585, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micrococcus luteus", "strain": "strain=ATCC 4698", "accession": "GCA_003417425.1", "taxid": 1270, "species_taxid": 1270, "relation_to_type": "type", "validated": true, "ani": 79.3699, "matched_fragments": 238, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter sedimenti", "strain": "strain=MIC A30", "accession": "GCA_011750795.2", "taxid": 2694931, "species_taxid": 2694931, "relation_to_type": "type", "validated": true, "ani": 78.2113, "matched_fragments": 199, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter jiangjiafuii", "strain": "strain=zg-ZUI227", "accession": "GCA_018622995.1", "taxid": 2817475, "species_taxid": 2817475, "relation_to_type": "type", "validated": true, "ani": 77.8885, "matched_fragments": 205, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arthrobacter jiangjiafuii", "strain": "strain=zg-ZUI227", "accession": "GCA_017898065.1", "taxid": 2817475, "species_taxid": 2817475, "relation_to_type": "type", "validated": true, "ani": 77.8472, "matched_fragments": 202, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Georgenia yuyongxinii", "strain": "strain=Z443", "accession": "GCA_006352065.1", "taxid": 2589797, "species_taxid": 2589797, "relation_to_type": "type", "validated": true, "ani": 77.1936, "matched_fragments": 186, "total_fragments": 762, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003687455.1", "gtdb_species": "s__Kocuria tytonicola", "ani": 100.0, "matched_fragments": 756, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.95", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000010285.1", "gtdb_species": "s__Kocuria rhizophila_A", "ani": 87.9929, "matched_fragments": 677, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_003226895.2", "gtdb_species": "s__Kocuria tytonis", "ani": 87.8503, "matched_fragments": 672, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "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_003667225.1", "gtdb_species": "s__Kocuria rhizophila", "ani": 87.7953, "matched_fragments": 630, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "97.11", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_006539885.1", "gtdb_species": "s__Kocuria varians", "ani": 86.533, "matched_fragments": 635, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007681555.1", "gtdb_species": "s__Kocuria salsicia", "ani": 85.9632, "matched_fragments": 649, "total_fragments": 762, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.09", "min_intra_species_ani": "95.42", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.009, "cell_length": -0.009, "doubling_h": null, "growth_tmp": 29.038, "optimum_tmp": 29.863, "optimum_ph": 7.416, "genome_size": 3128484.398, "gc_content": 71.521, "coding_genes": 2561.833, "rRNA16S_genes": 3.0, "tRNA_genes": 47.333, "gram_stain": 1.0, "sporulation": 0.125, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.058, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.941, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Kocuria", "tytonicola" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }