{ "type": "genome", "identifier": "GCF_004153545.1", "organism": "Serinicoccus sediminis", "title": "Serinicoccus sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004153545.1", "bioproject": "PRJNA224116", "biosample": "SAMN10824318", "wgs_master": "SDVA00000000.1", "refseq_category": "reference genome", "taxid": "2306021", "species_taxid": "2306021", "organism_name": "Serinicoccus sediminis", "infraspecific_name": "strain=GP-T3-3", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/11", "asm_name": "ASM415354v1", "asm_submitter": "Korea University", "gbrs_paired_asm": "GCA_004153545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/153/545/GCF_004153545.1_ASM415354v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3550960", "genome_size_ungapped": "3550960", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "104", "contig_count": "104", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004153545.1-RS_2024_03_21", "annotation_date": "2024-03-21", "total_gene_count": "3303", "protein_coding_gene_count": "3228", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-11", "dateModified": "2019-02-11", "datePublished": "2019-02-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Serinicoccus sediminis" ], "sample_taxid": [ "2306021" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Gopado" ], "sample_host_location_id": [], "data_size": "0.938 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)": "3550960", "Number of Sequences": "104", "Longest Sequences (bp)": "542602", "N50 (bp)": "205012", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.2", "Number of CDSs": "3241", "Average Protein Length": "332.9", "Coding Ratio (%)": "91.2", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Serinicoccus sediminis", "strain": "strain=GP-T3-3", "accession": "GCA_004153545.1", "taxid": 2306021, "species_taxid": 2306021, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1151, "total_fragments": 1154, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Serinicoccus chungangensis", "strain": "strain=CCUG 59777", "accession": "GCA_006337125.1", "taxid": 767452, "species_taxid": 767452, "relation_to_type": "type", "validated": true, "ani": 89.1389, "matched_fragments": 972, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus profundi", "strain": "strain=CGMCC 4.5582", "accession": "GCA_008001015.1", "taxid": 1078471, "species_taxid": 1078471, "relation_to_type": "type", "validated": true, "ani": 85.597, "matched_fragments": 902, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus profundi", "strain": "strain=MCCC 1A05965", "accession": "GCA_000224715.2", "taxid": 1078471, "species_taxid": 1078471, "relation_to_type": "type", "validated": true, "ani": 85.5165, "matched_fragments": 866, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus marinus", "strain": "strain=DSM 15273", "accession": "GCA_000421245.1", "taxid": 247333, "species_taxid": 247333, "relation_to_type": "type", "validated": true, "ani": 85.4517, "matched_fragments": 851, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus marinus", "strain": "strain=DSM 15273", "accession": "GCA_008386315.1", "taxid": 247333, "species_taxid": 247333, "relation_to_type": "type", "validated": true, "ani": 85.3766, "matched_fragments": 863, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus hydrothermalis", "strain": "strain=JLT9", "accession": "GCA_001685415.1", "taxid": 1758689, "species_taxid": 1758689, "relation_to_type": "type", "validated": true, "ani": 85.1046, "matched_fragments": 893, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus kebangsaanensis", "strain": "strain=P2D13-UKM", "accession": "GCA_008919445.1", "taxid": 2602069, "species_taxid": 2602069, "relation_to_type": "type", "validated": true, "ani": 83.8586, "matched_fragments": 845, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium pekingense", "strain": "strain=DSM 21552", "accession": "GCA_000421185.1", "taxid": 384677, "species_taxid": 384677, "relation_to_type": "type", "validated": true, "ani": 81.3994, "matched_fragments": 704, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium kibberense", "strain": "strain=DSM 17687", "accession": "GCA_006519705.1", "taxid": 282060, "species_taxid": 282060, "relation_to_type": "type", "validated": true, "ani": 81.1296, "matched_fragments": 655, "total_fragments": 1154, "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": 79.7796, "matched_fragments": 526, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium murale", "strain": "strain=DSM 22056", "accession": "GCA_003352835.1", "taxid": 1050153, "species_taxid": 1050153, "relation_to_type": "type", "validated": true, "ani": 78.6963, "matched_fragments": 328, "total_fragments": 1154, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004153545.1", "gtdb_species": "s__Serinicoccus sediminis", "ani": 100.0, "matched_fragments": 1151, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "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_006337125.1", "gtdb_species": "s__Serinicoccus chungangensis", "ani": 89.1389, "matched_fragments": 972, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "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_001483745.1", "gtdb_species": "s__Serinicoccus chungangensis_A", "ani": 89.1298, "matched_fragments": 963, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "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_008001015.1", "gtdb_species": "s__Serinicoccus profundi", "ani": 85.607, "matched_fragments": 901, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008386315.1", "gtdb_species": "s__Serinicoccus marinus", "ani": 85.4019, "matched_fragments": 861, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001685415.1", "gtdb_species": "s__Serinicoccus hydrothermalis", "ani": 85.1138, "matched_fragments": 892, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "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_008919445.1", "gtdb_species": "s__Serinicoccus sp008919445", "ani": 83.8393, "matched_fragments": 847, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus", "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_001942405.1", "gtdb_species": "s__Ornithinimicrobium sp001942405", "ani": 81.1873, "matched_fragments": 661, "total_fragments": 1154, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.63", "min_intra_species_ani": "97.63", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": -0.222, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 35.0, "optimum_ph": 8.0, "genome_size": 3476746.5, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Serinicoccus", "sediminis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }